From b148c5d32b74735babf7da2776781d22fa1e7cab Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Thu, 9 Jul 2026 10:49:54 +0100 Subject: [PATCH 1/7] Update docker image to 'standard' version --- docker-compose_armadillo.yml | 3 ++- docker-compose_opal.yml | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/docker-compose_armadillo.yml b/docker-compose_armadillo.yml index dba71daf8..bfc84e063 100644 --- a/docker-compose_armadillo.yml +++ b/docker-compose_armadillo.yml @@ -3,7 +3,8 @@ services: hostname: armadillo ports: - 8080:8080 - image: datashield/armadillo_citest:latest + image: molgenis/molgenis-armadillo:latest +# image: datashield/armadillo_citest:latest environment: LOGGING_CONFIG: 'classpath:logback-file.xml' AUDIT_LOG_PATH: '/app/logs/audit.log' diff --git a/docker-compose_opal.yml b/docker-compose_opal.yml index 70bffd8d1..8e6a560a3 100644 --- a/docker-compose_opal.yml +++ b/docker-compose_opal.yml @@ -1,6 +1,7 @@ services: opal: - image: datashield/opal_citest:latest + image: obiba/opal:latest +# image: datashield/opal_citest:latest ports: - 8443:8443 - 8080:8080 From 0507e04e2f3d11fde3193cae95fb1811c4b38675 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Mon, 13 Jul 2026 15:19:24 +0100 Subject: [PATCH 2/7] Switch images --- docker-compose_armadillo.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docker-compose_armadillo.yml b/docker-compose_armadillo.yml index bfc84e063..f0cf4a55b 100644 --- a/docker-compose_armadillo.yml +++ b/docker-compose_armadillo.yml @@ -18,6 +18,7 @@ services: default: hostname: default - image: datashield/rock_citest-permissive:latest +# image: datashield/rock_citest-permissive:latest + image: datashield/rock-tulip-donkey-permissive:3.0.0 environment: DEBUG: "FALSE" From 0e1bae5374ba2c24e64ee94a801ed35689e2e049 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Tue, 14 Jul 2026 11:17:13 +0100 Subject: [PATCH 3/7] Revert docker composition files --- docker-compose_armadillo.yml | 6 ++---- docker-compose_opal.yml | 3 +-- 2 files changed, 3 insertions(+), 6 deletions(-) diff --git a/docker-compose_armadillo.yml b/docker-compose_armadillo.yml index f0cf4a55b..dba71daf8 100644 --- a/docker-compose_armadillo.yml +++ b/docker-compose_armadillo.yml @@ -3,8 +3,7 @@ services: hostname: armadillo ports: - 8080:8080 - image: molgenis/molgenis-armadillo:latest -# image: datashield/armadillo_citest:latest + image: datashield/armadillo_citest:latest environment: LOGGING_CONFIG: 'classpath:logback-file.xml' AUDIT_LOG_PATH: '/app/logs/audit.log' @@ -18,7 +17,6 @@ services: default: hostname: default -# image: datashield/rock_citest-permissive:latest - image: datashield/rock-tulip-donkey-permissive:3.0.0 + image: datashield/rock_citest-permissive:latest environment: DEBUG: "FALSE" diff --git a/docker-compose_opal.yml b/docker-compose_opal.yml index 8e6a560a3..70bffd8d1 100644 --- a/docker-compose_opal.yml +++ b/docker-compose_opal.yml @@ -1,7 +1,6 @@ services: opal: - image: obiba/opal:latest -# image: datashield/opal_citest:latest + image: datashield/opal_citest:latest ports: - 8443:8443 - 8080:8080 From 2314d1634615ec298858da33cf730f98dc8d832e Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Mon, 17 Aug 2026 18:34:08 +0100 Subject: [PATCH 4/7] Switch to 'permissive' mode, and 'roxygen' version, --- DESCRIPTION | 2 +- NAMESPACE | 62 +++++++++++++++++++++++++++++++---------------------- 2 files changed, 37 insertions(+), 27 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index ff5813eda..b4673dba0 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -86,4 +86,4 @@ Suggests: DSLite Encoding: UTF-8 Language: en-GB -Config/roxygen2/version: 8.0.0 +Config/roxygen2/version: 8.1.0 diff --git a/NAMESPACE b/NAMESPACE index d0baa073b..cbfec6b50 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -121,31 +121,41 @@ export(ds.var) export(ds.vectorCalc) export(subsetHelper) import(DSI) -importFrom(DSI,datashield.aggregate) -importFrom(DSI,datashield.assign) +importFrom(DSI, + datashield.aggregate, + datashield.assign +) importFrom(assertthat,assert_that) -importFrom(cli,cli_abort) -importFrom(cli,cli_alert_danger) -importFrom(cli,cli_alert_info) -importFrom(cli,cli_alert_success) -importFrom(cli,cli_alert_warning) -importFrom(cli,cli_end) -importFrom(cli,cli_li) -importFrom(cli,cli_ol) -importFrom(cli,cli_text) -importFrom(cli,cli_ul) +importFrom(cli, + cli_abort, + cli_alert_danger, + cli_alert_info, + cli_alert_success, + cli_alert_warning, + cli_end, + cli_li, + cli_ol, + cli_text, + cli_ul +) importFrom(data.table,.SD) -importFrom(dplyr,"%>%") -importFrom(dplyr,all_of) -importFrom(dplyr,bind_rows) -importFrom(dplyr,case_when) -importFrom(dplyr,row_number) -importFrom(dplyr,where) -importFrom(purrr,map) -importFrom(purrr,map_lgl) -importFrom(purrr,pmap) -importFrom(purrr,pmap_lgl) -importFrom(stats,as.formula) -importFrom(stats,na.omit) -importFrom(stats,ts) -importFrom(stats,weighted.mean) +importFrom(dplyr, + "%>%", + all_of, + bind_rows, + case_when, + row_number, + where +) +importFrom(purrr, + map, + map_lgl, + pmap, + pmap_lgl +) +importFrom(stats, + as.formula, + na.omit, + ts, + weighted.mean +) From a836041bee7c856ccbe56c01366040acd3ba02ad Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Wed, 19 Aug 2026 10:51:13 +0100 Subject: [PATCH 5/7] Added 'Server package output' --- armadillo_azure-pipelines.yml | 9 ++++++++- opal_azure-pipelines.yml | 9 ++++++++- 2 files changed, 16 insertions(+), 2 deletions(-) diff --git a/armadillo_azure-pipelines.yml b/armadillo_azure-pipelines.yml index 4721bc81d..ed650b818 100644 --- a/armadillo_azure-pipelines.yml +++ b/armadillo_azure-pipelines.yml @@ -635,10 +635,17 @@ jobs: echo -e "R sessionInfo(): ############" R -e 'sessionInfo()' - sudo apt install tree -y + echo -e "\n#############################" + echo -e "Server packages: ############" + curl -s -u admin:admin -X GET http://localhost:8080/packages -o - | jq '.' + + echo -e "\n#############################" + echo -e "PWD: ############" pwd + echo -e "\n#############################" echo -e "File tree: ##################" + sudo apt install tree -y tree $(Pipeline.Workspace) displayName: 'Environment info' diff --git a/opal_azure-pipelines.yml b/opal_azure-pipelines.yml index 1bac20ea4..12f757496 100644 --- a/opal_azure-pipelines.yml +++ b/opal_azure-pipelines.yml @@ -551,8 +551,15 @@ jobs: echo -e "R sessionInfo(): ############" R -e 'sessionInfo()' - sudo apt install tree -y + echo -e "\n#############################" + echo -e "Server packages: ############" + curl -s -u admin:admin -X GET http://localhost:8080/packages -o - | jq '.' + + echo -e "\n#############################" + echo -e "PWD: ############" pwd + + sudo apt install tree -y echo -e "\n#############################" echo -e "File tree: ##################" tree $(Pipeline.Workspace) From aa97a9af02b062e97331f9a5ad2feb1d6d27ffea Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Wed, 19 Aug 2026 23:13:27 +0100 Subject: [PATCH 6/7] Added server packages --- azure-pipelines.yml | 9 ++++++++- opal_azure-pipelines.yml | 2 +- 2 files changed, 9 insertions(+), 2 deletions(-) diff --git a/azure-pipelines.yml b/azure-pipelines.yml index 1bac20ea4..b98eccf3a 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -551,8 +551,15 @@ jobs: echo -e "R sessionInfo(): ############" R -e 'sessionInfo()' - sudo apt install tree -y + echo -e "\n#############################" + echo -e "Server packages: ############" + R --no-echo -q -e "sink(nullfile(), type = c('output', 'message')); library(rjson); library(opalr); o <- opal.login('administrator','datashield_test&', url='http://localhost:8080/'); p <- oadmin.installed_packages(o); opal.logout(o); sink(NULL); cat(toJSON(p))" 2> /dev/null | jq '.' + + echo -e "\n#############################" + echo -e "PWD: ############" pwd + + sudo apt install tree -y echo -e "\n#############################" echo -e "File tree: ##################" tree $(Pipeline.Workspace) diff --git a/opal_azure-pipelines.yml b/opal_azure-pipelines.yml index 12f757496..b98eccf3a 100644 --- a/opal_azure-pipelines.yml +++ b/opal_azure-pipelines.yml @@ -553,7 +553,7 @@ jobs: echo -e "\n#############################" echo -e "Server packages: ############" - curl -s -u admin:admin -X GET http://localhost:8080/packages -o - | jq '.' + R --no-echo -q -e "sink(nullfile(), type = c('output', 'message')); library(rjson); library(opalr); o <- opal.login('administrator','datashield_test&', url='http://localhost:8080/'); p <- oadmin.installed_packages(o); opal.logout(o); sink(NULL); cat(toJSON(p))" 2> /dev/null | jq '.' echo -e "\n#############################" echo -e "PWD: ############" From 1b2afda8f87c89b023a5113e1c041f0b654bcba7 Mon Sep 17 00:00:00 2001 From: Stuart Wheater Date: Thu, 20 Aug 2026 11:35:58 +0100 Subject: [PATCH 7/7] Install rjson package in Azure Pipelines --- opal_azure-pipelines.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/opal_azure-pipelines.yml b/opal_azure-pipelines.yml index b98eccf3a..41d5dd595 100644 --- a/opal_azure-pipelines.yml +++ b/opal_azure-pipelines.yml @@ -553,7 +553,8 @@ jobs: echo -e "\n#############################" echo -e "Server packages: ############" - R --no-echo -q -e "sink(nullfile(), type = c('output', 'message')); library(rjson); library(opalr); o <- opal.login('administrator','datashield_test&', url='http://localhost:8080/'); p <- oadmin.installed_packages(o); opal.logout(o); sink(NULL); cat(toJSON(p))" 2> /dev/null | jq '.' + sudo R -q -e "install.packages(c('rjson'), dependencies=TRUE, repos='https://cloud.r-project.org')" + R --no-echo -q -e "sink(nullfile(), type = c('output', 'message')); library(rjson); library(opalr); o <- opal.login('administrator','datashield_test&', url='http://localhost:8080/'); p <- oadmin.installed_packages(o); opal.logout(o); sink(NULL); cat(toJSON(p))" | jq '.' echo -e "\n#############################" echo -e "PWD: ############"