diff --git a/.github/workflows/shinyapps_deploy.yml b/.github/workflows/shinyapps_deploy.yml index 7304da8e..95caabaf 100644 --- a/.github/workflows/shinyapps_deploy.yml +++ b/.github/workflows/shinyapps_deploy.yml @@ -48,23 +48,10 @@ jobs: run: | # has to activate each bash step source .venv/bin/activate - # use 'poetry' to install schematic dev schematic - # If commit is tagged for release or in main branch, install schematic from pypi - if [[ $GITHUB_REF_NAME == v*.*.* ]] || [[ $GITHUB_REF_NAME == main ]]; then - echo Installing pypi version of schematic - git clone --single-branch --branch main https://github.com/Sage-Bionetworks/schematic.git - cp schematic_config.yml schematic/config.yml - cd schematic - pip3 install schematicpy - else - pip3 install poetry - echo Installing develop branch of schematic from github - git clone --single-branch --branch develop https://github.com/Sage-Bionetworks/schematic.git - cp schematic_config.yml schematic/config.yml - cd schematic - poetry build - pip3 install dist/schematicpy-1.0.0-py3-none-any.whl - fi + echo Installing pypi version of schematic + git clone --single-branch --branch main https://github.com/Sage-Bionetworks/schematic.git + cp schematic_config.yml schematic/config.yml + pip3 install schematicpy - name: Set Configurations for Schematic shell: bash @@ -131,4 +118,14 @@ jobs: finally=close(configFileConn) ) rsconnect::setAccountInfo(rsConnectUser, rsConnectToken, rsConnectSecret) - rsconnect::deployApp(appName = appName) + # Get app names. If app exists, configure then deploy. Otherwise + # deploy then configure + apps <- rsconnect::applications()$name + if (appName %in% apps) { + rsconnect::configureApp(appName = appName, size = "xxxlarge", logLevel = "verbose") + rsconnect::deployApp(appName = appName) + } else { + rsconnect::deployApp(appName = appName) + rsconnect::configureApp(appName = appName, size = "xxxlarge", logLevel = "verbose") + } + diff --git a/functions/validationResult.R b/functions/validationResult.R index 92e6c31d..7db26368 100644 --- a/functions/validationResult.R +++ b/functions/validationResult.R @@ -121,7 +121,7 @@ validationResult <- function(anno.res, template, manifest = NULL, dashboard = FA # similar warnings in the same column should be concatenated from backend, like "['value1', 'value2', ...]" # extract the single quoted values from the warning string if (!is.null(warn[[4]])) { - warn_values <- gsub("^[^']*'|'\\],?$", "", strsplit(warn[[4]], "'(?=,)", perl = TRUE)[[1]]) + warn_values <- gsub("^[^']*'|'\\],?$", "", strsplit(as.character(warn[[4]]), "'(?=,)", perl = TRUE)[[1]]) } else { # if matchExactOne (set) warning exist, highlight entire column warn_values <- "ht_entire_column"