From ea478a34179f52c13bb798abd41d7ad96d1b1fc2 Mon Sep 17 00:00:00 2001 From: schuemie Date: Mon, 9 Oct 2023 08:31:31 +0200 Subject: [PATCH 1/2] Adding Github Action for weekly R check of main --- .../workflows/R_CMD_check_main_weekly.yaml | 64 +++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 .github/workflows/R_CMD_check_main_weekly.yaml diff --git a/.github/workflows/R_CMD_check_main_weekly.yaml b/.github/workflows/R_CMD_check_main_weekly.yaml new file mode 100644 index 00000000..8e610aac --- /dev/null +++ b/.github/workflows/R_CMD_check_main_weekly.yaml @@ -0,0 +1,64 @@ +on: + schedule: + - cron: '0 19 * * 0' # every Sunday at 7pm UTC + +name: 'R check' + +jobs: + R-CMD-check-main: + runs-on: ${{ matrix.config.os }} + + name: ${{ matrix.config.os }} (${{ matrix.config.r }}) + + strategy: + fail-fast: false + matrix: + config: + - {os: macOS-latest, r: 'release'} + + env: + GITHUB_PAT: ${{ secrets.GH_TOKEN }} + R_REMOTES_NO_ERRORS_FROM_WARNINGS: true + RSPM: ${{ matrix.config.rspm }} + CDM5_ORACLE_CDM54_SCHEMA: ${{ secrets.CDM5_ORACLE_CDM54_SCHEMA }} + CDM5_ORACLE_OHDSI_SCHEMA: ${{ secrets.CDM5_ORACLE_OHDSI_SCHEMA }} + CDM5_ORACLE_PASSWORD: ${{ secrets.CDM5_ORACLE_PASSWORD }} + CDM5_ORACLE_SERVER: ${{ secrets.CDM5_ORACLE_SERVER }} + CDM5_ORACLE_USER: ${{ secrets.CDM5_ORACLE_USER }} + CDM5_POSTGRESQL_CDM54_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_CDM54_SCHEMA }} + CDM5_POSTGRESQL_OHDSI_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_OHDSI_SCHEMA }} + CDM5_POSTGRESQL_PASSWORD: ${{ secrets.CDM5_POSTGRESQL_PASSWORD }} + CDM5_POSTGRESQL_SERVER: ${{ secrets.CDM5_POSTGRESQL_SERVER }} + CDM5_POSTGRESQL_USER: ${{ secrets.CDM5_POSTGRESQL_USER }} + CDM5_SQL_SERVER_CDM54_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_CDM54_SCHEMA }} + CDM5_SQL_SERVER_OHDSI_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_OHDSI_SCHEMA }} + CDM5_SQL_SERVER_PASSWORD: ${{ secrets.CDM5_SQL_SERVER_PASSWORD }} + CDM5_SQL_SERVER_SERVER: ${{ secrets.CDM5_SQL_SERVER_SERVER }} + CDM5_SQL_SERVER_USER: ${{ secrets.CDM5_SQL_SERVER_USER }} + CDM5_REDSHIFT_CDM54_SCHEMA: ${{ secrets.CDM5_REDSHIFT_CDM54_SCHEMA }} + CDM5_REDSHIFT_OHDSI_SCHEMA: ${{ secrets.CDM5_REDSHIFT_OHDSI_SCHEMA }} + CDM5_REDSHIFT_PASSWORD: ${{ secrets.CDM5_REDSHIFT_PASSWORD }} + CDM5_REDSHIFT_SERVER: ${{ secrets.CDM5_REDSHIFT_SERVER }} + CDM5_REDSHIFT_USER: ${{ secrets.CDM5_REDSHIFT_USER }} + + steps: + - uses: actions/checkout@v3 + + - uses: r-lib/actions/setup-r@v2 + with: + r-version: ${{ matrix.config.r }} + + - uses: r-lib/actions/setup-tinytex@v2 + + - uses: r-lib/actions/setup-pandoc@v2 + + - uses: r-lib/actions/setup-r-dependencies@v2 + with: + extra-packages: any::rcmdcheck + needs: check + + - uses: r-lib/actions/check-r-package@v2 + with: + args: 'c("--no-manual", "--as-cran")' + error-on: '"warning"' + check-dir: '"check"' From 3d5fd6d215b19d23ad39d183f2764aaa11e986d4 Mon Sep 17 00:00:00 2001 From: Jo Vanvoorden Date: Fri, 17 Nov 2023 07:42:11 +0100 Subject: [PATCH 2/2] Fix fromJSON correct method usage --- R/exportToJson.R | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/R/exportToJson.R b/R/exportToJson.R index 2d7721a4..d463780e 100755 --- a/R/exportToJson.R +++ b/R/exportToJson.R @@ -1250,7 +1250,7 @@ generateConditionReports <- function(conn, return() } - treemapData <- jsonlite::fromJSON(file = treemapFile) + treemapData <- jsonlite::fromJSON(treemapFile) uniqueConcepts <- unique(treemapData$CONCEPT_ID) totalCount <- length(uniqueConcepts) @@ -1334,7 +1334,7 @@ generateConditionEraReports <- function(conn, return() } - treemapData <- jsonlite::fromJSON(file = treemapFile) + treemapData <- jsonlite::fromJSON(treemapFile) uniqueConcepts <- unique(treemapData$CONCEPT_ID) totalCount <- length(uniqueConcepts) @@ -1413,7 +1413,7 @@ generateDrugEraReports <- function(conn, dbms, cdmDatabaseSchema, resultsDatabas return() } - treemapData <- jsonlite::fromJSON(file = treemapFile) + treemapData <- jsonlite::fromJSON(treemapFile) uniqueConcepts <- unique(treemapData$CONCEPT_ID) totalCount <- length(uniqueConcepts) @@ -1495,7 +1495,7 @@ generateDrugReports <- function(conn, return() } - treemapData <- jsonlite::fromJSON(file = treemapFile) + treemapData <- jsonlite::fromJSON(treemapFile) uniqueConcepts <- unique(treemapData$CONCEPT_ID) totalCount <- length(uniqueConcepts) @@ -1630,7 +1630,7 @@ generateProcedureReports <- function(conn, return() } - treemapData <- jsonlite::fromJSON(file = treemapFile) + treemapData <- jsonlite::fromJSON(treemapFile) uniqueConcepts <- unique(treemapData$CONCEPT_ID) totalCount <- length(uniqueConcepts) @@ -1985,14 +1985,14 @@ generateDashboardReport <- function(outputPath) { progress <- progress + 1 utils::setTxtProgressBar(progressBar, progress) - personReport <- jsonlite::fromJSON(file = paste(outputPath, "/person.json", sep = "")) + personReport <- jsonlite::fromJSON(paste(outputPath, "/person.json", sep = "")) output$SUMMARY <- personReport$SUMMARY output$GENDER_DATA <- personReport$GENDER_DATA progress <- progress + 1 utils::setTxtProgressBar(progressBar, progress) - opReport <- jsonlite::fromJSON(file = paste(outputPath, "/observationperiod.json", sep = "")) + opReport <- jsonlite::fromJSON(paste(outputPath, "/observationperiod.json", sep = "")) output$AGE_AT_FIRST_OBSERVATION_HISTOGRAM <- opReport$AGE_AT_FIRST_OBSERVATION_HISTOGRAM output$CUMULATIVE_DURATION <- opReport$CUMULATIVE_DURATION @@ -2110,7 +2110,7 @@ generateMeasurementReports <- function(conn, return() } - treemapData <- jsonlite::fromJSON(file = treemapFile) + treemapData <- jsonlite::fromJSON(treemapFile) uniqueConcepts <- unique(treemapData$CONCEPT_ID) totalCount <- length(uniqueConcepts) @@ -2265,7 +2265,7 @@ generateObservationReports <- function(conn, return() } - treemapData <- jsonlite::fromJSON(file = treemapFile) + treemapData <- jsonlite::fromJSON(treemapFile) uniqueConcepts <- unique(treemapData$CONCEPT_ID) totalCount <- length(uniqueConcepts) @@ -2382,7 +2382,7 @@ generateVisitReports <- function(conn, return() } - treemapData <- jsonlite::fromJSON(file = treemapFile) + treemapData <- jsonlite::fromJSON(treemapFile) uniqueConcepts <- unique(treemapData$CONCEPT_ID) totalCount <- length(uniqueConcepts) @@ -2557,7 +2557,7 @@ generateVisitDetailReports <- function(conn, return() } - treemapData <- jsonlite::fromJSON(file = treemapFile) + treemapData <- jsonlite::fromJSON(treemapFile) uniqueConcepts <- unique(treemapData$CONCEPT_ID) totalCount <- length(uniqueConcepts)