Merge pull request #743 from uz-leuven/issue-726

Fix fromJSON correct method usage

.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"'

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)