fixing namespacing in phevaluator.main server, updating code to creat…

…e PV data, updating PV data per new spec
OHDSI · Jun 29, 2023 · 2a72ff8 · 2a72ff8
1 parent 95be4fe
commit 2a72ff8
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Showing 3 changed files with 162 additions and 162 deletions.
diff --git a/R/phevaluator-main.R b/R/phevaluator-main.R
@@ -445,47 +445,47 @@ phevaluatorServer <- function(
       customColDefs <- utils::modifyList(phevalColList, buttonColDefs)
 
 
-      resultTableServer(id = ns("algorithmPerformanceResultsTable"),
-                        df = dataAlgorithmPerformance,
+      resultTableServer(id = "algorithmPerformanceResultsTable",
+                        df = dataAlgorithmPerformance(),
                         colDefsInput = customColDefs,
                         downloadedFileName = "algorithmPerformanceResultsTable-")
 
-      resultTableServer(id = ns("cohortDefinitionSetTable"),
+      resultTableServer(id = "cohortDefinitionSetTable",
                         df = dataCohortDefinitionSet,
                         colDefsInput = customColDefs,
                         downloadedFileName = "cohortDefinitionSetTable-")
 
-      resultTableServer(id = ns("diagnosticsTable"),
+      resultTableServer(id = "diagnosticsTable",
                         df = dataDiagnostics,
                         colDefsInput = customColDefs,
                         downloadedFileName = "diagnosticsTable-")
 
-      resultTableServer(id = ns("evaluationInputParametersTable"),
+      resultTableServer(id = "evaluationInputParametersTable",
                         df = dataEvalInputParams,
                         colDefsInput = customColDefs,
                         downloadedFileName = "evaluationInputParametersTable-")
 
-      resultTableServer(id = ns("modelCovariatesTable"),
+      resultTableServer(id = "modelCovariatesTable",
                         df = dataModelCovars,
                         colDefsInput = customColDefs,
                         downloadedFileName = "modelCovariatesTable-")
 
-      resultTableServer(id = ns("modelInputParametersTable"),
+      resultTableServer(id = "modelInputParametersTable",
                         df = dataModelInputParams,
                         colDefsInput = customColDefs,
                         downloadedFileName = "modelInputParametersTable-")
 
-      resultTableServer(id = ns("modelPerformanceTable"),
+      resultTableServer(id = "modelPerformanceTable",
                         df = dataModelPerformance,
                         colDefsInput = customColDefs,
                         downloadedFileName = "modelPerformanceTable-")
 
-      resultTableServer(id = ns("testSubjectsTable"),
+      resultTableServer(id = "testSubjectsTable",
                         df = dataTestSubjects,
                         colDefsInput = customColDefs,
                         downloadedFileName = "testSubjectsTable-")
 
-      resultTableServer(id = ns("testSubjectsCovariatesTable"),
+      resultTableServer(id = "testSubjectsCovariatesTable",
                         df = dataTestSubjectsCovars,
                         colDefsInput = customColDefs,
                         downloadedFileName = "testSubjectsCovariatesTable-")

diff --git a/extras/codeToCreatePhevaluatorDatabase.R b/extras/codeToCreatePhevaluatorDatabase.R
@@ -1,48 +1,48 @@
-# #load specification
-# 
-#  mypath <- "D:/shiny/resultModelSpecs"
-#  serverPV <- "tests/resources/pvDatabase/phevaluator.sqlite"
-#  
-#  #delete entire database
-#  unlink(serverPV)
-#  
-#  #load tje results data model spec
-#  specification <- ResultModelManager::loadResultsDataModelSpecifications(file.path(mypath,
-#                                                                                    "resultsDataModelSpecificationReordered.csv")
-#  )
-#  
-#  #create sql to generate schema
-#  sql <- ResultModelManager::generateSqlSchema(schemaDefinition = specification)
-#  
-#  #create the schema
-#  connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sqlite",
-#                                                                  server = serverPV)
-#  
-#  
-#  # #need to re run the below qns when re-making the database
-#  qns <- ResultModelManager::createQueryNamespace(connectionDetails = connectionDetails,
-#                                                  tableSpecification = specification,
-#                                                  tablePrefix = "",
-#                                                  database_schema = "main")
-#  #execute the SQL
-#  qns$executeSql(sql)
-#  
-#  
-#  #upload the results to the schema
-#  ResultModelManager::uploadResults(connectionDetails = connectionDetails,
-#                                    schema = "main",
-#                                    resultsFolder = file.path(mypath, "results"),
-#                                    tablePrefix = "",
-#                                    specifications = specification,
-#                                    purgeSiteDataBeforeUploading = F)
-# 
-# #DBI::dbConnect(RSQLite::SQLite(), dbname = "phevaluator.sqlite")
-# 
-# #create connection to DB
-# connection <- DatabaseConnector::connect(connectionDetails = connectionDetails)
-# 
-# #disconnect
-# DatabaseConnector::disconnect(connection)
+#load specification
+
+ mypath <- "D:/shiny/resultModelSpecs"
+ serverPV <- "tests/resources/pvDatabase/phevaluator.sqlite"
+
+ #delete entire database
+ unlink(serverPV)
+
+ #load tje results data model spec
+ specification <- ResultModelManager::loadResultsDataModelSpecifications(file.path(mypath,
+                                                                                   "resultsDataModelSpecificationReordered.csv")
+ )
+
+ #create sql to generate schema
+ sql <- ResultModelManager::generateSqlSchema(schemaDefinition = specification)
+
+ #create the schema
+ connectionDetails <- DatabaseConnector::createConnectionDetails(dbms = "sqlite",
+                                                                 server = serverPV)
+
+
+ # #need to re run the below qns when re-making the database
+ qns <- ResultModelManager::createQueryNamespace(connectionDetails = connectionDetails,
+                                                 tableSpecification = specification,
+                                                 tablePrefix = "",
+                                                 database_schema = "main")
+ #execute the SQL
+ qns$executeSql(sql)
+
+
+ #upload the results to the schema
+ ResultModelManager::uploadResults(connectionDetails = connectionDetails,
+                                   schema = "main",
+                                   resultsFolder = file.path(mypath, "results"),
+                                   tablePrefix = "",
+                                   specifications = specification,
+                                   purgeSiteDataBeforeUploading = F)
+
+#DBI::dbConnect(RSQLite::SQLite(), dbname = "phevaluator.sqlite")
+
+#create connection to DB
+connection <- DatabaseConnector::connect(connectionDetails = connectionDetails)
+
+#disconnect
+DatabaseConnector::disconnect(connection)
 
 
 
@@ -52,114 +52,114 @@
 
 # code to manually create test data
 
-resultsPV <- "D:/shiny/resultModelSpecs/results"
-serverPV <- "tests/resources/pvDatabase/phevaluator.sqlite"
-connectionDetailsPV <- DatabaseConnector::createConnectionDetails(
-  dbms = 'sqlite',
-  server = serverPV
-)
-connectionPV <- DatabaseConnector::connect(
-  connectionDetails = connectionDetailsPV,
-  dbms = 'sqlite',
-  user = NULL,
-  password = NULL,
-  server = serverPV,
-  port = NULL
-)
+# resultsPV <- "D:/shiny/resultModelSpecs/results"
+# serverPV <- "tests/resources/pvDatabase/phevaluator.sqlite"
+# connectionDetailsPV <- DatabaseConnector::createConnectionDetails(
+#   dbms = 'sqlite',
+#   server = serverPV
+# )
+# connectionPV <- DatabaseConnector::connect(
+#   connectionDetails = connectionDetailsPV,
+#   dbms = 'sqlite',
+#   user = NULL,
+#   password = NULL,
+#   server = serverPV,
+#   port = NULL
+# )
+# # 
+# DatabaseConnector::insertTable(
+#   connection = connectionPV,
+#   databaseSchema = 'main',
+#   tableName = 'PV_ALGORITHM_PERFORMANCE_RESULTS',
+#   data = read.csv(file.path(resultsPV, "pv_algorithm_performance_results.csv")),
+#   createTable = T, dropTableIfExists = T,
+#   camelCaseToSnakeCase = F
+# )
+# 
+# DatabaseConnector::insertTable(
+#   connection = connectionPV,
+#   databaseSchema = 'main',
+#   tableName = 'PV_COHORT_DEFINITION_SET',
+#   data = read.csv(file.path(resultsPV, "pv_cohort_definition_set.csv")),
+#   createTable = T, dropTableIfExists = T,
+#   camelCaseToSnakeCase = F
+# )
+# 
+# DatabaseConnector::insertTable(
+#   connection = connectionPV,
+#   databaseSchema = 'main',
+#   tableName = 'PV_DIAGNOSTICS',
+#   data = read.csv(file.path(resultsPV, "pv_diagnostics.csv")),
+#   createTable = T, dropTableIfExists = T,
+#   camelCaseToSnakeCase = F
+# )
+# 
+# DatabaseConnector::insertTable(
+#   connection = connectionPV,
+#   databaseSchema = 'main',
+#   tableName = 'PV_EVALUATION_INPUT_PARAMETERS',
+#   data = read.csv(file.path(resultsPV, "pv_evaluation_input_parameters.csv")),
+#   createTable = T, dropTableIfExists = T,
+#   camelCaseToSnakeCase = F
+# )
+# 
+# DatabaseConnector::insertTable(
+#   connection = connectionPV,
+#   databaseSchema = 'main',
+#   tableName = 'PV_MODEL_COVARIATES',
+#   data = read.csv(file.path(resultsPV, "pv_model_covariates.csv")),
+#   createTable = T, dropTableIfExists = T,
+#   camelCaseToSnakeCase = F
+# )
+# 
+# DatabaseConnector::insertTable(
+#   connection = connectionPV,
+#   databaseSchema = 'main',
+#   tableName = 'PV_MODEL_INPUT_PARAMETERS',
+#   data = read.csv(file.path(resultsPV, "pv_model_input_parameters.csv")),
+#   createTable = T, dropTableIfExists = T,
+#   camelCaseToSnakeCase = F
+# )
+# 
+# DatabaseConnector::insertTable(
+#   connection = connectionPV,
+#   databaseSchema = 'main',
+#   tableName = 'PV_MODEL_PERFORMANCE',
+#   data = read.csv(file.path(resultsPV, "pv_model_performance.csv")),
+#   createTable = T, dropTableIfExists = T,
+#   camelCaseToSnakeCase = F
+# )
+# 
+# DatabaseConnector::insertTable(
+#   connection = connectionPV,
+#   databaseSchema = 'main',
+#   tableName = 'PV_MODEL_RUN_TIME_VALUES',
+#   data = read.csv(file.path(resultsPV, "pv_model_run_time_values.csv")),
+#   createTable = T, dropTableIfExists = T,
+#   camelCaseToSnakeCase = F
+# )
+# 
+# DatabaseConnector::insertTable(
+#   connection = connectionPV,
+#   databaseSchema = 'main',
+#   tableName = 'PV_TEST_SUBJECTS',
+#   data = read.csv(file.path(resultsPV, "pv_test_subjects.csv")),
+#   createTable = T, dropTableIfExists = T,
+#   camelCaseToSnakeCase = F
+# )
+# 
+# DatabaseConnector::insertTable(
+#   connection = connectionPV,
+#   databaseSchema = 'main',
+#   tableName = 'PV_TEST_SUBJECTS_COVARIATES',
+#   data = read.csv(file.path(resultsPV, "pv_test_subjects_covariates.csv")),
+#   createTable = T, dropTableIfExists = T,
+#   camelCaseToSnakeCase = F
+# )
+# 
+# 
+# 
 # 
-DatabaseConnector::insertTable(
-  connection = connectionPV,
-  databaseSchema = 'main',
-  tableName = 'PV_ALGORITHM_PERFORMANCE_RESULTS',
-  data = read.csv(file.path(resultsPV, "pv_algorithm_performance_results.csv")),
-  createTable = T, dropTableIfExists = T,
-  camelCaseToSnakeCase = F
-)
-
-DatabaseConnector::insertTable(
-  connection = connectionPV,
-  databaseSchema = 'main',
-  tableName = 'PV_COHORT_DEFINITION_SET',
-  data = read.csv(file.path(resultsPV, "pv_cohort_definition_set.csv")),
-  createTable = T, dropTableIfExists = T,
-  camelCaseToSnakeCase = F
-)
-
-DatabaseConnector::insertTable(
-  connection = connectionPV,
-  databaseSchema = 'main',
-  tableName = 'PV_DIAGNOSTICS',
-  data = read.csv(file.path(resultsPV, "pv_diagnostics.csv")),
-  createTable = T, dropTableIfExists = T,
-  camelCaseToSnakeCase = F
-)
-
-DatabaseConnector::insertTable(
-  connection = connectionPV,
-  databaseSchema = 'main',
-  tableName = 'PV_EVALUATION_INPUT_PARAMETERS',
-  data = read.csv(file.path(resultsPV, "pv_evaluation_input_parameters.csv")),
-  createTable = T, dropTableIfExists = T,
-  camelCaseToSnakeCase = F
-)
-
-DatabaseConnector::insertTable(
-  connection = connectionPV,
-  databaseSchema = 'main',
-  tableName = 'PV_MODEL_COVARIATES',
-  data = read.csv(file.path(resultsPV, "pv_model_covariates.csv")),
-  createTable = T, dropTableIfExists = T,
-  camelCaseToSnakeCase = F
-)
-
-DatabaseConnector::insertTable(
-  connection = connectionPV,
-  databaseSchema = 'main',
-  tableName = 'PV_MODEL_INPUT_PARAMETERS',
-  data = read.csv(file.path(resultsPV, "pv_model_input_parameters.csv")),
-  createTable = T, dropTableIfExists = T,
-  camelCaseToSnakeCase = F
-)
-
-DatabaseConnector::insertTable(
-  connection = connectionPV,
-  databaseSchema = 'main',
-  tableName = 'PV_MODEL_PERFORMANCE',
-  data = read.csv(file.path(resultsPV, "pv_model_performance.csv")),
-  createTable = T, dropTableIfExists = T,
-  camelCaseToSnakeCase = F
-)
-
-DatabaseConnector::insertTable(
-  connection = connectionPV,
-  databaseSchema = 'main',
-  tableName = 'PV_MODEL_RUN_TIME_VALUES',
-  data = read.csv(file.path(resultsPV, "pv_model_run_time_values.csv")),
-  createTable = T, dropTableIfExists = T,
-  camelCaseToSnakeCase = F
-)
-
-DatabaseConnector::insertTable(
-  connection = connectionPV,
-  databaseSchema = 'main',
-  tableName = 'PV_TEST_SUBJECTS',
-  data = read.csv(file.path(resultsPV, "pv_test_subjects.csv")),
-  createTable = T, dropTableIfExists = T,
-  camelCaseToSnakeCase = F
-)
-
-DatabaseConnector::insertTable(
-  connection = connectionPV,
-  databaseSchema = 'main',
-  tableName = 'PV_TEST_SUBJECTS_COVARIATES',
-  data = read.csv(file.path(resultsPV, "pv_test_subjects_covariates.csv")),
-  createTable = T, dropTableIfExists = T,
-  camelCaseToSnakeCase = F
-)
-
-
-
-
 
 
 

diff --git a/tests/resources/pvDatabase/phevaluator.sqlite b/tests/resources/pvDatabase/phevaluator.sqlite