Merge branch 'develop'

# Conflicts:
#	inst/doc/DbiAndDbplyr.pdf

.Rbuildignore

@@ -14,3 +14,5 @@ compare_versions
 _pkgdown.yml
 docs
 .github
+errorReportSql.txt
+^CRAN-SUBMISSION$

.github/workflows/R_CMD_check_Hades.yaml

@@ -53,7 +53,7 @@ jobs:
       CDM5_SPARK_CONNECTION_STRING: ${{ secrets.CDM5_SPARK_CONNECTION_STRING }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -114,7 +114,7 @@ jobs:
 
     steps:
 
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 0
 

.github/workflows/R_CMD_check_main.yaml → .github/workflows/R_CMD_check_main_weekly.yaml

@@ -1,8 +1,8 @@
 on:
   schedule:
-    - cron: '0 8 * * 2' # every Tuesday at 8 am UTC
+    - cron: '0 3 * * 0' # every Sunday at 3am UTC
 
-name: 'R check main'
+name: 'R check'
 
 jobs:
   R-CMD-check-main:
@@ -45,7 +45,7 @@ jobs:
       CDM5_SPARK_CONNECTION_STRING: ${{ secrets.CDM5_SPARK_CONNECTION_STRING }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-r@v2
         with:

CRAN-SUBMISSION

@@ -0,0 +1,3 @@
+Version: 6.0.0
+Date: 2023-01-30 10:59:45 UTC
+SHA: 352a46f3b48247aaf2c39336f719015996b05b42

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: DatabaseConnector
 Type: Package
 Title: Connecting to Various Database Platforms
-Version: 5.1.0
-Date: 2022-09-23
+Version: 6.0.0
+Date: 2023-01-30
 Authors@R: c(
     person("Martijn", "Schuemie", email = "[email protected]", role = c("aut", "cre")),
     person("Marc", "Suchard", role = c("aut")),
@@ -14,21 +14,24 @@ Authors@R: c(
   )
 Description: An R 'DataBase Interface' ('DBI') compatible interface to various database platforms ('PostgreSQL', 'Oracle', 'Microsoft SQL Server', 
     'Amazon Redshift', 'Microsoft Parallel Database Warehouse', 'IBM Netezza', 'Apache Impala', 'Google BigQuery', 'Snowflake', 'Spark', and 'SQLite'). Also includes support for
-    fetching data as 'Andromeda' objects. Uses 'Java Database Connectivity' ('JDBC') to connect to databases (except SQLite).
+    fetching data as 'Andromeda' objects. Uses either 'Java Database Connectivity' ('JDBC') or other DB I drivers to connect to databases.
 SystemRequirements: Java version 8 or higher (https://www.java.com/)
 Depends:
-    R (>= 2.10)
+    R (>= 4.0.0)
 Imports:
     rJava,
-    SqlRender (>= 1.8.3),
+    SqlRender (>= 1.12.0),
     methods,
     stringr,
     readr,
     rlang,
     utils,
     DBI (>= 1.0.0),
     urltools,
-    bit64
+    bit64,
+    checkmate,
+    digest,
+    dbplyr (>= 2.3.0)
 Suggests:
     aws.s3,
     R.utils,
@@ -40,11 +43,17 @@ Suggests:
     RSQLite,
     ssh,
     Andromeda,
-    dplyr
+    dplyr,
+    RPostgres,
+    odbc,
+    duckdb,
+    pool,
+    ParallelLogger
 License: Apache License
 VignetteBuilder: knitr
 URL: https://ohdsi.github.io/DatabaseConnector/, https://github.com/OHDSI/DatabaseConnector
 BugReports: https://github.com/OHDSI/DatabaseConnector/issues
 Copyright: See file COPYRIGHTS
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
+Roxygen: list(markdown = TRUE)
 Encoding: UTF-8

NAMESPACE

@@ -13,33 +13,48 @@ S3method(lowLevelQuerySqlToAndromeda,default)
 S3method(renderTranslateQueryApplyBatched,DatabaseConnectorDbiConnection)
 S3method(renderTranslateQueryApplyBatched,default)
 export(DatabaseConnectorDriver)
+export(assertTempEmulationSchemaSet)
+export(computeDataHash)
 export(connect)
 export(createConnectionDetails)
+export(createDbiConnectionDetails)
 export(createZipFile)
+export(dateAdd)
+export(dateDiff)
+export(dateFromParts)
+export(day)
 export(dbms)
 export(disconnect)
 export(downloadJdbcDrivers)
 export(dropEmulatedTempTables)
+export(eoMonth)
 export(executeSql)
 export(existsTable)
+export(extractQueryTimes)
 export(getAvailableJavaHeapSpace)
 export(getTableNames)
+export(inDatabaseSchema)
 export(insertTable)
 export(isSqlReservedWord)
 export(lowLevelExecuteSql)
 export(lowLevelQuerySql)
 export(lowLevelQuerySqlToAndromeda)
+export(month)
 export(querySql)
 export(querySqlToAndromeda)
 export(renderTranslateExecuteSql)
 export(renderTranslateQueryApplyBatched)
 export(renderTranslateQuerySql)
 export(renderTranslateQuerySqlToAndromeda)
+export(requiresTempEmulation)
+export(year)
+exportClasses("Microsoft SQL Server")
 exportClasses(DatabaseConnectorConnection)
 exportClasses(DatabaseConnectorDbiConnection)
+exportClasses(DatabaseConnectorDbiResult)
 exportClasses(DatabaseConnectorDriver)
 exportClasses(DatabaseConnectorJdbcConnection)
-exportClasses(DatabaseConnectorResult)
+exportClasses(DatabaseConnectorJdbcResult)
 exportMethods(dbAppendTable)
 exportMethods(dbCanConnect)
 exportMethods(dbClearResult)
@@ -50,6 +65,7 @@ exportMethods(dbDisconnect)
 exportMethods(dbExecute)
 exportMethods(dbExistsTable)
 exportMethods(dbFetch)
+exportMethods(dbGetInfo)
 exportMethods(dbGetQuery)
 exportMethods(dbGetRowCount)
 exportMethods(dbGetRowsAffected)

NEWS.md

@@ -1,3 +1,41 @@
+DatabaseConnector 6.0.0
+=======================
+
+Changes:
+
+1. Complete overhaul of DBI interface. DBI functions now apply translation to all incoming SQL, thus making the DatabaseConnector DBI interface an interface to a virtual database platform speaking OHDSISql as defined in `SqlRender`. This should aid write once - execute everywhere code development. It also allows using `dbplyr` with `DatabaseConnector`.
+
+2. Adding `requiresTempEmulation()` and `assertTempEmulationSchemaSet()` functions.
+
+3. The `dropEmulatedTempTables()` function can be called on all platforms (it doesn't do anything on platforms not requiring temp table emulation).
+
+4. Ensuring `dbms()`, `insertTable()`, `renderTranslateExecuteSql()`, `renderTranslateQuerySql()`, and `renderTranslateQuerySqlToAndromeda()` functions work with connection pool objects.
+
+5. Adding logging at 'TRACE' level for performance profiling using the `ParallelLogger` package. Use `options(LOG_DATABASECONNECTOR_SQL = TRUE)` to enable. The query times can be automatically extracted using the new `extractQueryTimes()` function.
+
+6. Adding the `computeDataHash()` function.
+
+7. The `inserTable()` function now converts logical fields to integer fields (and throws a warning if it does so).
+
+8. The `dbListTables()` and `getTableNames()` functions return results in lowercase instead of uppercase for consistency with DBI functions. 
+
+9. Throwing informative error if user calls `createConnectionDetails()` with credential arguments that cannot be evaluated in a multi-threading setting.
+
+10. Supporting external tables on RedShift.
+
+11. Adding support for ODBC connections to Spark.
+
+12. Querying to Andromeda when using a DBI driver (instead of a JDBC driver) now also uses batching to avoid running out of memory.
+
+13. Adding `appendToTable` argument to `querySqlToAndromeda()`, `renderTranslateQuerySqlToAndromeda()`, and `lowLevelQuerySqlToAndromeda()`.
+
+
+
+Bugfixes:
+
+1. Fix error when calling `insertTable()` and all column names require quotes.
+
+
 DatabaseConnector 5.1.0
 =======================