NEWS

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cs9 2025.3.6

• Automatically logging when tasks start running.

cs9 2025.2.24

New Features

• Added get_config_log() function to retrieve configuration log entries from the config_log table.
  • Supports optional filtering by surveillance system (ss), task name (task), and date range (start_date, end_date).
  • Returns a data.table with the filtered entries.

Improvements

• Updated update_config_log() to also route custom messages (...) to the message() function for clearer console output.

cs9 2025.2.21

• Added update_config_log function. Logs configuration updates including surveillance system (ss), task name (task), and a custom message.

cs9 2024.6.17

• Allows for CS9_DBCONFIG_ROLE_CREATE_TABLE in environmental variables.

• When running in parallel, a seed is set according to the index of the first analysis in each plan.

cs9 2024.6.6

• Partition table names are now 'xxxpartitionxxx' not 'PARTITION'

cs9 2024.3.7

• Including confirm_insert_via_nrow in DBtables. Checks nrow() before insert and after insert. If nrow() has not increased sufficiently, then attempt an upsert.

cs9 2023.8.1

• cs9::path now uses _interactive instead of interactive.

cs9 2023.5.3

• In R 4.3.0 as.character(lubridate::now()) adds microseconds, which breaks the SQL upload. This is now replaced by cstime::now_c().

cs9 2023.4.14

• Changed "success" to "succeeded" in update_config_tasks_stats

cs9 2023.4.13

• DBPartitionedTableExtended_v9$info() bug fixed with argument collapse=TRUE.
• Inclusion of confirm_indexes in DBPartitionedTableExtended_v9.

cs9 2023.4.12

• DBPartitionedTableExtended_v9$nrow() now has a new argument collapse=FALSE that provides partion-specific results
• DBPartitionedTableExtended_v9$info() now includes sizes in MB

cs9 2023.4.3

• Bug fix in DBPartitionedTableExtended_v9$nrow()

cs9 2023.4.2

• Extension of DBPartitionedTableExtended_v9 so that it is easier to use multiple partitioning variables.

cs9 2023.4.1

• Inclusion of partitions_randomized in DBPartitionedTableExtended_v9 so that when running in parallel, the database tables don't get locked.
• Inclusion of remove_table in DBPartitionedTableExtended_v9
• Fixed an error in RAM calculation in parallel for get_config_tasks_stats

cs9 2023.3.31

• DBTableExtended_v9 now automatically includes a column for all tables, called auto_last_updated_datetime, which is automatically calculated each time that row is changed.
• Creation of DBPartitionedTableExtended_v9, which allows for one dataset to be partitioned amongst multiple SQL tables automatically.

cs9 2023.3.8

• SurveillanceSystem_v9 constructor now takes in an argument called implementation_version, which can be used to identify what version of analytics code is currently being run.
• update_config_last_updated has now been replaced by update_config_tables_last_updated (which contains when the tables were last updated) and config_tasks_stats (which contains all the runtimes of the tasks).
• SurveillanceSystem_v9 now uses an internal R6 class DBTableExtended_v9 (which extends csdb::DBTable_v9) instead of using csdb::DBTable_v9 directly. DBTableExtended_v9 calls update_config_last_updated after altering a database table.

cs9 2023.3.7

• sc8 is deprecated in favor of cs9.

cs9 26.5.13

New Features

• TaskJob R6 class and run_task_sequentially_as_callr_bg_using_load_all() wrapper. A drop-in alternative to run_task_sequentially_as_rstudio_job_using_load_all() that works in editors without RStudio's job API (notably Positron, which does not implement runScriptJob). Spawns the task in a fresh callr::r_bg() process so the current environment is not polluted, captures output via a pipe, and streams it back to the calling R console (prefixed with the task name) via later::later() polling. Includes $start(), $wait(), $is_alive(), $status(), $tail(), $kill().

cs9 25.8.21

Documentation

• Organized pkgdown reference documentation with logical function groupings
• Enhanced reference structure with clear categories for different types of functions
• Improved pkgdown configuration for better navigation of package documentation

cs9 25.7.31

New Features

• Enhanced environment variable validation with detailed diagnostic function check_environment_setup()
• Improved graceful degradation for CRAN compatibility - package loads with limited functionality when database infrastructure is not available
• Context-aware environment variable validation with clear user guidance
• Robust error handling in package loading process

Improvements

• Updated system environment configuration handling
• Comprehensive startup messages guide users through configuration issues
• Enhanced database connection error handling
• Improved package loading sequence with better error isolation

Documentation

• Comprehensive installation vignette explaining infrastructure requirements
• Enhanced function documentation with CRAN-compatible examples
• Clear guidance on functionality available in different deployment scenarios
• Added comprehensive package-level documentation (?cs9)
• Enhanced check_environment_setup() documentation with detailed examples
• Updated vignettes with CRAN vs. full setup guidance

CRAN Preparation

• Removed fhiplot dependency (replaced with standard R functions)
• Fixed non-portable file names in vignettes directory
• Cleaned up build artifacts and hidden files
• Updated LICENSE file copyright year to 2025
• Created vignette precompiler system for maintainable documentation
• Verified graceful degradation in minimal environments

Bug Fixes

• Fixed package loading issues in environments without database configuration
• Improved error messages for missing environment variables
• Enhanced database table setup error handling

cs9 8.0.2

• Allows for multiple databases to be used for different access levels.
• copy_into_new_table_where now also copies indexes.
• V8 schemas now have a nice print function.
• V8 redirects now have a nice print function.
• copy_into_new_table_where uses tablock.
• upsert_at_end_of_each_plan and insert_at_end_of_each_plan can now take named lists as the return value from the action_fn.
• Custom progressr handler.

cs9 8.0.1

• When using sc8::add_task_from_config_v8 the schema list is checked to make sure they are actually schemas. This will solve the issue where people incorrectly add non-existent schemas to the task.
• insert_data, upsert_data, drop_all_rows_and_then_insert_data are now the recommended ways of inserting data
• addin_load_production
• schemas now use load_folder_fn, which should dynamically check if a user has permission to write to a folder, solving permissions errors
• Including tm_get_schema_names
• Both granularity_time AND granularity_geo are now included in db censors
• Requires R >= 4.1.0
• sc8::config$plan_attempt_index now exists. When running plans in parallel, if a plan fails it is retried five times. This lets a user track which attempt they are on. This is mostly useful so that emails and smses are only sent when sc8::config$plan_attempt_index==1
• (Disabled) TABLOCK is disabled right now due to issues where data would not be uploaded.
• (Disabled) Data is sorted before sending it to bcp to speed up in/upserts.

cs9 8.0.0

• Release of schema redirects that allow for restricted and anonymous datasets to be seamlessly used by people with different access rights
• Consistent naming of task_from_config_v8 and add_schema_v8

cs9 7.1.4

• db_insert_data, db_upsert_data, db_drop_all_rows_and_then_upsert_data are now the recommended ways of inserting data

cs9 7.1.3

• update_config_datetime and get_config_datetime now automatically record database table updates as well

cs9 7.1.2

• Updating default db schemas to be more explicit with the useage of isotime.

cs9 7.1.1

• qsenc_save and qsenc_read to save/read to/from encrypted files.

cs9 7.1.0

• task_from_config_v3 sets a new direction for creation of tasks and management of tasks
• describe_tasks and describe_schemas help with automatic documentation

cs9 7.0.8

• task_inline_v1 allows for easy inline task creation
• Corresponding RStudio addin for inline tasks that copy from one db table to another

cs9 7.0.7

• copy_into_new_table_where allows for the creation of a new table from an old table
• Including task_from_config_v2
• First RStudio addin

cs9 7.0.6

• write_data_infile now checks for Infinite/NaN values and sets them to NA

cs9 7.0.5

• Task now includes action_before_fn and action_after_fn

cs9 7.0.4

• validator_field_contents_sykdomspulsen now allows baregion as a valid granularity_geo

cs9 7.0.3

• tm_get_plans_argsets_as_dt provides an overview of the plans and argsets within a task

cs9 7.0.2

• keep_rows_where now also retains the PK constraints