Move test data out of package space and remove tests of schema files

.gitignore

@@ -1,3 +1,4 @@
+.vscode/
 .Rproj.user
 .Rhistory
 .RData

DESCRIPTION

@@ -37,7 +37,6 @@ License: Apache License (>= 2)
 Encoding: UTF-8
 LazyData: true
 Imports:
-    bit64,
     dplyr,
     jsonlite,
     lubridate,

NAMESPACE

@@ -4,7 +4,6 @@ export(connect_to_rcc_billing_db)
 export(draft_communication_record_from_line_item)
 export(fix_data_in_invoice_line_item)
 export(fix_data_in_invoice_line_item_communication)
-export(fix_data_in_redcap_log_event)
 export(fix_data_in_redcap_projects)
 export(fix_data_in_redcap_user_information)
 export(get_bad_emails_from_log)

R/data.R

@@ -33,74 +33,6 @@
 #' @source \url{https://github.com/ctsit/rcc.billing/issues/3}
 "invoice_line_item_test_data"
 
-#' Sample data for service_instance table
-#'
-#' @format
-#' \describe{
-#'   \item{service_instance_id}{the primary key}
-#'   \item{service_type_code}{a numeric code that uniquely identifies the service_type}
-#'   \item{service_identifier}{either a redcap project ID, or redcap username}
-#'   \item{ctsi_study_id}{CSBT’s unique identifier for a service}
-#'   \item{active}{a boolean indicating if we expect to continue billing for this service}
-#' }
-#'
-#' @source \url{https://github.com/ctsit/rcc.billing/issues/2}
-"service_instance_test_data"
-
-#' Sample data for service_type table
-#'
-#' @format
-#' \describe{
-#'   \item{service_type_code}{a numeric code that uniquely identifies the service_type}
-#'   \item{service_type}{short name describing the service_type, in snake case}
-#'   \item{price}{price for one unit of the service, in US dollars}
-#'   \item{billing_frequency}{frequency at which this service ir billed, in months}
-#' }
-#'
-#' @source \url{https://github.com/ctsit/rcc.billing/issues/1}
-"service_type_test_data"
-
-#' @title invoice_line_item_communications_test_data
-#' @description A test dataset for testing functions that write or read invoice_line_item_communications
-#' @format A data frame with 26 rows and 32 variables:
-#' \describe{
-#'   \item{\code{id}}{double: the primary key}
-#'   \item{\code{service_identifier}}{character: either a redcap project ID, or redcap username}
-#'   \item{\code{service_type_code}}{double: a numeric code that uniquely identifies the service_type}
-#'   \item{\code{service_instance_id}}{character: a numeric code that uniquely identifies the service_instance}
-#'   \item{\code{ctsi_study_id}}{double: CSBT's unique identifier for a service}
-#'   \item{\code{name_of_service}}{character: name of the service}
-#'   \item{\code{name_of_service_instance}}{character: name of the study}
-#'   \item{\code{other_system_invoicing_comments}}{character: additional invoice information, either project url, or sponsor and pi}
-#'   \item{\code{price_of_service}}{double: price of the service, in US dollars}
-#'   \item{\code{qty_provided}}{double: quantity provided}
-#'   \item{\code{amount_due}}{double: amount due, in US dollars}
-#'   \item{\code{fiscal_year}}{character: fiscal year of the invoice}
-#'   \item{\code{month_invoiced}}{character: month of the invoice}
-#'   \item{\code{pi_last_name}}{character: last name of the person invoiced}
-#'   \item{\code{pi_first_name}}{character: first name of the person invoiced}
-#'   \item{\code{pi_email}}{character: email of the person invoiced}
-#'   \item{\code{gatorlink}}{character: gatorlink of the person invoiced}
-#'   \item{\code{crc_number}}{double: Clinical Research Center number}
-#'   \item{\code{ids_number}}{character: Investigational Drug Service number}
-#'   \item{\code{ocr_number}}{character: Office of Clinical Research study number}
-#'   \item{\code{invoice_number}}{double: invoice number}
-#'   \item{\code{je_number}}{character: journal entry number}
-#'   \item{\code{je_posting_date}}{POSIXct: journal entry posting date}
-#'   \item{\code{reason}}{character: reason for the invoice}
-#'   \item{\code{status}}{character: status of the invoice}
-#'   \item{\code{created}}{POSIXct: created at timestamp}
-#'   \item{\code{updated}}{POSIXct: updated at timestamp}
-#'   \item{\code{sender}}{character: message sender, typically an email address}
-#'   \item{\code{recipient}}{character: message recipient, typically an email address}
-#'   \item{\code{date_sent}}{POSIXct: date CTSI sent the message}
-#'   \item{\code{date_received}}{POSIXct: date CTSIT received the email}
-#'   \item{\code{script_name}}{character: the script that created this record}
-#' }
-#'
-#' @source \url{https://github.com/ctsit/rcc.billing/issues/7}
-"invoice_line_item_communications_test_data"
-
 #' @title CTS-IT Staff
 #' @description usernames of CTS-IT staff
 #' @format A data frame with 6 rows and 1 variable:
@@ -434,87 +366,6 @@
 #' }
 "projects_table_fragment"
 
-#' @title redcap_user_information_test_data
-#' @description Test dataset for redcap_user_information
-#' @format A data frame with 5 rows and 49 variables:
-#' \describe{
-#'   \item{\code{ui_id}}{integer primary key}
-#'   \item{\code{username}}{character redcap username}
-#'   \item{\code{user_email}}{character primary email address}
-#'   \item{\code{user_email2}}{character}
-#'   \item{\code{user_email3}}{character}
-#'   \item{\code{user_phone}}{character}
-#'   \item{\code{user_phone_sms}}{character}
-#'   \item{\code{user_firstname}}{character}
-#'   \item{\code{user_lastname}}{character}
-#'   \item{\code{user_inst_id}}{character}
-#'   \item{\code{super_user}}{integer}
-#'   \item{\code{account_manager}}{integer}
-#'   \item{\code{access_system_config}}{integer}
-#'   \item{\code{access_system_upgrade}}{integer}
-#'   \item{\code{access_external_module_install}}{integer}
-#'   \item{\code{admin_rights}}{integer}
-#'   \item{\code{access_admin_dashboards}}{integer}
-#'   \item{\code{user_creation}}{double}
-#'   \item{\code{user_firstvisit}}{double}
-#'   \item{\code{user_firstactivity}}{double}
-#'   \item{\code{user_lastactivity}}{double}
-#'   \item{\code{user_lastlogin}}{double}
-#'   \item{\code{user_suspended_time}}{double}
-#'   \item{\code{user_expiration}}{double}
-#'   \item{\code{user_access_dashboard_view}}{double}
-#'   \item{\code{user_access_dashboard_email_queued}}{character}
-#'   \item{\code{user_sponsor}}{character}
-#'   \item{\code{user_comments}}{character}
-#'   \item{\code{allow_create_db}}{integer}
-#'   \item{\code{email_verify_code}}{character}
-#'   \item{\code{email2_verify_code}}{character}
-#'   \item{\code{email3_verify_code}}{character}
-#'   \item{\code{datetime_format}}{character}
-#'   \item{\code{number_format_decimal}}{character}
-#'   \item{\code{number_format_thousands_sep}}{character}
-#'   \item{\code{csv_delimiter}}{character}
-#'   \item{\code{two_factor_auth_secret}}{character}
-#'   \item{\code{display_on_email_users}}{integer}
-#'   \item{\code{two_factor_auth_twilio_prompt_phone}}{integer}
-#'   \item{\code{two_factor_auth_code_expiration}}{integer}
-#'   \item{\code{api_token}}{character}
-#'   \item{\code{messaging_email_preference}}{character}
-#'   \item{\code{messaging_email_urgent_all}}{integer}
-#'   \item{\code{messaging_email_ts}}{double}
-#'   \item{\code{messaging_email_general_system}}{integer}
-#'   \item{\code{messaging_email_queue_time}}{double}
-#'   \item{\code{ui_state}}{character}
-#'   \item{\code{api_token_auto_request}}{integer}
-#'   \item{\code{fhir_data_mart_create_project}}{integer}
-#' }
-#' @details DETAILS
-"redcap_user_information_test_data"
-
-#' @title redcap_log_event_test_data
-#' @description a named list of redcap_log_event tables with project lifecycle test data
-#' @format A named list of 10 dataframes each with a 0 or more rows of 15 variables.
-#'   Each dataframe is structured as described here.
-#' \describe{
-#'   \item{\code{log_event_id}}{integer primary key}
-#'   \item{\code{project_id}}{integer REDCap project_id}
-#'   \item{\code{ts}}{double a timestamp in the format YYYYMMDDHHMMSS in local time}
-#'   \item{\code{user}}{character the REDCap username who initiated this event}
-#'   \item{\code{ip}}{character IP address of that REDCap user}
-#'   \item{\code{page}}{character relative REDCap URL that initiated this event}
-#'   \item{\code{event}}{character the type of event. e.g DATA_EXPORT, DELETE, ERROR, INSERT, MANAGE, OTHER, UPDATE}
-#'   \item{\code{object_type}}{character a REDCap object type e.g., NA, redcap_arms, redcap_auth, redcap_data, redcap_docs, redcap_event_forms, redcap_events, redcap_events_metadata, redcap_metadata, redcap_metadata_temp, redcap_projects, redcap_user_rights}
-#'   \item{\code{sql_log}}{character the SQL code executed during this event}
-#'   \item{\code{pk}}{character the primary key of the effected object}
-#'   \item{\code{event_id}}{integer the REDCap event_id if relevant}
-#'   \item{\code{data_values}}{character}
-#'   \item{\code{description}}{character description of the event}
-#'   \item{\code{legacy}}{integer}
-#'   \item{\code{change_reason}}{character}
-#' }
-#' @details DETAILS
-"redcap_log_event_test_data"
-
 #' @title csbt_column_names
 #' @description Column names useful for CTSI-IT billing
 #' @format A data frame with 12 rows and 2 variables:
@@ -524,25 +375,6 @@
 #'}
 "csbt_column_names"
 
-#' @title invoice_line_item_reasons
-#' @description Provides text for new invoice line items
-#' @format A data frame with 3 rows and 2 variables:
-#' \describe{
-#'   \item{\code{code}}{character: A short, static name for the string}
-#'   \item{\code{label}}{character: A friendly human-readable string}
-#'}
-"invoice_line_item_reasons"
-
-#' @title invoice_line_item_statuses
-#' @description Describes valid invoice line item statuses
-#' @format A data frame with 5 rows and 2 variables:
-#' \describe{
-#'   \item{\code{status}}{character: A short, static name for the status code}
-#'   \item{\code{description}}{character: A human-readable description of the status}
-#'}
-#' @details DETAILS
-"invoice_line_item_statuses"
-
 #' @title fiscal_years
 #' @description A dataframe of fiscal years and labels from 2019-2020 to 2039-2040
 #' @format A data frame with 21 rows and 2 variables:
@@ -558,14 +390,3 @@
 #' @format A vector with 9 elements
 #' @details DETAILS
 "log_event_tables"
-
-#' @title redcap_rights_test_data
-#' @description A named list of dataframes used to test the functions written for redcap_rights.R
-#' @format A named list of 3 dataframes:
-#' \describe{
-#'   \item{\code{redcap_user_information}}{REDCap Core table}
-#'   \item{\code{redcap_user_rights}}{REDCap Core table}
-#'   \item{\code{redcap_user_roles}}{REDCap Core table}
-#' }
-#' @details DETAILS
-"redcap_rights_test_data"

R/transform.R

@@ -175,39 +175,6 @@ fix_data_in_redcap_user_information <- function(data) {
   return(mutate_columns_to_posixct(data, time_columns))
 }
 
-#' fix_data_in_redcap_log_event
-#'
-#' Fixes column data types that can vary between MySQL/MariaDB and SQLite3.
-#' This allows testing in SQLite3 while production is MariaDB
-#'
-#' @param data - a dataframe containing data from the redcap_log_event tables
-#'
-#' @return The input dataframe with revised data types
-#' @export
-#'
-#' @examples
-#' \dontrun{
-#' fix_data_in_redcap_log_event(redcap_log_event_test_data)
-#' }
-fix_data_in_redcap_log_event <- function(data) {
-  integer64_columns <- c(
-    "ts"
-  )
-  if (nrow(data) == 0) { # zero-row SQLite3 tables get the wrong data type on ts
-    result <- data |>
-      dplyr::mutate(
-        dplyr::across(
-          dplyr::any_of(integer64_columns),
-          bit64::as.integer64
-        )
-      )
-  } else {
-    result <- data
-  }
-
-  return(result)
-}
-
 #' Renames columns of a dataframe from CTSIT format to CSBT format
 #'
 #' Excludes non-CSBT columns and renames CTSIT column names to the corresponding CSBT names.