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redcapAPI (development version)

redcapAPI 2.12.0

Breaking changes

  • unlockREDCap upstream dependency on shelter now default to 'SHELTER_' prefix when looking for ENV variable overrides.

Minor improvements and fixes

  • exportDags, exportFieldNames, exportProjectInformation, exportReportsTyped, importDags, writeDataForImport, and exportRecordsTyped now have a csv_delimiter parameter to control delimiter utilized.
  • importMetaData bug fix when given duplicate names to exit and warn user properly.
  • redcapUserRoleStructure allows new alerts, api_modules, and data_quality_resolution attributes.
  • exportUsers properly handles the columns random_setup, random_dashboard and random_perform.
  • importUsers and exportUsers weren't handling data_access_group assignment properly.
  • exportUserRoles now avoids errors when user role access columns are missing from export responses.
  • exportFileRepositoryListing returns a data.frame with 6 columns (was 4) from REDCap version 16.0.8 and up.
  • redcapConnection has better documentation on setting the CSV delimiter and this is respected through most calls except for ones that have been shown to be hard coded to commas by REDCap.

DEPRECATION NOTICES

A future release of version 3.0.0 will introduce several breaking changes!

  • The exportRecords function interface will be replaced. Please switch your processes to exportRecordsTyped
  • The importRecords function interface will be replaced to utilize castForImport to prepare data for import. Validation logs will no longer be printed.
  • The redcapFactor class is being discontinued with all its supporting methods (including redcapFactorFlip). Please use recastRecords instead.
  • The recodeCheck function is being discontinued. Please use recastRecords instead.

2.11.5

  • prepUserImportData_validateAllFormsPresent and prepUserImportData_extractFormName functions are removed.
  • Enhanced logging of exporting records to include record_id and other non-PHI info.
  • Updated user role permissions to use new numbering scheme based on REDCap version.
  • unlockREDCap adds trailing slash to url if not present.
  • importUsers improved error message when invalid columns are provided.
  • Added data_access_group_label to allowed user attributes.
  • Added data_quality_resolution to allowed user attributes. It may be unnecessary.

2.11.4

  • Updated to allow for project_pi_email as an allowed field of project info.
  • Updated to allow for data_access_group as part of user role assignment.

2.11.3

  • Added injectable log function for use in production environments or debugging.

2.11.2

  • Fixed bug in exportDataQuality when no quality issues exist.
  • Deprecated functions exportProjectInfo and exportBundle have been removed.
  • Fixed offline test that was having issue on Windows.
  • Fixed bug in exportFilesMultiple.

2.11.1

  • Better handling of unexpected html responses from REDCap.
  • Improved CSV formatting for API imports. Properly deals with escaped quoting.
  • Allow for overlapping mapping in radio import validation.
  • Restored debug mode for API call/response. Just add config=list(options=list(verbose=TRUE)) to unlockREDCap or any call.
  • Added experimental exportSAS.

2.11.0

  • unlockREDCap internal code is now in package shelter.

2.10.3

  • Update missingSummary to support "missing checkbox" under special branching scenario.

2.10.2

  • When a project is deleted, the records no longer show in the logs as deleted with the current version of REDCap (15.2.0). Removed test of logs for deleted records

2.10.1

  • unlockREDCap no longer changes console focus
  • Vectorized renameRecord and exportFieldNames
  • Exporting connectAndCheck function to establish connections
  • Improved error messages when misspecified URL is provided.
  • Fix for redirected URLs

2.10.0

  • Replace httr dependency with curl

2.9.4

  • Minor code refactoring
  • Add test case for CI environment
  • Implemented GitHub Actions for automated source code checks.

2.9.3

  • REDCap 14.4.0 changed user role structure.

2.9.2

  • Improved date and datetime validation
  • Bug fix for importMetaData validation
  • Refactored error handling on API calls to reduce code footprint.
  • Added redcap_survey_identifier to system field list.
  • Bug fix for handling fields ending in '_complete' that are not form related.
  • Added batching method for exportLogging.

2.9.1

  • Added additional supported arguments to deleteRecords.
  • Changed the default to dag=FALSE for exportRecordsTyped.
  • exportRecordsTyped more robust against some forms of corrupted meta data.
  • Added a new feature exportDataQuality for pulling queries from the DataQuality module.

2.9.0

  • Refactor of missingSummary to use exportRecordsTyped. This is a breaking change in prep of 3.0.0.
  • Added handling of url redirects (301,302) on makeApiCall.

2.8.5

  • importRecords stops when provided fields not in the project.
  • Filtering empty records will use mapping if available
  • Minor export optimizations for records.
  • unlockREDCap will now search for ENV variables.
  • New importFileToRecord which will import a file and create the record if it doesn't exist.

2.8.4

  • Patch to reading HTTP data. When non UTF-8 characters are sent, they get mapped to '□'.

2.8.3

  • Patch to date range handling that was breaking on new REDCap projects since version 14.0.2 of the REDCap server.
  • Improved speed / memory usage for empty row exclusion.
  • Checkbox field labels now follow the pattern '[field_label] (choice=[choice_label])'
  • Fixed checkbox handling to be consistent with data export tool.
  • Added skip_validation function to complement raw_cast.

2.8.2

  • Extends casting and validation to text fields validated with the BioPortal Ontology service.
  • Extends casting and validation to sql fields.
  • Adds valSkip, allowing for validation to be skipped for a field type.
  • Adds castLogical casting function.
  • Adds four vignettes for getting started with using unlockREDCap and exportRecordsTyped.
  • Added helper function changedRecords.
  • Added assembleCodebook, which mimics the codebook in the REDCap UI in the form of a data frame.

2.8.1

  • New functions for project management: createRedcapProject, exportProjectXml
  • Additional timeout trap for request retry strategy.
  • Reports of data failing validation checks now include a link to the form with the failing data.
  • Major cleanup to remove messages on successful function execution. Many return values are changed to be consistent and be TRUE/FALSE if possible.
  • Bug fix: The repeat_instance argument of exportFiles is now included in the API call.
  • New Vignette: vignette("redcapAPI-offline-connection")
  • Adds exportFilesMultiple to facilitate exporting multiple files in a familiar interface.
  • Bug fix: Batching records no longer has the potential to produce duplicated records when a record ID has data in multiple events. (See Issue 262)
  • Extends preserveProject and adds readPreservedProject to assist with preparing data for offline users.

2.8.0

  • Changed importArms and importEvents to use data argument for consistency. Backward compatible via ....
  • Added several functions for manipulating DAGs.
  • Fixed bug in zero coded fields. NOTE: It is impossible to handle every possible case as the definition of zero coded fields in REDCap can be inconsistent.
  • Fixed issue in importUsers where existing roles might get dropped on an update. Now handles the multiple API calls seemlessly to properly handle user roles.
  • Fixed issue with decimal validation.
  • Added renameRecord function.
  • Fixed issue with preserving missing values in preparing checkbox fields for import
  • Added default_cast_no_factor, a list of casting functions that may be used to cast fields without casting any fields to factors. It comes with an equivalent alias default_cast_character.
  • Documentation has been standardized. Related methods are now documented in the same help file.
  • Add several functions for exporting Survey links and return codes
  • Replaced deprecated function with_mock with with_mocked_bindings

2.7.5

  • added filter_empty_rows flag to exportRecordsTyped.

2.7.4

  • Fixed upper/lower case for AND/OR in parseBranchingLogic
  • Added a system field type for mapping with castLabel and castRaw.
  • DAGs are added to connection cache.
  • Timeout on connections defaults to 5m.
  • Clearer error message on connection closed.
  • export/import handles the 'now' and 'today' validation words for dates and date/times.
  • unlockREDCap: major refactor / rewrite. Many edges cases handled gracefully with better error messaging. Now with less password requests.

2.7.3

  • dags: Added ability to get DAG information from connection object, e.g. rcon$dags()
  • exportBulkRecords: When no forms are specified, it defaults to all instruments for the project.
  • importRecords: Got rid of warning about dropping fields that were already dropped.
  • mChoiceCast: Added configurable dropping of choice fields that were aggregated. Defaults to drop.
  • unlockREDCap: Defaults to RStudio password prompt if available. Uses askpass option. General improvements in error messages.

2.7.2

  • Spelling/Grammar cleanup
  • envir parameter allows passing a number of the environment
  • New functions use pre-existing error handling strategy.

2.7.1

Version bump for CRAN publication

2.7.0

  • The new function exportRecordsTyped is now available as a replacement for the existing exportRecords. It is a breaking change in interface--but provides far better stability in calling--full inversion of control over casting, retries through the connection object, and a clear error report as part of the final dataframe. Please take a moment to read the documentation on exportRecordsTyped and start moving over to using it over exportRecords.
  • bundle argument has been removed from all API methods. (It is no longer needed, thanks to caching). Backward compatibility is unaffected.
  • Introduces the offlineConnection function, which creates the redcapOfflineConnection object. This connection object can be built using either data frames structured like those received from the API methods, or the CSV files downloaded from the REDCap UI. The object function in the same way as an API connection with caching. Meta data can be retrieved via rcon$metadata(), etc..
  • added castForImport. Recasts a data.frame back into the expected text values.
  • added exportReportsTyped. Similar to exportRecordsTyped. * Helper function exportBulkRecords for bulk calls to exportRecordsTyped.

2.6.2

  • Added retry parameter to connection object. On timeouts and gateway failures it retries 5 times now by default.
  • Cleanup from emergency patches.

2.6.1

  • Emergency fix. REDCap latest version changed its API calling syntax.
  • Fix to choice name parsing when only a single choice is specified.
  • Fix to importMethod validators when event=NULL

2.6.0

  • A set of functions to deal with file import / export in REDCap
    • exportFileRepositoryListing
    • exportFromFileRepository
    • exportFileRepository
    • importToFileRepository
    • deleteFromFileRepository
    • createFileRepositoryFolder
    • importFileRepository
    • deleteFileRepository

2.5.0

  • IMPORTANT: The upcoming 3.0.0 release will be a breaking change for exportRecords. This is needed for full inversion of control to the user over type casting.
  • Fully removed deprecated redcapDbConnection
  • Added a drop= argument to exportRecords and exportReports. These columns are dropped before returning.
  • Metadata is cached in the connection object. In addition to token, url, and config elements, the following are also made available:
    • metadata
    • arms
    • events
    • fieldnames
    • mapping
    • users
    • version
    • projectInformation each of these has a companion function
    • has_* (returns a logical indicating if the element has been cached)
    • flush_* (removes the cached value)
    • refresh_* (replaces the cached value with a fresh call to the API) There are also flush_all and refresh_all methods.
  • New method: exportLogging
  • Fixed minor bugs in validations and improved documentation
  • Fixed bug in formatting vectors for API calls in multiple places #33
  • Removed stringr and tidyr as dependencies
  • Removed unused version argument from checkbox_suffix
  • Fixed error thrown in export_users when labels=TRUE
  • Greatly expanded test coverage
  • mChoice class addition if Hmisc is installed

2.4.2

  • Added a missingSummary function that deals with branching logic.
  • Fixed bug in delete records.
  • Fixed bug date handling for NA in date conversion of time_hh_mm_ss

2.4.0

  • Added handlers overrides for type conversion based on REDCap field type.

2.3.3

Transfer from Benjamin Nutter to VUMC Biostatistics.

2.3.0

  • Bug fix: Unmapped suffixes do not cause crashes, only warnings.

2.2.0

  • BREAKING CHANGE: The dev_allocate and prod_allocate elements of the object returned by allocationTable have been named dev_allocation and prod_allocation, respectively.
  • Bug fix: importRecords now handles data with repeating forms correctly.
  • New feature: UTF-8 Characters may be stripped from the data dictionary.

2.1.0 (2018-03-03)

  • Bug fix: Add [form]_complete fields
  • Bug fix: Include [form]_complete fields in Reports
  • New feature: [form]_complete fields may be explicitly requested.
  • New feature: Automatic selection of [form]_complete fields may be turned off.

2.0.0 (2017-01-18)

  • redcapDbConnection methods are being deprecated. To our knowledge, no one is using these methods, and we do not believe they would work as previously coded anyway. The methods definitions continue to be reserved although they will likely not be developed in the foreseeable future (if at all). Please file an issue on GitHub if you feel such methods would be of use.
  • redcapProjectInfo is being deprecated, as it will inevitably create confusion with the API method exportProjectInformation. The replacement function is exportBundle.
  • export bundles are now placed into the option redcap_bundle by default. For now, exportBundle will also return that same object. This is to prevent back-compatibility problems with existing code but will change at a future date.
  • Added several new API functions. All functions up to REDCap 6.5.0 are included.
  • Optional arguments that previously had no default now default to NULL. There should be no change in behavior related to this change.
  • Further standardization to documentation. Each function has three new sections: "From the REDCap Documentation" which gives the description of the function as taken from the REDCap documentation; "REDCap Version" which gives the versions of REDCap for which the function is known to operate; and "Known REDCap Limitations" which documents any bugs or other limitations that may be encountered when working with the API
  • the fieldToVar function now operates on a switch statement instead of a sequence of if else blocks. It also incorporates a for loop in place of the lapply and <<- structure.
  • Error checking, when feasible, makes use of the checkmate package.
  • exportVersion will now return "5.12.2" for all versions of REDCap less than 6.0.0. While it is admittedly odd, this allows for consistent logical comparisons of of versions and allows better control of the package's behavior over multiple versions of REDCap.
  • REDCap variables that can reasonably be treated as factors are given an additional class, redcapFactor, that inherits whatever class the variable becomes on export. For example, if factors = TRUE, the new class will be c("redcapFactor", "factor"), otherwise, it may be something similar to c("redcapFactor", "numeric"). This is done to assist in converting factors back and forth between classes as needed (particular when using redcapFactorFlip).
  • A package option is added for how to manage errors returned by the API. This is used to assist in dealing with errors relating to bugs in the API and/or the user's version of REDCap. For instance, if an API method doesn't exist for the user's version of REDCap, the user can control if a hard error is returned, or if a NULL value is returned. See ?redcap_error for details.
  • Codebase has been standardized and given a cleaner format (yeah, that's totally subjective)

1.3.5 (2017-01-20)

  • Bug fixes from @tobadia. (Issue #79)

1.3.2 (2015-12-09)

  • Bug fix. Changed the call to fieldToVar in exportReports; was incorrectly referencing the meta_data field names. Thanks to Will Campbell for finding this bug.

1.3.1 (2015-07-05)

  • Changed the default config argument in redcapConnection from config=list() to config=httr::config().
  • Added code to allow all errors from apiCall to be returned correctly.

1.3 (2015-03-04)

  • The Maintainer has been changed to Stephen Lane
  • Bug fix: The REDCap API Error message for exportEvents, exportArms, and exportMappings changed between versions 5.x and 6.0. In 5.x, the error message is "You cannot export arms for classic projects." In 6.0+, it is "ERROR: You cannot export arms for classic projects." The change causes exportEvents, exportArms, and exportMappings to cast an error instead of returning the character string with the error. The bug fix accommodates the error messages from both 5.x and 6.0+.

1.2 (2015-02-01)

  • Code has been rewritten to make use of the roxygen2 documentation style.
  • The function 'allocationTable' is added. This assists in producing allocation tables for the randomization module.
  • Offline versions for 'exportRecords' and 'allocationTable' are included. These produce output identical to the API calls, but operate based on the csv's downloaded via the user interface.

1.1 (2014-10-01)

  • redcapAPI now depends on R 3.0.0 or higher
  • A bug fix was added. When specifying the 'fields' and 'forms' arguments in 'exportRecords', only the variables in 'fields' were being converted to the appropriate data types. This has been corrected.
  • redcapAPI requires Hmisc 3.14-6 or higher. This is a consequence of the following item. Please update your Hmisc package.
  • The Hmisc package was moved from the Suggests field to the Imports field. This reflects the addition of some of the label functions in Hmisc being explicitly exported, making them available to import.

1.0.1 (2014-10-20)

  • Bug fix: in importRecords meta data was not previously exported when a project info object was not provided. This is now corrected
  • Bug fix: in exportRecords and exportReports, the checkbox labels weren't being returned as factor levels when checkboxLabels=TRUE. The behavior is now consistent with expectations.
  • Bug fix: in compareRedcapVersion, a logical check was failing due to an omitted argument in grepl. This has been corrected.
  • added function apiCall. This wraps a call to tryCatch. If a Gnu/TLS recv error is returned, the encoding is changed from 'gzip' to 'identity' to successfully retrieve the API response.
  • tryCatch calls are added to redcapProjectInfo to prevent fatal errors when one of the API functions casts an error. The output is modified to indicate where the problem occurred. This is most likely to affect exportUsers. An unresolved issue behind this is logged in the issues on GitHub.