Description
I am not sure if you want to support this given that it effects pretty old versions of REDCap, and I am not sure when Vanderbilt fixed the root cause, but redcap_read() presently fails when trying to read records on older versions of REDCap circa v7.3.5.
Specifically, I am trying to read data from a v7.3.5 instance of REDCap, and redcap_read() fails with the following:
Warning: The following named parsers don't match the column names: has_repeating_instruments_or_events, missing_data_codes, external_modules, bypass_branching_erase_field_prompt1 rows were read from REDCap in 0.3 seconds. The http status code was 200.
Warning: Unknown or uninitialised column: `has_repeating_instruments_or_events`.Error in if (d_proj$has_repeating_instruments_or_events[1]) { :
argument is of length zero
I have traced the issue to a pairing of what the REDCap API returns and this commit on 2022-10-08. That is, redcap_read() broke for v7.3.5 with this commit.
The underlying issue is that redcap_metadata_internal() expects a long list of columns to be returned, but the API does not return all of them for older versions of the API.
Here are the expected columns:
col_types <- readr::cols(
project_id = readr::col_integer(),
project_title = readr::col_character(),
creation_time = readr::col_datetime(format = ""),
production_time = readr::col_datetime(format = ""),
in_production = readr::col_logical(),
project_language = readr::col_character(),
purpose = readr::col_integer(),
purpose_other = readr::col_character(),
project_notes = readr::col_character(),
custom_record_label = readr::col_character(),
secondary_unique_field = readr::col_character(),
is_longitudinal = readr::col_logical(),
has_repeating_instruments_or_events = readr::col_logical(),
surveys_enabled = readr::col_logical(),
scheduling_enabled = readr::col_logical(),
record_autonumbering_enabled = readr::col_logical(),
randomization_enabled = readr::col_logical(),
ddp_enabled = readr::col_logical(),
project_irb_number = readr::col_character(),
project_grant_number = readr::col_character(),
project_pi_firstname = readr::col_character(),
project_pi_lastname = readr::col_character(),
display_today_now_button = readr::col_logical(),
missing_data_codes = readr::col_character(),
external_modules = readr::col_character(),
bypass_branching_erase_field_prompt = readr::col_character(),
.default = readr::col_character()
)
names(col_types$cols)
#> [1] "project_id" "project_title"
#> [3] "creation_time" "production_time"
#> [5] "in_production" "project_language"
#> [7] "purpose" "purpose_other"
#> [9] "project_notes" "custom_record_label"
#> [11] "secondary_unique_field" "is_longitudinal"
#> [13] "has_repeating_instruments_or_events" "surveys_enabled"
#> [15] "scheduling_enabled" "record_autonumbering_enabled"
#> [17] "randomization_enabled" "ddp_enabled"
#> [19] "project_irb_number" "project_grant_number"
#> [21] "project_pi_firstname" "project_pi_lastname"
#> [23] "display_today_now_button" "missing_data_codes"
#> [25] "external_modules" "bypass_branching_erase_field_prompt"Created on 2023-02-03 with reprex v2.0.2
And here are the actual columns returned:
library(RCurl)
result <- postForm(
uri='https://redcap.wustl.edu/redcap/.../api/',
token='XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX',
content='project',
format='csv',
returnFormat='json'
)
names(
readr::read_csv(
I(result),
show_col_types = FALSE
)
)
#> [1] "project_id" "project_title"
#> [3] "creation_time" "production_time"
#> [5] "in_production" "project_language"
#> [7] "purpose" "purpose_other"
#> [9] "project_notes" "custom_record_label"
#> [11] "secondary_unique_field" "is_longitudinal"
#> [13] "surveys_enabled" "scheduling_enabled"
#> [15] "record_autonumbering_enabled" "randomization_enabled"
#> [17] "ddp_enabled" "project_irb_number"
#> [19] "project_grant_number" "project_pi_firstname"
#> [21] "project_pi_lastname" "display_today_now_button"Created on 2023-02-03 with reprex v2.0.2
A setdiff() would show the missing columns are those listed in the part of the message produced by read_csv():
- has_repeating_instruments_or_events
- missing_data_codes
- external_modules
- bypass_branching_erase_field_prompt
The actual stopping error happens later in redcap_metadata_internal() when there is an attempt to check d_proj$has_repeating_instruments_or_events[1] which is NULL on account of not having been returned by the API.
I have a solution that produces the expected d_proj object with NA for the missing columns, but before I initiated a pull request, I wanted to see if this was something you wanted to support.
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