basics of eav

ref #420

playgrounds/eav-playground-2.R

@@ -0,0 +1,138 @@
+rm(list=ls(all=TRUE)) #Clear the memory of variables from previous run. This is not called by knitr, because it's above the first chunk.
+
+# ---- load-sources ------------------------------------------------------------
+
+# ---- load-packages -----------------------------------------------------------
+library("magrittr")
+requireNamespace("httr")
+requireNamespace("dplyr")
+requireNamespace("readr")
+requireNamespace("testit")
+
+# ---- declare-globals ---------------------------------------------------------
+redcap_uri <- "https://bbmc.ouhsc.edu/redcap/api/"
+token <- "9A81268476645C4E5F03428B8AC3AA7B"  # PHI-free demo: simple static
+token <- "5007DC786DBE39CE77ED8DD0C68069A6"  # PHI-free demo: Checkboxes 1
+# token <- "CCB7E11837D41126D67C744F97389E04"  # PHI-free demo: super-wide --3,000 columns
+# token <- "5C1526186C4D04AE0A0630743E69B53C"  # PHI-free demo: super-wide #3--35,000 columns
+# token <- "56F43A10D01D6578A46393394D76D88F"  # PHI-free demo: Repeating Instruments --Sparse
+
+raw_or_label <- "raw"
+export_data_access_groups_string <- "false"
+
+# ---- load-data ---------------------------------------------------------------
+system.time(
+  ds_expected <- REDCapR::redcap_read_oneshot(redcap_uri, token)$data
+)
+
+system.time({
+  ds_metadata <- REDCapR:::redcap_metadata_internal(redcap_uri, token)$d_variable
+  ds_variable <- REDCapR::redcap_variables(redcap_uri, token)$data
+
+  post_body <- list(
+    token                        = token,
+    content                      = "record",
+    format                       = "csv",
+    type                         = "eav"#,
+    # rawOrLabel                   = raw_or_label,
+    # rawOrLabelHeaders            = raw_or_label_headers,
+    # exportDataAccessGroups       = export_data_access_groups,
+    # filterLogic                  = filter_logic,
+    # dateRangeBegin               = datetime_range_begin,
+    # dateRangeEnd                 = datetime_range_end,
+    # exportBlankForGrayFormStatus = blank_for_gray_form_status
+    # record, fields, forms & events are specified below
+  )
+  kernel <- REDCapR:::kernel_api(
+    redcap_uri      = redcap_uri,
+    post_body       = post_body,
+    config_options  = NULL
+    # config_options  = config_options,
+    # encoding        = http_response_encoding,
+    # handle_httr     = handle_httr
+  )
+})
+
+# ds_eav$field_name
+testit::assert(sort(ds_metadata$field_name) == sort(colnames(ds_expected)))
+testthat::expect_setequal( ds_metadata$field_name, colnames(ds_expected))
+
+# ---- tweak-data --------------------------------------------------------------
+
+ds_eav <-
+  readr::read_csv(
+    file            = I(kernel$raw_text),
+    col_types       = readr::cols(.default = readr::col_character()),
+    # locale          = locale,
+    show_col_types  = FALSE
+  )
+
+if (!"event_id" %in% colnames(ds_eav)) {
+  ds_eav$event_id <- "dummy_1"
+}
+
+ds_eav_possible <-
+  ds_eav %>%
+  tidyr::expand(
+    tidyr::nesting(record, event_id),
+    tidyr::crossing(field_name = ds_metadata$field_name)
+  )
+
+# distinct_checkboxes <-
+#   ds_metadata %>%
+#   dplyr::filter(.data$field_type == "checkbox") %>%
+#   dplyr::pull(.data$field_name)
+#
+# ds_possible_checkbox_rows  <-
+#   tidyr::crossing(
+#     field_name = distinct_checkboxes,
+#     record     = unique(ds_eav$record),
+#     field_type = "checkbox",
+#     event_id   =  unique(ds_eav$event_id)
+#   )
+
+# variables_to_keep <-
+#   ds_metadata %>%
+#   dplyr::select(.data$field_name) %>%
+#   dplyr::union(
+#     ds_variable %>%
+#       dplyr::select(field_name = .data$export_field_name) %>%
+#       dplyr::filter(grepl("^\\w+?_complete$", .data$field_name))
+#   ) %>%
+#   dplyr::pull(.data$field_name) #%>% rev()
+
+ds_eav_2 <-
+  ds_eav %>%
+  dplyr::rename(field_name_base = field_name) %>%
+  dplyr::left_join(
+    ds_metadata %>%
+      dplyr::distinct(.data$field_name_base, .data$field_type), # .data$field_name,
+    by = "field_name_base"
+  ) %>%
+  dplyr::mutate(
+    field_name = dplyr::if_else(!is.na(.data$field_type) & (.data$field_type == "checkbox"), paste0(.data$field_name_base , "___", .data$value), .data$field_name_base )
+  ) %>%
+  dplyr::mutate(
+    value      = dplyr::if_else(!is.na(.data$field_type) & (.data$field_type == "checkbox"), as.character(!is.na(.data$value)), .data$value)
+  ) %>%
+  dplyr::right_join(ds_eav_possible, by = c("record", "event_id", "field_name"))
+
+
+
+. <- NULL # For the sake of avoiding an R CMD check note.
+# ds <-
+  ds_eav_2 %>%
+  dplyr::select(-.data$field_type, -.data$field_name_base) %>%
+  # dplyr::select(-.data$redcap_repeat_instance) %>%        # TODO: need a good fix for repeats
+  # tidyr::drop_na(event_id) %>%                            # TODO: need a good fix for repeats
+  tidyr::pivot_wider(
+    # id_cols   = c(record, event_id),
+    names_from  = field_name,
+    values_from = value
+  ) #%>%
+  # dplyr::select(.data = ., !!intersect(variables_to_keep, colnames(.)))
+
+ds_2 <-
+  ds %>%
+  dplyr::mutate_if(is.character, ~type.convert(., as.is = FALSE)) %>%
+  dplyr::mutate_if(is.factor   , as.character)