Merge pull request #136 from RConsortium/copilot/purge-rds-usage

Completely remove RDS format usage per FDA feedback

Author: bms63

.github/workflows/lint.yml

@@ -117,7 +117,9 @@ jobs:
           }
           lints <- lint_dir(
             "pilot5-submission/pilot5-programs", 
-            linters_with_defaults(line_length_linter = line_length_linter(120L)),
+            linters_with_defaults(line_length_linter = line_length_linter(120L),
+            pipe_consistency_linter = NULL
+            ),
             exclusions = exclusions_list
             )
           saveRDS(lints, file = "lints.rds")

.lintr

@@ -1,6 +1,11 @@
 linters: linters_with_defaults(
-    line_length_linter(120) 
+    line_length_linter(120),
+    pipe_consistency_linter = pipe_consistency_linter(pipe = "%>%")
   )
 exclusions: list(
-  "pilot5-submission/pilot5-programs/pilot5-helper-fcns.r"
+  "pilot5-submission/pilot5-programs/pilot5-helper-fcns.r",
+  "adrg/llm-adrg-utils/util.R",
+  "adrg/llm-adrg-utils/llm_prompts.R",
+  "adrg/llm-adrg-utils/llm_pipeline.qmd",
+  "adrg/llm-adrg-utils/llm_api.R"
   )

adrg/_adrg.qmd

@@ -270,9 +270,9 @@ As a temporary workaround, FDA requested that Conformance Summaries should be ge
 
 The xpts were generated as follows:
 
-* ADaM programs read in sdtm `.json` files
-* ADaM programs wrote out `.rds` files
-* A program converted these `.rds` files to `.json` and then to `.xpt`
+* ADaM programs read in sdtm `.json` files directly
+* ADaM programs wrote out `.json` files directly
+* A program converted these `.json` files to `.xpt`
 * `.xpt` files were validated by P21C
 
 | Check ID | Diagnostic Message                                                           | Dataset | Count | Explanation                                                                                                                                                                             |
@@ -285,11 +285,11 @@ The xpts were generated as follows:
 
 The datasetson 1.0 `.json` files were generated as follows:
 
-* ADaM programs read in sdtm `.json` files
+* ADaM programs read in sdtm `.json` files directly
   * `.json` files were created using datasetjson 1.1 standard
-* ADaM programs wrote out `.rds` files
-* A program converted these `.rds` files to `.json` and then to `.xpt`
+* ADaM programs wrote out `.json` files directly
   * `.json` files were created using datasetjson 1.1 standard
+* `.json` files were converted to `.xpt` files
 * `.xpt` files were converted to by P21C `.json` files using 1.0 standard
 * `.json` files were validated by P21C
 
@@ -674,22 +674,7 @@ which will load all helper functions for datasets and displays into your global
 source(file.path(path$programs, "pilot5-helper-fcns.r"))
 ```
 
-4. Convert sdtm JSON files to rds files. The sdtm files are in json transport file format 
-and need to be converted to rds files to run the ADaM programs.
-
-Run the following code:
-
-```r
-sdtm_files <- list.files(
-  path = file.path(path$sdtm),
-  pattern = "\\.json$",
-  full.names = TRUE
-)
-
-convert_json_to_rds(sdtm_files, output_dir = file.path(path$sdtm))
-```
-
-5. Execute ADaM programs as seen in the order below:
+4. Execute ADaM programs as seen in the order below:
 
  - `adsl.r`
  - `adadas.r`
@@ -698,13 +683,13 @@ convert_json_to_rds(sdtm_files, output_dir = file.path(path$sdtm))
  - `adtte.r`
 
 You can use the following command to quickly execute each ADaM dataset. Just change
-the name of the dataset in the command. Rds files will be created for each ADaM in the `adamdata` folder and in your global environment.
+the name of the dataset in the command. Datasetjson files will be created for each ADaM in the `pilot5-datasetjson` output folder and the dataset will be loaded in your global environment.
 
 ```r
 source(file.path(path$programs, "adsl.r"))
 ```
 
-6. Execute Display programs as seen in the order below:
+5. Execute Display programs as seen in the order below:
 
  - `tlf-demographic.r`
  - `tlf-efficacy.r`