incorporating fl metadata function into vignettes

ecohealthalliance · Aug 28, 2024 · 88c2513 · 88c2513
1 parent d94489e
commit 88c2513
Show file tree

Hide file tree

Showing 7 changed files with 31 additions and 61 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -23,6 +23,7 @@ Imports:
     arsenal,
     containerTemplateUtils (>= 0.0.0.9006),
     dplyr,
+    frictionless,
     googledrive,
     googlesheets4,
     here,

diff --git a/NAMESPACE b/NAMESPACE
@@ -14,6 +14,7 @@ export(detect_language)
 export(download_dropbox)
 export(download_googledrive_files)
 export(dropbox_upload)
+export(expand_frictionless_metadata)
 export(get_dropbox_val_logs)
 export(get_odk_form_schema)
 export(get_odk_responses)

diff --git a/R/create_structural_metadata.R b/R/create_structural_metadata.R
@@ -179,10 +179,10 @@ create_structural_metadata <- function(data,
 #' @param additional_elements data frame. OPTIONAL Empty tibble with structural
 #' metadata elements and their types.
 #'
+#' @note See vignette on metadata for examples
+#'
 #' @return data.frame
 #' @export
-#'
-#' @examples
 update_structural_metadata <- function(data,metadata,primary_key = "", foreign_key = "",additional_elements = tibble::tibble()){
 
   existing_fkeys <- metadata |>

diff --git a/man/update_structural_metadata.Rd b/man/update_structural_metadata.Rd
diff --git a/vignettes/data_examples/my_data.csv b/vignettes/data_examples/my_data.csv
@@ -1,11 +1,11 @@
 "date","measurement","measured_by","site_name","key"
-2024-08-26,22,"Johana","c",1
-2024-08-27,94,"Collin","c",2
-2024-08-28,85,"Collin","b",3
-2024-08-29,63,"Collin","d",4
-2024-08-30,92,"Collin","e",5
-2024-08-31,8,"Collin","a",6
-2024-09-01,96,"Collin","e",7
-2024-09-02,53,"Johana","b",8
-2024-09-03,11,"Johana","a",9
-2024-09-04,97,"Johana","d",10
+2024-08-26,29,"Johana","b",1
+2024-08-27,53,"Johana","e",2
+2024-08-28,71,"Johana","d",3
+2024-08-29,43,"Collin","e",4
+2024-08-30,93,"Johana","b",5
+2024-08-31,4,"Collin","d",6
+2024-09-01,74,"Johana","e",7
+2024-09-02,13,"Johana","c",8
+2024-09-03,46,"Johana","e",9
+2024-09-04,44,"Collin","a",10
diff --git a/vignettes/metadata.Rmd b/vignettes/metadata.Rmd
@@ -157,7 +157,8 @@ descriptive_metadata <- list (
 
 # create a new client 
 cli <- deposits::depositsClient$new(service = "zenodo",
-                                    metadata = descriptive_metadata, sandbox = TRUE)
+                                    metadata = descriptive_metadata,
+                                    sandbox = TRUE)
 
 
 # create a new deposit item - this  creates a placeholder in zenodo
@@ -168,58 +169,22 @@ cli$deposit_new()
 # this will make a datapackage.json item in data_examples
 cli$deposit_add_resource(path = "data_examples/my_data.csv")
 
+## open the 
+
 # Take a peak at the `datapackage.json` file - you'll see the first section
 # describes the csv file, the second section describes the data in the csv,
 # the third section contains the descriptive metadata we created
 
-# Add in your metadata
-
-data_package <- frictionless::read_package("data_examples/datapackage.json")
-
-# get the schema for a resource in the data package 
-my_data_schema <- data_package|>
-                    get_schema("my_data")
-
-
-## build up schema based on structural metadata
-
-for(idx in 1:length(my_data_schema$fields)){
-  # item to build out
-  x <- my_data_schema$fields[[idx]]
-  for(idy in 1:length(structural_metadata)){
-
-     y <- structural_metadata[idx,idy][[1]]
-    # get property name
-     property_to_add_name <- names(structural_metadata)[idy]
-
-     # skip properties that already exist
-     if(property_to_add_name %in% names(x)){
-      next()
-     }
-
-    property_to_add_value <- y
-    names(property_to_add_value) <- property_to_add_name
-    x <- c(x, property_to_add_value)
-  }
-
-  # update 
-   my_data_schema$fields[[idx]] <- x
-}
-
-# update the datapackage.json
-data_package <- data_package|>
-   frictionless::remove_resource("my_data") |>
-   frictionless::add_resource(resource_name = "my_data",
-               data = "data_examples/my_data.csv", 
-               schema = my_data_schema,
-              )
-
-# write the datapackage.json
-frictionless::write_package(data_package,directory = "data_examples/")
-
-# upload to zenodo - this creates a draft deposit in Zenodo 
+# Add your structural metadata to the frictionless metadata
+
+expand_frictionless_metadata(structural_metadata = structural_metadata,
+                             resource_name = "my_data", # name of the file with no extension
+                             resource_path = "data_examples/my_data.csv",
+                             data_package_path = "data_examples/datapackage.json")
+
+# upload to zenodo - this creates a **draft** deposit in Zenodo 
 cli$deposit_upload_file(path = "data_examples/")
 
-# there are methods for embargoing or restricting 
+# there are methods for embargoing or restricting deposits in {deposits}
 
 ```
diff --git a/vignettes/metadata_examples/structural_metadata.csv b/vignettes/metadata_examples/structural_metadata.csv
@@ -3,4 +3,4 @@
 "measurement","distance to ephemeral pan from livestock pen","meters","https://schema.org/Distance",NA,FALSE,FALSE
 "measured_by","A person who measured the distance",NA,"https://schema.org/name",NA,FALSE,TRUE
 "site_name","Name of site",NA,"https://schema.org/name",NA,FALSE,TRUE
-"key",NA,NA,NA,NA,TRUE,FALSE
+"key","unique id for each row",NA,"https://schema.org/identifier",NA,TRUE,FALSE