Merge pull request #49 from ecohealthalliance/feature/update_friction…

…less_metadata adding update metadata function
ecohealthalliance · Sep 4, 2024 · b7b615e · b7b615e
2 parents 3160453 + 8aa4218
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: ohcleandat
 Type: Package
 Title: One Health Data Cleaning and Quality Checking Package
-Version: 0.3.5
+Version: 0.3.6
 Authors@R: c(
     person("Collin", "Schwantes", email = "schwantes@ecohealthalliance.org", role = c("cre", "aut"), comment = c(ORCID = "0000-0003-4014-4896")),
     person("Johana", "Teigen", email = "teigen@ecohealthalliance.org", role = "aut", comment = c(ORCID = "0000-0002-6209-2321")),

diff --git a/NAMESPACE b/NAMESPACE
@@ -31,6 +31,7 @@ export(read_excel_all_sheets)
 export(read_googlesheets)
 export(remove_deletions)
 export(set_diff)
+export(update_frictionless_metadata)
 export(update_structural_metadata)
 export(validation_checks)
 importFrom(dplyr,"%>%")

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,7 @@
+# ohcleandat 0.3.6
+
+* Adds a function to update the descriptive metadata in a frictionless datapackage
+
 # ohcleandat 0.3.5
 
 # ohcleandat 0.3.4

diff --git a/R/update_frictionless_metadata.R b/R/update_frictionless_metadata.R
@@ -0,0 +1,40 @@
+#' Update descriptive metadata in frictionless datapackage
+#'
+#' This function overwrites the descriptive metadata associated with a
+#' frictionless datapackage. It does *NOT* validate the metadata, or check
+#' for conflicts with existing descriptive metadata. It is very easy to create
+#' invalid metadata.
+#'
+#' @param descriptive_metadata List of descriptive metadata terms.
+#' @param data_package_path Character. Path to datapackage.json file
+#'
+#' @return invisibly writes datapackage.json
+#' @export
+#'
+#' @examples
+#' \dontrun{
+#' descriptive_metadata <- list (
+#' title = "Example Dataset",
+#' description = "This is the abstract but it needs more detail",
+#' creator = list (list (name = "A. Person"), list (name = "B. Person"),
+#' list (name = "C. Person"),list (name = "F. Person"))
+#' # , accessRights = "open"
+#' )
+#' update_frictionless_metadata(descriptive_metadata = descriptive_metadata,
+#'                              data_package_path = "data_examples/datapackage.json"
+#' )
+#' }
+update_frictionless_metadata <- function(descriptive_metadata,
+                                         data_package_path){
+
+  data_package <- frictionless::read_package(data_package_path)
+
+  data_package_dir <- dirname(data_package_path)
+
+  data_package$metadata <- descriptive_metadata
+
+  # write the datapackage.json
+  frictionless::write_package(data_package,directory = data_package_dir)
+
+  invisible()
+}
diff --git a/man/update_frictionless_metadata.Rd b/man/update_frictionless_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"
-2024-08-26,29,"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
+2024-08-26,38,"Collin","b",1
+2024-08-27,64,"Johana","a",2
+2024-08-28,94,"Johana","e",3
+2024-08-29,75,"Johana","a",4
+2024-08-30,49,"Collin","d",5
+2024-08-31,78,"Collin","d",6
+2024-09-01,93,"Johana","b",7
+2024-09-02,2,"Johana","c",8
+2024-09-03,91,"Johana","c",9
+2024-09-04,27,"Johana","a",10
diff --git a/vignettes/metadata.Rmd b/vignettes/metadata.Rmd
@@ -185,9 +185,25 @@ expand_frictionless_metadata(structural_metadata = structural_metadata,
                              resource_path = "data_examples/my_data.csv",
                              data_package_path = "data_examples/datapackage.json")
 
+
+## OOPs actually I need to add more to the description
+
+descriptive_metadata <- list (
+    title = "Example Dataset",
+    description = "This is the abstract but it needs more detail",
+    creator = list (list (name = "A. Person"), list (name = "B. Person"),list (name = "C. Person"),list (name = "F. Person"))
+    # , accessRights = "open"
+)
+update_frictionless_metadata(descriptive_metadata = descriptive_metadata,
+                             data_package_path = "data_examples/datapackage.json"
+)
+
+cli$deposit_fill_metadata(descriptive_metadata)
+# update deposit hangs if the descriptive metadata is not properly formatted, even after correction
 # upload to zenodo - this creates a **draft** deposit in Zenodo 
 cli$deposit_upload_file(path = "data_examples/")
 
 # there are methods for embargoing or restricting deposits in {deposits}
 
+
 ```