Merge pull request #597 from Sage-Bionetworks/fds-1852-upload-file-an…

…notations Fds 1852 add file_annotations_upload to model/submit
Sage-Bionetworks · May 14, 2024 · acc8e63 · acc8e63
2 parents a2ca2d9 + 4de36bd
commit acc8e63
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Showing 18 changed files with 238 additions and 35 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -6,7 +6,7 @@ Authors: Rongrong Chai, Xengie Doan, Milen Nikolov, Sujay Patil, Robert Allaway,
 License: file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Imports: httr, dplyr, jsonlite, shinyjs, yaml, promises, readr
 Suggests: 
     covr
diff --git a/R/schematic_rest_api.R b/R/schematic_rest_api.R
@@ -221,8 +221,18 @@ manifest_validate <- function(url="http://localhost:3001/v1/model/validate",
 #' @param schema_url URL to a schema jsonld 
 #' @param data_type Type of dataset
 #' @param dataset_id Synapse ID of existing manifest
-#' @param access_token Synapse login cookie, PAT, or API key.
-#' @param csv_file Filepath of csv to validate
+#' @param restrict_rules Default = FALSE
+#' @param access_token Synapse login cookie, PAT, or API key
+#' @param json_str Json string to submit
+#' @param asset_view Synapse fileview
+#' @param manifest_record_type Default = "table_and_file"
+#' @param file_name Name of file
+#' @param table_manipulation Default = "replace"
+#' @param hide_blanks Default = FALSE
+#' @param table_column_names Default = "class_and_label"
+#' @param annotation_keys Default = "class_and_label"
+#' @param data_model_labels Default = "class_and_label"
+#' @param upload_file_annotations Default = TRUE
 #' 
 #' @returns TRUE if successful upload or validate errors if not.
 #' @export
@@ -240,7 +250,8 @@ model_submit <- function(url="http://localhost:3001/v1/model/submit",
                          hide_blanks=FALSE,
                          table_column_names="class_label",
                          annotation_keys="class_label",
-                         data_model_labels="class_label") {
+                         data_model_labels="class_label",
+                         file_annotations_upload=TRUE) {
   req <- httr::POST(url,
                     httr::add_headers(Authorization = sprintf("Bearer %s", access_token)),
                     query=list(
@@ -255,7 +266,8 @@ model_submit <- function(url="http://localhost:3001/v1/model/submit",
                       table_column_names=table_column_names,
                       annotation_keys=annotation_keys,
                       data_model_labels=data_model_labels,
-                      hide_blanks=hide_blanks),
+                      hide_blanks=hide_blanks,
+                      file_annotations_upload=file_annotations_upload),
                     body=list(file_name=httr::upload_file(file_name))
                     #body=list(file_name=file_name)
   )

diff --git a/man/get_asset_view_table.Rd b/man/get_asset_view_table.Rd
diff --git a/man/get_synapse_table_names.Rd b/man/get_synapse_table_names.Rd
diff --git a/man/manifest_generate.Rd b/man/manifest_generate.Rd
diff --git a/man/manifest_populate.Rd b/man/manifest_populate.Rd
diff --git a/man/manifest_validate.Rd b/man/manifest_validate.Rd
diff --git a/man/model_component_requirements.Rd b/man/model_component_requirements.Rd
diff --git a/man/model_submit.Rd b/man/model_submit.Rd
diff --git a/man/storage_dataset_files.Rd b/man/storage_dataset_files.Rd
diff --git a/man/storage_project_datasets.Rd b/man/storage_project_datasets.Rd
diff --git a/man/storage_projects.Rd b/man/storage_projects.Rd
diff --git a/man/synapse_download_file_handle.Rd b/man/synapse_download_file_handle.Rd
diff --git a/man/synapse_entity_children.Rd b/man/synapse_entity_children.Rd
diff --git a/man/synapse_get_project_scope.Rd b/man/synapse_get_project_scope.Rd
diff --git a/man/synapse_projects_user.Rd b/man/synapse_projects_user.Rd