Merge pull request #588 from Sage-Bionetworks/FDS-1402-schematic-disp…

…lay-name Fds 1402 schematic display name
Sage-Bionetworks · Feb 28, 2024 · dac61ba · dac61ba
2 parents 8478a21 + a2789ab
commit dac61ba
Show file tree

Hide file tree

Showing 5 changed files with 709 additions and 556 deletions.
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -10,36 +10,6 @@ repos:
     # codemeta must be above use-tidy-description when both are used
     # -   id: codemeta-description-updated
     -   id: use-tidy-description
-    -   id: spell-check
-        exclude: >
-          (?x)^(
-          .*\.[rR]|
-          .*\.feather|
-          .*\.jpeg|
-          .*\.pdf|
-          .*\.png|
-          .*\.py|
-          .*\.RData|
-          .*\.rds|
-          .*\.Rds|
-          .*\.Rproj|
-          .*\.sh|
-          (.*/|)\.gitignore|
-          (.*/|)\.gitlab-ci\.yml|
-          (.*/|)\.lintr|
-          (.*/|)\.pre-commit-.*|
-          (.*/|)\.Rbuildignore|
-          (.*/|)\.Renviron|
-          (.*/|)\.Rprofile|
-          (.*/|)\.travis\.yml|
-          (.*/|)appveyor\.yml|
-          (.*/|)NAMESPACE|
-          (.*/|)renv/settings\.dcf|
-          (.*/|)renv\.lock|
-          (.*/|)WORDLIST|
-          \.github/workflows/.*|
-          data/.*|
-          )$
     -   id: lintr
     -   id: readme-rmd-rendered
     -   id: parsable-R

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -7,6 +7,6 @@ License: file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
-Imports: httr, dplyr, jsonlite
+Imports: httr, dplyr, jsonlite, shinyjs, yaml, promises, readr
 Suggests: 
     covr
diff --git a/R/schematic_rest_api.R b/R/schematic_rest_api.R
@@ -54,11 +54,16 @@ manifest_download <- function(url = "http://localhost:3001/v1/manifest/download"
 #' @returns a URL to a google sheet
 #' @export
 manifest_generate <- function(url="http://localhost:3001/v1/manifest/generate",
-                              schema_url="https://raw.githubusercontent.com/ncihtan/data-models/main/HTAN.model.jsonld", #nolint
-                              title, data_type,
-                              use_annotations="false", dataset_id=NULL,
-                              asset_view, output_format, access_token = NULL,
-                              strict_validation = FALSE) {
+                              schema_url,
+                              title,
+                              data_type,
+                              use_annotations="false",
+                              dataset_id=NULL,
+                              asset_view,
+                              output_format,
+                              access_token = NULL,
+                              strict_validation = FALSE,
+                              data_model_labels = "class_label") {
 
   req <- httr::GET(url,
                    httr::add_headers(Authorization = sprintf("Bearer %s", access_token)),
@@ -70,7 +75,8 @@ manifest_generate <- function(url="http://localhost:3001/v1/manifest/generate",
                      dataset_id=dataset_id,
                      asset_view=asset_view,
                      output_format=output_format,
-                     strict_validation = strict_validation
+                     strict_validation = strict_validation,
+                     data_model_labels = data_model_labels
                    ))
 
   check_success(req)
@@ -87,15 +93,20 @@ manifest_generate <- function(url="http://localhost:3001/v1/manifest/generate",
 #' @param csv_file Filepath of csv to validate
 #' @export
 manifest_populate <- function(url="http://localhost:3001/v1/manifest/populate",
-                              schema_url="https://raw.githubusercontent.com/ncihtan/data-models/main/HTAN.model.jsonld", #notlint
-                              data_type, title, return_excel=FALSE, csv_file) {
+                              schema_url,
+                              data_type,
+                              title,
+                              return_excel=FALSE,
+                              data_model_labels = "class_label",
+                              csv_file) {
 
   req <- httr::POST(url,
                     query=list(
                       schema_url=schema_url,
                       data_type=data_type,
                       title=title,
-                      return_excel=return_excel),
+                      return_excel=return_excel,
+                      data_model_labels=data_model_labels),
                     body=list(csv_file=httr::upload_file(csv_file, type = "text/csv"))
   )
   check_success(req)
@@ -114,9 +125,14 @@ manifest_populate <- function(url="http://localhost:3001/v1/manifest/populate",
 #' @returns An empty list() if sucessfully validated. Or a list of errors.
 #' @export
 manifest_validate <- function(url="http://localhost:3001/v1/model/validate",
-                              schema_url="https://raw.githubusercontent.com/ncihtan/data-models/main/HTAN.model.jsonld", #nolint
-                              data_type, file_name, restrict_rules=FALSE, project_scope = NULL,
-                              access_token, asset_view = NULL) {
+                              schema_url,
+                              data_type,
+                              file_name,
+                              restrict_rules=FALSE,
+                              project_scope = NULL,
+                              access_token,
+                              asset_view = NULL,
+                              data_model_labels = "class_label") {
 
   flattenbody <- function(x) {
     # A form/query can only have one value per name, so take
@@ -144,7 +160,8 @@ manifest_validate <- function(url="http://localhost:3001/v1/model/validate",
                        data_type=data_type,
                        restrict_rules=restrict_rules,
                        project_scope = project_scope,
-                       asset_view = asset_view)),
+                       asset_view = asset_view,
+                       data_model_labels = data_model_labels)),
                     body=list(file_name=httr::upload_file(file_name))
   )
 
@@ -180,10 +197,20 @@ manifest_validate <- function(url="http://localhost:3001/v1/model/validate",
 #' @returns TRUE if successful upload or validate errors if not.
 #' @export
 model_submit <- function(url="http://localhost:3001/v1/model/submit",
-                         schema_url="https://raw.githubusercontent.com/ncihtan/data-models/main/HTAN.model.jsonld", #notlint
-                         data_type, dataset_id, restrict_rules=FALSE, access_token, json_str=NULL, asset_view,
-                         use_schema_label=TRUE, manifest_record_type="table_and_file", file_name,
-                         table_manipulation="replace", hide_blanks=FALSE) {
+                         schema_url,
+                         data_type,
+                         dataset_id,
+                         restrict_rules=FALSE,
+                         access_token,
+                         json_str=NULL,
+                         asset_view,
+                         manifest_record_type="table_and_file",
+                         file_name,
+                         table_manipulation="replace",
+                         hide_blanks=FALSE,
+                         table_column_names="class_label",
+                         annotation_keys="class_label",
+                         data_model_labels="class_label") {
   req <- httr::POST(url,
                     httr::add_headers(Authorization = sprintf("Bearer %s", access_token)),
                     query=list(
@@ -193,9 +220,10 @@ model_submit <- function(url="http://localhost:3001/v1/model/submit",
                       restrict_rules=restrict_rules,
                       json_str=json_str,
                       asset_view=asset_view,
-                      use_schema_label=use_schema_label,
                       manifest_record_type=manifest_record_type,
                       table_manipulation=table_manipulation,
+                      table_column_names=table_column_names,
+                      annotation_keys=annotation_keys,
                       hide_blanks=hide_blanks),
                     body=list(file_name=httr::upload_file(file_name))
                     #body=list(file_name=file_name)
@@ -215,14 +243,17 @@ model_submit <- function(url="http://localhost:3001/v1/model/submit",
 #' @returns A list of required components associated with the source component.
 #' @export
 model_component_requirements <- function(url="http://localhost:3001/v1/model/component-requirements",
-                                         schema_url, source_component,
-                                         as_graph = FALSE) {
+                                         schema_url,
+                                         source_component,
+                                         as_graph = FALSE,
+                                         data_model_labels = "class_label") {
 
   req <- httr::GET(url,
                    query =  list(
                      schema_url = schema_url,
                      source_component = source_component,
-                     as_graph = as_graph
+                     as_graph = as_graph,
+                     data_model_labels = data_model_labels
                    ))
 
   check_success(req)
@@ -344,11 +375,14 @@ get_asset_view_table <- function(url="http://localhost:3001/v1/storage/assets/ta
 #' @export
 #' @importFrom httr GET content
 graph_by_edge_type <- function(url = "https://schematic-dev.api.sagebionetworks.org/v1/schemas/get/graph_by_edge_type",
-                               schema_url, relationship = "requiresDependency") {
+                               schema_url,
+                               relationship = "requiresDependency",
+                               data_model_labels = "class_label") {
   req <- httr::GET(url = url,
                    query = list(
                      schema_url = schema_url,
-                     relationship = relationship
+                     relationship = relationship,
+                     data_model_labels = data_model_labels
                    ))
   httr::content(req)
 }