Testing schema changes work (#205)

Necessary changes to app that arose during testing deployment.
Sage-Bionetworks · Jun 8, 2023 · 2350f7e · 2350f7e
1 parent 0f321bc
commit 2350f7e
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Showing 11 changed files with 2,347 additions and 144 deletions.
diff --git a/.Rprofile b/.Rprofile
@@ -7,4 +7,4 @@
   )
 }
 
-source("renv/activate.R")
+source("renv/activate.R")
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -26,7 +26,7 @@ LazyData: true
 RoxygenNote: 7.2.3
 Suggests: 
     spelling,
-    testthat,
+    testthat (>= 3.0.0),
     devtools,
     usethis,
     renv

diff --git a/R/app_server.R b/R/app_server.R
@@ -42,22 +42,22 @@ app_server <- function( input, output, session ) {
 
   # generate dashboard configuration from dataFlow schema
   dash_config <- dfamodules::generate_dashboard_config(schema_url = global_config$schema_url,
-                                                       display_names = list(contributor = "Contributor",
-                                                                            entityId = "Synapse ID",
-                                                                            dataset = "Data Type",
-                                                                            dataset_name = "Dataset Folder Name",
-                                                                            num_items = "Number of Items in Manifest",
-                                                                            release_scheduled = "Release Date",
-                                                                            embargo = "Embargo",
-                                                                            standard_compliance = "QC Checks",
-                                                                            released = "Released",
-                                                                            data_portal = "Data Portal",
-                                                                            Component = NA),
+                                                       # display_names = list(contributor = "Contributor",
+                                                       #                      entityId = "Synapse ID",
+                                                       #                      dataset = "Data Type",
+                                                       #                      dataset_name = "Dataset Folder Name",
+                                                       #                      num_items = "Number of Items in Manifest",
+                                                       #                      release_scheduled = "Release Date",
+                                                       #                      embargo = "Embargo",
+                                                       #                      standard_compliance = "QC Checks",
+                                                       #                      released = "Released",
+                                                       #                      data_portal = "Data Portal",
+                                                       #                      Component = NA),
                                                        icon = TRUE,
-                                                       na_replace = list(num_items = "No Manifest",
-                                                                         release_scheduled = "Not Scheduled",
-                                                                         embargo = "No Embargo",
-                                                                         dataset = "No Manifest"),
+                                                       # na_replace = list(num_items = "No Manifest",
+                                                       #                   release_scheduled = "Not Scheduled",
+                                                       #                   embargo = "No Embargo",
+                                                       #                   dataset = "No Manifest"),
                                                        base_url = global_config$api_base_url)
 
   # download data flow status manifest

diff --git a/inst/data_model/dataflow_component.csv b/inst/data_model/dataflow_component.csv
@@ -0,0 +1,14 @@
+Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules
+dataFlow,Describes data flow status,,"Component, contributor, entityId, dataset_name, dataset, num_items, release_scheduled, embargo, standard_compliance, data_portal, released",,TRUE,DataType,,,
+contributor,Storage project that dataset is contained in,,,,TRUE,DataProperty,,,str
+entityId,Synapse unique ID,,,,TRUE,DataProperty,,,str
+dataset_name,Unique dataset name,,,,TRUE,DataProperty,,,str
+dataset,Type of dataset,,,,TRUE,DataProperty,,,str
+num_items,Number of files contained in a manifest,,,,TRUE,DataProperty,,,int
+release_scheduled,Date that a dataset is scheduled for release,,,,TRUE,DataProperty,,,date
+embargo,Date that indicates when a dataset is released from embargo,,,,TRUE,DataProperty,,,date
+standard_compliance,Has dataset passed standard validation checks,"TRUE, FALSE",,,TRUE,DataProperty,,,str
+data_portal,"Has dataset been published to data portal
+","TRUE, FALSE",,,TRUE,DataProperty,,,str
+released,"Has this dataset been released
+","TRUE, FALSE",,,TRUE,DataProperty,,,str
diff --git a/inst/data_flow_component.jsonld → inst/data_model/dataflow_component.jsonld b/inst/data_flow_component.jsonld → inst/data_model/dataflow_component.jsonld
diff --git a/inst/datatable_dashboard_config.json b/inst/datatable_dashboard_config.json
diff --git a/inst/global.json b/inst/global.json
@@ -1,6 +1,6 @@
 {
     "asset_view": "syn50896957",
-    "manifest_dataset_id": "syn50900267",
-    "schema_url": "https://raw.githubusercontent.com/Sage-Bionetworks/data_flow/dev-schema-changes/inst/data_flow_component.jsonld",
-    "api_base_url": "https://schematic-staging.api.sagebionetworks.org"
+    "manifest_dataset_id": "syn51673148",
+    "schema_url": "https://raw.githubusercontent.com/Sage-Bionetworks/data_flow/dev-schema-changes-testing/inst/data_model/dataflow_component_testing.jsonld",
+    "api_base_url": "https://schematic-dev.api.sagebionetworks.org"
   }
diff --git a/inst/testing/datatable_dashboard_config.json b/inst/testing/datatable_dashboard_config.json
diff --git a/inst/testing/synapse_storage_manifest_dataflow.csv b/inst/testing/synapse_storage_manifest_dataflow.csv
diff --git a/tests/testing_data/dataflow_component_testing.csv b/tests/testing_data/dataflow_component_testing.csv
@@ -0,0 +1,13 @@
+Attribute,Description,Valid Values,DependsOn,Properties,Required,Parent,DependsOn Component,Source,Validation Rules
+dataFlow,Describes data flow status,,"Component, contributor, entityId, dataset_name, dataset, num_items, embargo, release_scheduled, testing_str, testing_log, testing_num, testing_date",,TRUE,DataType,,,
+contributor,Storage project that dataset is contained in,,,,TRUE,DataProperty,,,str
+entityId,Synapse unique ID,,,,TRUE,DataProperty,,,str
+dataset_name,Unique dataset name,,,,TRUE,DataProperty,,,str
+dataset,Type of dataset,,,,TRUE,DataProperty,,,str
+num_items,Number of files contained in a manifest,,,,TRUE,DataProperty,,,int
+embargo,Date of embargo,,,,TRUE,DataProperty,,,date
+release_scheduled,Date of scheduled release,,,,TRUE,DataProperty,,,date
+testing_str,TEST STRING,,,,TRUE,DataProperty,,,str
+testing_log,TEST LOGICAL,"TRUE, FALSE",,,TRUE,DataProperty,,,str
+testing_num,TEST NUMBER,,,,TRUE,DataProperty,,,num
+testing_date,TEST DATE,,,,TRUE,DataProperty,,,date
-Original file line number
+Diff line change
@@ Expand Up / @@ -7,4 +7,4 @@ @@
       )
     }
-    source("renv/activate.R")
+    source("renv/activate.R")