From ec5eb1f80add9c8f9f43744728b731db53fc84d2 Mon Sep 17 00:00:00 2001
From: eblondel <emmanuel.blondel1@gmail.com>
Date: Thu, 12 Oct 2023 00:00:54 +0200
Subject: [PATCH] fix #370 + integration test

---
 .../workflows/config_metadata_ncml.json       | 23 +++++++++++
 inst/extdata/workflows/workflows.csv          |  3 +-
 inst/metadata/entity/entity_handler_ncml.R    |  4 +-
 tests/testthat/test_config_metadata_ncml.R    | 41 +++++++++++++++++++
 4 files changed, 68 insertions(+), 3 deletions(-)
 create mode 100644 inst/extdata/workflows/config_metadata_ncml.json
 create mode 100644 tests/testthat/test_config_metadata_ncml.R

diff --git a/inst/extdata/workflows/config_metadata_ncml.json b/inst/extdata/workflows/config_metadata_ncml.json
new file mode 100644
index 00000000..0da4eddc
--- /dev/null
+++ b/inst/extdata/workflows/config_metadata_ncml.json
@@ -0,0 +1,23 @@
+{
+  "profile": {
+    "id": "my-workflow",
+    "name": "My workflow",
+    "project": "Test geoflow project",
+    "organization": "My organization",
+    "logos": [
+      "https://via.placeholder.com/300x150.png/09f/fff?text=geoflow"
+      ],
+    "mode": "entity"
+  },
+  "metadata": {
+    "entities": [
+      {
+        "handler": "ncml",
+        "source": "https://galilee.univ-reunion.fr/thredds/ncml/dataStations/La_Reunion/saintjosephmairie/saintjosephmairie_aggregated.ncml?catalog=https%3A%2F%2Fgalilee.univ-reunion.fr%2Fthredds%2Fcatalog%2FdataStations%2FLa_Reunion%2Fsaintjosephmairie%2Fcatalog.html&dataset=station%2FLa_Reunion%2Fsaintjosephmairie%2Fsaintjosephmairie_aggregated.ncml"
+      }
+    ],
+    "contacts" : []
+  },
+  "software": [],
+  "actions": []
+}
diff --git a/inst/extdata/workflows/workflows.csv b/inst/extdata/workflows/workflows.csv
index 976ba133..634f0518 100644
--- a/inst/extdata/workflows/workflows.csv
+++ b/inst/extdata/workflows/workflows.csv
@@ -16,4 +16,5 @@ config_metadata_gsheets_sdi_geoserver_geotiff_directory.json,Load metadata entit
 config_metadata_ocs.json,Load metadata entities/contacts/dictionary from CSV files hosted on a cloud supporting OCS API (eg. nextcloud/owncloud)
 config_metadata_dataverse.json,Load metadata entities/contacts from Dataverse records
 config_metadata_zenodo.json,Load metadata entities/contacts from Zenodo deposits/records
-config_metadata_zenodo_with_options.json,Load metadata entities/contacts from Zenodo deposits/records (with options declared to fetch from public records and by DOI)
\ No newline at end of file
+config_metadata_zenodo_with_options.json,Load metadata entities/contacts from Zenodo deposits/records (with options declared to fetch from public records and by DOI)
+config_metadata_ncml.json,Load a metadata entity/contacts from a NCML source
\ No newline at end of file
diff --git a/inst/metadata/entity/entity_handler_ncml.R b/inst/metadata/entity/entity_handler_ncml.R
index 6f225cde..56de1e9d 100644
--- a/inst/metadata/entity/entity_handler_ncml.R
+++ b/inst/metadata/entity/entity_handler_ncml.R
@@ -86,7 +86,7 @@ handle_entities_ncml <- function(handler, source, config, handle = TRUE){
   
   
   #identifiers
-  entity$setIdentifier("id", basename(source_name))
+  entity$setIdentifier("id", basename(attr$full_name$value))
   
   doi <- attr$identifier_product_doi$value
   if(!is.null(doi)){
@@ -98,7 +98,7 @@ handle_entities_ncml <- function(handler, source, config, handle = TRUE){
   if(!is.null(title)){
     entity$setTitle("title", title)
   }else{
-    entity$setTitle("title",basename(source_name))  
+    entity$setTitle("title",basename(attr$full_name$value))  
   }
   
   #description
diff --git a/tests/testthat/test_config_metadata_ncml.R b/tests/testthat/test_config_metadata_ncml.R
new file mode 100644
index 00000000..21d548a8
--- /dev/null
+++ b/tests/testthat/test_config_metadata_ncml.R
@@ -0,0 +1,41 @@
+# test_config_metadata_ncml.R
+# Author: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
+#
+# Description: Integration tests for config_metadata_ncml.json workflow
+#=======================
+require(geoflow, quietly = TRUE)
+require(testthat)
+
+#init
+test_that("init",{
+  testthat::skip_on_cran()
+  cfg_file = system.file("extdata/workflows/config_metadata_ncml.json", package = "geoflow")
+  CFG <- geoflow::initWorkflow(cfg_file)
+  expect_is(CFG$metadata$content, "list")
+  expect_equal(length(CFG$metadata$content), 1L)
+  expect_equal(names(CFG$metadata$content), "entities")
+  expect_equal(length(CFG$metadata$content$entities), 1L)
+  expect_equal(length(CFG$getEntities()), 1L)
+  expect_equal(length(CFG$actions), 0L)
+})
+
+#debug
+test_that("debug",{
+  testthat::skip_on_cran()
+  cfg_file = system.file("extdata/workflows/config_metadata_ncml.json", package = "geoflow")
+  DEBUG <- geoflow::debugWorkflow(cfg_file, entityIndex = 1, dir = ".")
+  expect_equal(names(DEBUG), c("config", "entity"))
+  expect_is(DEBUG$config, "list")
+  expect_is(DEBUG$entity, "geoflow_entity")
+})
+
+#execute
+test_that("execute",{
+  #testthat::skip_on_cran()
+  #cfg_file = system.file("extdata/workflows/config_metadata_ncml.json", package = "geoflow")
+  #execution
+  #EXEC <- geoflow::executeWorkflow(cfg_file, dir = ".")
+  #expect_true(dir.exists(EXEC))
+  #expect_true(file.exists(file.path(EXEC, "job.json")))
+  #expect_true(file.exists(file.path(EXEC, "job-logs.txt")))
+})