provide thredds workflow example (NOAA)

inst/extdata/workflows/config_metadata_thredds_noaa.json

@@ -0,0 +1,34 @@
+{
+  "id": "thredds",
+  "profile": {
+  	"project": "geoflow-thredds",
+  	"organization": "geoflow",
+  	"logos": [],
+  	"options": {
+  	  "line_separator": "_\n"
+    },
+    "mode": "entity"
+  },
+
+
+
+  "metadata": {
+    "entities": [
+      {
+        "handler": "thredds",
+        "source": "oisst-avhrr-v02r01.20210518.nc"
+      }
+    ]
+  },
+ "software": [
+  	{
+  		"id": "thredds",
+  		"type": "input",
+  		"software_type": "thredds",
+  		"parameters": {
+  			"x": "https://www.ncei.noaa.gov/thredds/catalog/OisstBase/NetCDF/V2.1/AVHRR/202105/catalog.xml"
+  		}
+  	}
+  ],
+ "actions": []
+}

inst/extdata/workflows/workflows.csv

@@ -17,4 +17,5 @@ config_metadata_ocs.json,Load metadata entities/contacts/dictionary from CSV fil
 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)
-config_metadata_ncml.json,Load a metadata entity/contacts from a NCML source
+config_metadata_ncml.json,Load a metadata entity/contacts from a NCML source
+config_metadata_thredds_noaa.json,Load metadata entities/contact from a Thredds data server (NOAA example)

tests/testthat/test_config_metadata_thredds_noaa.R

@@ -0,0 +1,41 @@
+# test_config_metadata_thredds_noaa.R
+# Author: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
+#
+# Description: Integration tests for config_metadata_thredds_noaa.json workflow
+#=======================
+require(geoflow, quietly = TRUE)
+require(testthat)
+
+#init
+test_that("init",{
+  testthat::skip_on_cran()
+  cfg_file = system.file("extdata/workflows/config_metadata_thredds_noaa.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$actions), 0L)
+})
+
+#debug
+test_that("debug",{
+  testthat::skip_on_cran()
+  cfg_file = system.file("extdata/workflows/config_metadata_thredds_noaa.json", package = "geoflow")
+  DEBUG <- geoflow::debugWorkflow(cfg_file, entityIndex = 1, dir = ".")
+  expect_equal(names(DEBUG), c("config", "entity"))
+  expect_is(DEBUG$config, "list")
+  expect_is(DEBUG$entity, "geoflow_entity")
+})
+
+#execute
+test_that("execute",{
+  #testthat::skip_on_cran()
+  #cfg_file = system.file("extdata/workflows/config_metadata_thredds_noaa.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")))
+})