More tests.

tests/data/samplesheets/missing_metadata.csv

@@ -0,0 +1,4 @@
+sample,sample_name,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8
+sample1,"ABC",,1.2,1.3,,1.5,1.6,,1.8
+sample2,,2.1,,2.3,2.4,,2.6,2.7,
+sample3,"GHI",3.1,3.2,,3.4,3.5,,3.7,3.8

tests/pipelines/integration.nf.test

@@ -175,4 +175,70 @@ nextflow_pipeline {
             assert output.contains("Unspecified transformation '--transformation'. Exiting now.")
         }
     }
+
+    test("Basic lock - missing metadata") {
+        tag "pipeline_missing_metadata"
+
+        when {
+            params {
+                input = "$baseDir/tests/data/samplesheets/missing_metadata.csv"
+                outdir = "results"
+
+                transformation = "lock"
+            }
+        }
+
+        then {
+            assert workflow.success
+            assert path("$launchDir/results").exists()
+
+            // Check Locked Results
+            def locked = path("$launchDir/results/lock/locked.csv")
+            assert locked.exists()
+
+            assert locked.text.contains("sample_id,irida_id,metadata_1,metadata_2,metadata_3,metadata_4,metadata_5,metadata_6,metadata_7,metadata_8")
+            assert locked.text.contains("ABC,sample1,,1.2,1.3,,1.5,1.6,,1.8")
+            assert locked.text.contains("sample2,sample2,2.1,,2.3,2.4,,2.6,2.7,")
+            assert locked.text.contains("GHI,sample3,3.1,3.2,,3.4,3.5,,3.7,3.8")
+
+            // Check IRIDA Next JSON Output
+            def iridanext_json = path("$launchDir/results/iridanext.output.json").json
+            def iridanext_metadata = iridanext_json.metadata.samples
+
+            assert iridanext_metadata.size() == 3 
+
+            assert iridanext_metadata.containsKey("ABC")
+            assert iridanext_metadata.ABC.irida_id == "sample1"
+            assert iridanext_metadata.ABC.metadata_1 == ""
+            assert iridanext_metadata.ABC.metadata_2 == "1.2"
+            assert iridanext_metadata.ABC.metadata_3 == "1.3"
+            assert iridanext_metadata.ABC.metadata_4 == ""
+            assert iridanext_metadata.ABC.metadata_5 == "1.5"
+            assert iridanext_metadata.ABC.metadata_6 == "1.6"
+            assert iridanext_metadata.ABC.metadata_7 == ""
+            assert iridanext_metadata.ABC.metadata_8 == "1.8"
+
+            assert iridanext_metadata.containsKey("sample2")
+            assert iridanext_metadata.sample2.irida_id == "sample2"
+            assert iridanext_metadata.sample2.metadata_1 == "2.1"
+            assert iridanext_metadata.sample2.metadata_2 == ""
+            assert iridanext_metadata.sample2.metadata_3 == "2.3"
+            assert iridanext_metadata.sample2.metadata_4 == "2.4"
+            assert iridanext_metadata.sample2.metadata_5 == ""
+            assert iridanext_metadata.sample2.metadata_6 == "2.6"
+            assert iridanext_metadata.sample2.metadata_7 == "2.7"
+            assert iridanext_metadata.sample2.metadata_8 == ""
+
+            assert iridanext_metadata.containsKey("GHI")
+            assert iridanext_metadata.GHI.irida_id == "sample3"
+            assert iridanext_metadata.GHI.metadata_1 == "3.1"
+            assert iridanext_metadata.GHI.metadata_2 == "3.2"
+            assert iridanext_metadata.GHI.metadata_3 == ""
+            assert iridanext_metadata.GHI.metadata_4 == "3.4"
+            assert iridanext_metadata.GHI.metadata_5 == "3.5"
+            assert iridanext_metadata.GHI.metadata_6 == ""
+            assert iridanext_metadata.GHI.metadata_7 == "3.7"
+            assert iridanext_metadata.GHI.metadata_8 == "3.8"
+        }
+    }
 }