feat: demonstrate that array fields work in meta

nextflow-io · Dec 21, 2023 · 69f6c8f · 69f6c8f
1 parent 90d2053
commit 69f6c8f
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Showing 4 changed files with 94 additions and 74 deletions.
diff --git a/plugins/nf-validation/src/test/nextflow/validation/SamplesheetConverterTest.groovy b/plugins/nf-validation/src/test/nextflow/validation/SamplesheetConverterTest.groovy
@@ -212,9 +212,9 @@ class SamplesheetConverterTest extends Dsl2Spec{
 
         then:
         noExceptionThrown()
-        stdout.contains("[[${this.getRootString()}/src/testResources/testDir/testFile.txt, ${this.getRootString()}/src/testResources/testDir2/testFile2.txt], [${this.getRootString()}/src/testResources/testDir, ${this.getRootString()}/src/testResources/testDir2], [${this.getRootString()}/src/testResources/testDir, ${this.getRootString()}/src/testResources/testDir2/testFile2.txt], [string1, string2], [25, 26], [25, 26.5], [false, true], [1, 2, 3], [true], [${this.getRootString()}/src/testResources/testDir/testFile.txt], [[${this.getRootString()}/src/testResources/testDir/testFile.txt]]]" as String)
-        stdout.contains("[[], [], [], [string1, string2], [25, 26], [25, 26.5], [], [1, 2, 3], [false, true, false], [${this.getRootString()}/src/testResources/testDir/testFile.txt], [[${this.getRootString()}/src/testResources/testDir/testFile.txt]]]" as String)
-        stdout.contains("[[], [], [], [string1, string2], [25, 26], [25, 26.5], [], [1, 2, 3], [false, true, false], [${this.getRootString()}/src/testResources/testDir/testFile.txt], [[${this.getRootString()}/src/testResources/testDir/testFile.txt], [${this.getRootString()}/src/testResources/testDir/testFile.txt, ${this.getRootString()}/src/testResources/testDir2/testFile2.txt]]]" as String)
+        stdout.contains("[[array_meta:null], [${this.getRootString()}/src/testResources/testDir/testFile.txt, ${this.getRootString()}/src/testResources/testDir2/testFile2.txt], [${this.getRootString()}/src/testResources/testDir, ${this.getRootString()}/src/testResources/testDir2], [${this.getRootString()}/src/testResources/testDir, ${this.getRootString()}/src/testResources/testDir2/testFile2.txt], [string1, string2], [25, 26], [25, 26.5], [false, true], [1, 2, 3], [true], [${this.getRootString()}/src/testResources/testDir/testFile.txt], [[${this.getRootString()}/src/testResources/testDir/testFile.txt]]]" as String)
+        stdout.contains("[[array_meta:[look, an, array, in, meta]], [], [], [], [string1, string2], [25, 26], [25, 26.5], [], [1, 2, 3], [false, true, false], [${this.getRootString()}/src/testResources/testDir/testFile.txt], [[${this.getRootString()}/src/testResources/testDir/testFile.txt]]]" as String)
+        stdout.contains("[[array_meta:null], [], [], [], [string1, string2], [25, 26], [25, 26.5], [], [1, 2, 3], [false, true, false], [${this.getRootString()}/src/testResources/testDir/testFile.txt], [[${this.getRootString()}/src/testResources/testDir/testFile.txt], [${this.getRootString()}/src/testResources/testDir/testFile.txt, ${this.getRootString()}/src/testResources/testDir2/testFile2.txt]]]" as String)
     }
 
     def 'arrays should work fine - JSON' () {
@@ -238,9 +238,9 @@ class SamplesheetConverterTest extends Dsl2Spec{
 
         then:
         noExceptionThrown()
-        stdout.contains("[[${this.getRootString()}/src/testResources/testDir/testFile.txt, ${this.getRootString()}/src/testResources/testDir2/testFile2.txt], [${this.getRootString()}/src/testResources/testDir, ${this.getRootString()}/src/testResources/testDir2], [${this.getRootString()}/src/testResources/testDir, ${this.getRootString()}/src/testResources/testDir2/testFile2.txt], [string1, string2], [25, 26], [25, 26.5], [false, true], [1, 2, 3], [true], [${this.getRootString()}/src/testResources/testDir/testFile.txt], [[${this.getRootString()}/src/testResources/testDir/testFile.txt]]]" as String)
-        stdout.contains("[[], [], [], [string1, string2], [25, 26], [25, 26.5], [], [1, 2, 3], [false, true, false], [${this.getRootString()}/src/testResources/testDir/testFile.txt], [[${this.getRootString()}/src/testResources/testDir/testFile.txt]]]" as String)
-        stdout.contains("[[], [], [], [string1, string2], [25, 26], [25, 26.5], [], [1, 2, 3], [false, true, false], [${this.getRootString()}/src/testResources/testDir/testFile.txt], [[${this.getRootString()}/src/testResources/testDir/testFile.txt], [${this.getRootString()}/src/testResources/testDir/testFile.txt, ${this.getRootString()}/src/testResources/testDir2/testFile2.txt]]]" as String)
+        stdout.contains("[[array_meta:null], [${this.getRootString()}/src/testResources/testDir/testFile.txt, ${this.getRootString()}/src/testResources/testDir2/testFile2.txt], [${this.getRootString()}/src/testResources/testDir, ${this.getRootString()}/src/testResources/testDir2], [${this.getRootString()}/src/testResources/testDir, ${this.getRootString()}/src/testResources/testDir2/testFile2.txt], [string1, string2], [25, 26], [25, 26.5], [false, true], [1, 2, 3], [true], [${this.getRootString()}/src/testResources/testDir/testFile.txt], [[${this.getRootString()}/src/testResources/testDir/testFile.txt]]]" as String)
+        stdout.contains("[[array_meta:[look, an, array, in, meta]], [], [], [], [string1, string2], [25, 26], [25, 26.5], [], [1, 2, 3], [false, true, false], [${this.getRootString()}/src/testResources/testDir/testFile.txt], [[${this.getRootString()}/src/testResources/testDir/testFile.txt]]]" as String)
+        stdout.contains("[[array_meta:null], [], [], [], [string1, string2], [25, 26], [25, 26.5], [], [1, 2, 3], [false, true, false], [${this.getRootString()}/src/testResources/testDir/testFile.txt], [[${this.getRootString()}/src/testResources/testDir/testFile.txt], [${this.getRootString()}/src/testResources/testDir/testFile.txt, ${this.getRootString()}/src/testResources/testDir2/testFile2.txt]]]" as String)
     }
 
     def 'array errors before channel conversion - YAML' () {

diff --git a/plugins/nf-validation/src/testResources/correct_arrays.json b/plugins/nf-validation/src/testResources/correct_arrays.json
@@ -1,72 +1,79 @@
 [
-    {
-      "field_1": [
-        "src/testResources/testDir/testFile.txt",
-        "src/testResources/testDir2/testFile2.txt"
+  {
+    "field_1": [
+      "src/testResources/testDir/testFile.txt",
+      "src/testResources/testDir2/testFile2.txt"
+    ],
+    "field_2": [
+      "src/testResources/testDir",
+      "src/testResources/testDir2"
+    ],
+    "field_3": [
+      "src/testResources/testDir",
+      "src/testResources/testDir2/testFile2.txt"
+    ],
+    "field_4": [
+      "string1",
+      "string2"
+    ],
+    "field_5": [
+      25,
+      26
+    ],
+    "field_6": [
+      25,
+      26.5
+    ],
+    "field_7": [
+      false,
+      true
+    ],
+    "field_9": [
+      true
+    ]
+  },
+  {
+    "field_4": [
+      "string1",
+      "string2"
+    ],
+    "field_5": [
+      25,
+      26
+    ],
+    "field_6": [
+      25,
+      26.5
+    ],
+    "field_12": [
+      "look",
+      "an",
+      "array",
+      "in",
+      "meta"
+    ]
+  },
+  {
+    "field_4": [
+      "string1",
+      "string2"
+    ],
+    "field_5": [
+      25,
+      26
+    ],
+    "field_6": [
+      25,
+      26.5
+    ],
+    "field_11": [
+      [
+        "src/testResources/testDir/testFile.txt"
       ],
-      "field_2": [
-        "src/testResources/testDir",
-        "src/testResources/testDir2"
-      ],
-      "field_3": [
-        "src/testResources/testDir",
+      [
+        "src/testResources/testDir/testFile.txt",
         "src/testResources/testDir2/testFile2.txt"
-      ],
-      "field_4": [
-        "string1",
-        "string2"
-      ],
-      "field_5": [
-        25,
-        26
-      ],
-      "field_6": [
-        25,
-        26.5
-      ],
-      "field_7": [
-        false,
-        true
-      ],
-      "field_9": [
-        true
-      ]
-    },
-    {
-      "field_4": [
-        "string1",
-        "string2"
-      ],
-      "field_5": [
-        25,
-        26
-      ],
-      "field_6": [
-        25,
-        26.5
-      ]
-    },
-    {
-      "field_4": [
-        "string1",
-        "string2"
-      ],
-      "field_5": [
-        25,
-        26
-      ],
-      "field_6": [
-        25,
-        26.5
-      ],
-      "field_11": [
-        [
-          "src/testResources/testDir/testFile.txt"
-        ],
-        [
-          "src/testResources/testDir/testFile.txt",
-          "src/testResources/testDir2/testFile2.txt"
-        ]
       ]
-    }
-  ]
+    ]
+  }
+]
diff --git a/plugins/nf-validation/src/testResources/correct_arrays.yaml b/plugins/nf-validation/src/testResources/correct_arrays.yaml
@@ -30,6 +30,12 @@
   field_6:
     - 25
     - 26.5
+  field_12:
+    - look
+    - an
+    - array
+    - in
+    - meta
 - field_4:
     - string1
     - string2

diff --git a/plugins/nf-validation/src/testResources/schema_input_with_arrays.json b/plugins/nf-validation/src/testResources/schema_input_with_arrays.json
@@ -95,6 +95,13 @@
                     }
                 },
                 "default": [["src/testResources/testDir/testFile.txt"]] 
+            },
+            "field_12": {
+                "type": "array",
+                "items": {
+                    "type": "string"
+                },
+                "meta": ["array_meta"]
             }
         },
         "required": ["field_4", "field_6"]
-Original file line number
+Diff line change
@@ Expand Up / @@ -30,6 +30,12 @@ @@
       field_6:
         - 25
         - 26.5
+      field_12:
+        - look
+        - an
+        - array
+        - in
+        - meta
     - field_4:
         - string1
         - string2
@@ Expand Down @@