rework example5 to have unsupported vocabs in data dict

- example5 previously wasn't used anywhere and was conceptually a duplicate of example9
neurobagel · Dec 19, 2024 · 75329c0 · 75329c0
1 parent 4dc9f8b
commit 75329c0
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Showing 6 changed files with 54 additions and 104 deletions.
diff --git a/tests/data/README.md b/tests/data/README.md
@@ -8,8 +8,8 @@
 | 2 | valid, unique `participant` and `session` IDs | same as example 1 | pass |
 | 3 | same as example 2 | valid BIDS data dictionary, BUT: does not contain Neurobagel `"Annotations"` key | fail |
 | 4 | valid, has additional columns not described in `.json` | same as example 1 | pass |
-| 5 | valid, has additional unique value, not annotated in `.json` | same as example 1 | fail |
-| 6 | valid, same as example 5. has assessment tool columns | valid, contains `"MissingValues"` attribute for categorical variable | pass |
+| 5 | valid, has assessment tool columns | invalid, has TermURLs from unsupported vocabularies | fail |
+| 6 | valid, same as example 5. | valid, contains `"MissingValues"` attribute for categorical variable | pass |
 | invalid | valid, only exists to be used together with the (invalid) .json | invalid, missing the `"TermURL"` attribute for identifiers | fail |
 | 7 | has fewer columns than are annotated in `.json` | same as example 1 | fail |
 | 8 | valid, based on ex2 has multiple participant_id columns | valid, based on ex2 multiple participant_id column annotations | fail* |

diff --git a/tests/data/example22.json b/tests/data/example22.json
diff --git a/tests/data/example22.tsv b/tests/data/example22.tsv
diff --git a/tests/data/example5.json b/tests/data/example5.json
@@ -39,7 +39,50 @@
                     "TermURL": "ncit:C94342",
                     "Label": "Healthy Control"
                 }
-            }
+            },
+            "MissingValues": ["OTHER"]
+        }
+    },
+    "tool_item1": {
+        "Description": "item 1 scores for an imaginary tool",
+        "Annotations": {
+            "IsAbout": {
+                "TermURL": "nb:Assessment",
+                "Label": "Assessment tool"
+            },
+            "IsPartOf": {
+                "TermURL": "unknownvocab:1234",
+                "Label": "Imaginary tool"
+            },
+            "MissingValues": ["missing"]
+        }
+    },
+    "tool_item2": {
+        "Description": "item 2 scores for an imaginary tool",
+        "Annotations": {
+            "IsAbout": {
+                "TermURL": "nb:Assessment",
+                "Label": "Assessment tool"
+            },
+            "IsPartOf": {
+                "TermURL": "unknownvocab:1234",
+                "Label": "Imaginary tool"
+            },
+            "MissingValues": ["missing"]
+        }
+    },
+    "other_tool_item1": {
+        "Description": "item 1 scores for a different imaginary tool",
+        "Annotations": {
+            "IsAbout": {
+                "TermURL": "nb:Assessment",
+                "Label": "Assessment tool"
+            },
+            "IsPartOf": {
+                "TermURL": "cogatlas:4321",
+                "Label": "A different imaginary tool"
+            },
+            "MissingValues": ["none"]
         }
     }
 }
diff --git a/tests/data/example5.tsv b/tests/data/example5.tsv
@@ -1,5 +1,7 @@
-participant_id	session_id	group
-sub-01	ses-01	PAT
-sub-01	ses-02	PAT
-sub-02	ses-01	OTHER
-sub-02	ses-02	CTRL
+participant_id	session_id	group	tool_item1	tool_item2	other_tool_item1
+sub-01	ses-01	PAT	11.0	"missing"	"none"
+sub-01	ses-02	PAT	"missing"	12.0	"none"
+sub-02	ses-01	OTHER	"missing"	"missing"	"none"
+sub-02	ses-02	OTHER	"missing"	"missing"	"none"
+sub-03	ses-01	CTRL	10.0	8.0	"ok"
+sub-03	ses-02	CTRL	10.0	8.0	"bad"
diff --git a/tests/integration/test_cli_pheno.py b/tests/integration/test_cli_pheno.py
@@ -117,7 +117,7 @@ def test_pheno_valid_inputs_run_successfully(
             ["do not have unique combinations of participant and session IDs"],
         ),
         (
-            "example22",
+            "example5",
             LookupError,
             [
                 "unsupported vocabulary namespace prefixes",