From ac745e678815bdf7a0e8965f48ee28e0cff32448 Mon Sep 17 00:00:00 2001
From: Chris Markiewicz <effigies@gmail.com>
Date: Tue, 5 Nov 2024 13:45:44 -0500
Subject: [PATCH] schema: Update metaschema, fix errors caught by metaschema

---
 src/metaschema.json                           | 12 +++++++++++
 src/schema/rules/files/atlas/derivatives.yaml | 20 +++++++++----------
 src/schema/rules/files/deriv/imaging.yaml     | 20 +++++++++----------
 3 files changed, 32 insertions(+), 20 deletions(-)

diff --git a/src/metaschema.json b/src/metaschema.json
index aab0f487c1..23c858543a 100644
--- a/src/metaschema.json
+++ b/src/metaschema.json
@@ -361,6 +361,18 @@
               "required": ["core", "tables"],
               "additionalProperties": false
             },
+            "atlas": {
+              "type": "object",
+              "patternProperties": {
+                "^[a-z_]+$": {
+                  "type": "object",
+                  "patternProperties": {
+                    "^[a-zA-Z0-9_]+$": { "$ref": "#/definitions/suffixRule" }
+                  }
+                }
+              },
+              "additionalProperties": false
+            },
             "deriv": {
               "type": "object",
               "patternProperties": {
diff --git a/src/schema/rules/files/atlas/derivatives.yaml b/src/schema/rules/files/atlas/derivatives.yaml
index 7c03ae25eb..3c6eef8595 100644
--- a/src/schema/rules/files/atlas/derivatives.yaml
+++ b/src/schema/rules/files/atlas/derivatives.yaml
@@ -92,7 +92,7 @@ anat_parametric_discrete_segmentation:
     cohort: optional
     space: optional
     atlas: optional
-    segmentation: option
+    segmentation: optional
     scale: optional
     resolution: optional
     density: optional
@@ -112,7 +112,7 @@ anat_nonparametric_discrete_segmentation:
     cohort: optional
     space: optional
     atlas: optional
-    segmentation: option
+    segmentation: optional
     scale: optional
     resolution: optional
     density: optional
@@ -132,7 +132,7 @@ func_discrete_segmentation:
     cohort: optional
     space: optional
     atlas: optional
-    segmentation: option
+    segmentation: optional
     scale: optional
     resolution: optional
     density: optional
@@ -147,7 +147,7 @@ dwi_discrete_segmentation:
     cohort: optional
     space: optional
     atlas: optional
-    segmentation: option
+    segmentation: optional
     scale: optional
     resolution: optional
     density: optional
@@ -162,7 +162,7 @@ anat_parametric_probabilistic_segmentation:
     cohort: optional
     space: optional
     atlas: optional
-    segmentation: option
+    segmentation: optional
     scale: optional
     resolution: optional
     density: optional
@@ -178,7 +178,7 @@ anat_nonparametric_probabilistic_segmentation:
     cohort: optional
     space: optional
     atlas: optional
-    segmentation: option
+    segmentation: optional
     scale: optional
     resolution: optional
     density: optional
@@ -194,7 +194,7 @@ func_probabilistic_segmentation:
     cohort: optional
     space: optional
     atlas: optional
-    segmentation: option
+    segmentation: optional
     scale: optional
     resolution: optional
     density: optional
@@ -210,7 +210,7 @@ dwi_probabilistic_segmentation:
     cohort: optional
     space: optional
     atlas: optional
-    segmentation: option
+    segmentation: optional
     scale: optional
     resolution: optional
     density: optional
@@ -232,7 +232,7 @@ anat_parametic_discrete_surface:
     cohort: optional
     space: optional
     atlas: optional
-    segmentation: option
+    segmentation: optional
     scale: optional
     resolution: optional
     density: optional
@@ -253,7 +253,7 @@ anat_nonparametic_discrete_surface:
     cohort: optional
     space: optional
     atlas: optional
-    segmentation: option
+    segmentation: optional
     scale: optional
     resolution: optional
     density: optional
diff --git a/src/schema/rules/files/deriv/imaging.yaml b/src/schema/rules/files/deriv/imaging.yaml
index f1a6cc63f6..5da448e324 100644
--- a/src/schema/rules/files/deriv/imaging.yaml
+++ b/src/schema/rules/files/deriv/imaging.yaml
@@ -101,7 +101,7 @@ anat_parametric_discrete_segmentation:
     cohort: optional
     space: optional
     atlas: optional
-    segmentation: option
+    segmentation: optional
     scale: optional
     resolution: optional
     density: optional
@@ -121,7 +121,7 @@ anat_nonparametric_discrete_segmentation:
     cohort: optional
     space: optional
     atlas: optional
-    segmentation: option
+    segmentation: optional
     scale: optional
     resolution: optional
     density: optional
@@ -141,7 +141,7 @@ func_discrete_segmentation:
     cohort: optional
     space: optional
     atlas: optional
-    segmentation: option
+    segmentation: optional
     scale: optional
     resolution: optional
     density: optional
@@ -156,7 +156,7 @@ dwi_discrete_segmentation:
     cohort: optional
     space: optional
     atlas: optional
-    segmentation: option
+    segmentation: optional
     scale: optional
     resolution: optional
     density: optional
@@ -171,7 +171,7 @@ anat_parametric_probabilistic_segmentation:
     cohort: optional
     space: optional
     atlas: optional
-    segmentation: option
+    segmentation: optional
     scale: optional
     resolution: optional
     density: optional
@@ -187,7 +187,7 @@ anat_nonparametric_probabilistic_segmentation:
     cohort: optional
     space: optional
     atlas: optional
-    segmentation: option
+    segmentation: optional
     scale: optional
     resolution: optional
     density: optional
@@ -203,7 +203,7 @@ func_probabilistic_segmentation:
     cohort: optional
     space: optional
     atlas: optional
-    segmentation: option
+    segmentation: optional
     scale: optional
     resolution: optional
     density: optional
@@ -219,7 +219,7 @@ dwi_probabilistic_segmentation:
     cohort: optional
     space: optional
     atlas: optional
-    segmentation: option
+    segmentation: optional
     scale: optional
     resolution: optional
     density: optional
@@ -241,7 +241,7 @@ anat_parametic_discrete_surface:
     cohort: optional
     space: optional
     atlas: optional
-    segmentation: option
+    segmentation: optional
     scale: optional
     resolution: optional
     density: optional
@@ -262,7 +262,7 @@ anat_nonparametic_discrete_surface:
     cohort: optional
     space: optional
     atlas: optional
-    segmentation: option
+    segmentation: optional
     scale: optional
     resolution: optional
     density: optional