Merge pull request ome#71 from jluethi/380_alphanumeric_well_images

Relax the allowed names of images in wells

Author: joshmoore

index.md

@@ -1547,7 +1547,11 @@ The `well` object MUST contain an `images` key
 whose value MUST be an array of JSON objects specifying all fields of views for a given well.
 Each image object MUST contain a `path` key
 whose value MUST be a string specifying the path to the field of view.
-The `path` MUST contain only alphanumeric characters, MUST be case-sensitive, and MUST NOT be a duplicate of any other `path` in the `images` array.
+The `path` MUST be case-sensitive, and MUST NOT be a duplicate of any other `path` in the `images` list.
+The `path` MUST follow [Zarr node name naming conventions](https://github.com/zarr-developers/zarr-specs/blob/main/docs/v3/core/index.rst#node-names) including the recommended limitations of characters to ensure consistency across different storage systems and programming languages. 
+Specifically: The `path` MUST NOT consist only of periods (like `.` or `..`) or start with the reserved prefix `__`; 
+The `path` MUST NOT be an empty string and MUST NOT contain `/` characters; 
+The `path` MUST only use characters in the sets `a-z`, `A-Z`, `0-9`, `-`, `_`, `.`. 
 If multiple acquisitions were performed in the plate,
 it MUST contain an `acquisition` key whose value MUST be an integer identifying the acquisition
 which MUST match one of the acquisition JSON objects defined in the [plate metadata](#plate-md).

schemas/well.schema

@@ -25,7 +25,14 @@
                   "path": {
                     "description": "The path for this field of view subgroup",
                     "type": "string",
-                    "pattern": "^[A-Za-z0-9]+$"
+                    "minLength": 1,
+                    "pattern": "^[A-Za-z0-9_.-]+$",
+                    "not": {
+                      "anyOf": [
+                        { "pattern": "^\\.+$" },
+                        { "pattern": "^__" }
+                      ]
+                    }
                   }
                 },
                 "required": [

tests/attributes/spec/invalid/well/forbidden_path_1.json

@@ -0,0 +1,15 @@
+{
+  "well": {
+    "images": [
+      {
+        "path": "."
+      }
+    ]
+  },
+  "_conformance": {
+    "schema": {
+      "id": "schemas/well.schema"
+    },
+    "description": "Tests for the well JSON schema: "
+  }
+}

tests/attributes/spec/invalid/well/forbidden_path_2.json

@@ -0,0 +1,15 @@
+{
+  "well": {
+    "images": [
+      {
+        "path": ".."
+      }
+    ]
+  },
+  "_conformance": {
+    "schema": {
+      "id": "schemas/well.schema"
+    },
+    "description": "Tests for the well JSON schema: "
+  }
+}

tests/attributes/spec/invalid/well/forbidden_path_3.json

@@ -0,0 +1,15 @@
+{
+  "well": {
+    "images": [
+      {
+        "path": "__something"
+      }
+    ]
+  },
+  "_conformance": {
+    "schema": {
+      "id": "schemas/well.schema"
+    },
+    "description": "Tests for the well JSON schema: "
+  }
+}

tests/attributes/spec/invalid/well/forbidden_path_4.json

@@ -0,0 +1,15 @@
+{
+  "well": {
+    "images": [
+      {
+        "path": "!@#$%^&*()+={}[]"
+      }
+    ]
+  },
+  "_conformance": {
+    "schema": {
+      "id": "schemas/well.schema"
+    },
+    "description": "Tests for the well JSON schema: "
+  }
+}

tests/attributes/spec/valid/well/minimal_path_special_char.json

@@ -0,0 +1,18 @@
+{
+  "ome": {
+    "version": "0.6.dev2",
+    "well": {
+      "images": [
+        {
+          "path": "0_a-b.image"
+        }
+      ]
+    }
+  },
+  "_conformance": {
+    "schema": {
+      "id": "schemas/well.schema"
+    },
+    "description": "Tests for the well JSON schema: "
+  }
+}

version_history.md

@@ -8,6 +8,12 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 
+## [Unreleased]
+
+### Changed
+
+- Changed the constraints for valid `path` values in `wells` for HCS plates to allow some non-alphanumeric characters.
+
 ## [0.6.dev3] - 2025-01-27
 
 ### Changed