From 767b64235f26086cb1cdfdcd2d1a486a8a43621e Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Thu, 6 Jun 2024 13:51:12 +0100
Subject: [PATCH] Fix format.matches for v0.5

---
 ome_zarr/format.py | 21 ++++++++++++++++++++-
 ome_zarr/io.py     |  8 +++-----
 ome_zarr/reader.py | 10 +++++++++-
 3 files changed, 32 insertions(+), 7 deletions(-)

diff --git a/ome_zarr/format.py b/ome_zarr/format.py
index 8d4238b0..2f0acc67 100644
--- a/ome_zarr/format.py
+++ b/ome_zarr/format.py
@@ -8,6 +8,8 @@
 
 LOGGER = logging.getLogger("ome_zarr.format")
 
+NGFF_URL_0_5 = "https://ngff.openmicroscopy.org/0.5"
+
 
 def format_from_version(version: str) -> "Format":
     for fmt in format_implementations():
@@ -24,6 +26,7 @@ def format_implementations() -> Iterator["Format"]:
     """
     Return an instance of each format implementation, newest to oldest.
     """
+    yield FormatV05()
     yield FormatV04()
     yield FormatV03()
     yield FormatV02()
@@ -353,7 +356,7 @@ def version(self) -> str:
 
     @property
     def version_key(self) -> str:
-        return "https://ngff.openmicroscopy.org/0.5"
+        return NGFF_URL_0_5
 
     def init_store(self, path: str, mode: str = "r") -> FSStore:
         """
@@ -376,5 +379,21 @@ def init_store(self, path: str, mode: str = "r") -> FSStore:
         print("Created v0.5 store %s(%s, %s, %s)" % (cls, path, mode, kwargs))
         return store
 
+    def matches(self, metadata: dict) -> bool:
+        """Version 0.5+ defined by version_key (URL)"""
+        version = self._get_metadata_version(metadata)
+        LOGGER.debug("%s matches %s?", self.version, version)
+        return version == self.version_key
+    
+    def _get_metadata_version(self, metadata: dict) -> Optional[str]:
+        """
+        For version 0.5+ we use the NGFF_URL_0_5 key
+
+        Returns the version of the first object found in the metadata,
+        checking for 'multiscales', 'plate', 'well' etc
+        """
+        if self.version_key in metadata.get("attributes", {}):
+            return self.version_key
+
 
 CurrentFormat = FormatV05
diff --git a/ome_zarr/io.py b/ome_zarr/io.py
index f9e81c8d..0c7e56a7 100644
--- a/ome_zarr/io.py
+++ b/ome_zarr/io.py
@@ -71,7 +71,7 @@ def __init__(
         #         loader = CurrentFormat()
 
         self.__init_metadata()
-        print("init self.__metadata", self.__metadata)
+        print("ZarrLocation init self.__metadata", self.__metadata)
         detected = detect_format(self.__metadata, loader)
         LOGGER.debug("ZarrLocation.__init__ %s detected: %s", self.__path, detected)
         if detected != self.__fmt:
@@ -110,20 +110,18 @@ def __init_metadata(self) -> None:
             # NB: zarr_format not supported in Group.open() or Array.open() yet
             # We want to use zarr_format=None to handle v2 or v3
             zarr_group = Group.open(self.__store)  #, zarr_format=None)
-            self.zgroup: JSONDict = zarr_group.metadata.to_dict()
+            self.zgroup = zarr_group.metadata.to_dict()
             self.__metadata = self.zgroup
         except FileNotFoundError:
             # group doesn't exist yet, try array
             try:
                 zarr_array = Array.open(self.__store)  #, zarr_format=None)
-                self.zarray: JSONDict = zarr_array.metadata.to_dict()
+                self.zarray = zarr_array.metadata.to_dict()
                 self.__metadata = self.zarray
             except (ValueError, KeyError, FileNotFoundError):
                 # exceptions raised may change here?
-                print("__init_metadata DOESN'T EXIST", self.__store)
                 self.__exists = False
                 
-        print("__init_metadat EXISTS?", self.__exists, self.__metadata)
         # self.zarray: JSONDict = await self.get_json(".zarray")
         # self.zgroup: JSONDict = await self.get_json(".zgroup")
         # v3_json = await self.get_json("zarr.json")
diff --git a/ome_zarr/reader.py b/ome_zarr/reader.py
index 55f84ec0..4ace8237 100644
--- a/ome_zarr/reader.py
+++ b/ome_zarr/reader.py
@@ -9,7 +9,7 @@
 import numpy as np
 
 from .axes import Axes
-from .format import format_from_version
+from .format import format_from_version, NGFF_URL_0_5
 from .io import ZarrLocation
 from .types import JSONDict
 
@@ -176,6 +176,11 @@ def __init__(self, node: Node) -> None:
             LOGGER.debug(v)
 
     def lookup(self, key: str, default: Any) -> Any:
+
+        # Handle zarr V3 where everything is under "attributes"
+        if NGFF_URL_0_5 in self.zarr.root_attrs.get("attributes", {}):
+            return self.zarr.root_attrs.get("attributes", {}).get(NGFF_URL_0_5, {}).get(key, default)
+
         return self.zarr.root_attrs.get(key, default)
 
 
@@ -270,9 +275,12 @@ class Multiscales(Spec):
     @staticmethod
     def matches(zarr: ZarrLocation) -> bool:
         """is multiscales metadata present?"""
+
         if zarr.zgroup:
             if "multiscales" in zarr.root_attrs:
                 return True
+            if "multiscales" in (zarr.root_attrs.get("attributes", {}).get(NGFF_URL_0_5, {})):
+                return True
         return False
 
     def __init__(self, node: Node) -> None: