From 08e12f784e085adbf4ca6d384720443108f96cb6 Mon Sep 17 00:00:00 2001
From: jmoore <josh@glencoesoftware.com>
Date: Wed, 13 Apr 2022 14:55:15 +0200
Subject: [PATCH] Add support for HCS output

- skip parsing if plates exist
- temporarily remove HashSHA1 due to parsing error
  (https://github.com/ome/bioformats/issues/3810)
- insert MetadataOnly after Channel for validation
  (https://github.com/glencoesoftware/bioformats2raw/issues/137)
---
 src/ome_zarr_metadata/spec.py | 39 +++++++++++++++++++++++++++++------
 1 file changed, 33 insertions(+), 6 deletions(-)

diff --git a/src/ome_zarr_metadata/spec.py b/src/ome_zarr_metadata/spec.py
index 0365941..7bbbf11 100644
--- a/src/ome_zarr_metadata/spec.py
+++ b/src/ome_zarr_metadata/spec.py
@@ -32,11 +32,14 @@ def __init__(self, node: Node) -> None:
         super().__init__(node)
         try:
             data = self.handle(node)
-            for idx, image in enumerate(data.images):
-                series = node.zarr.create(str(idx))
-                assert series.exists()
-                _logger.info(f"found {series}")
-                node.add(series)
+            if data.plates:
+                _logger.info("Plates detected. Skipping implicit loading")
+            else:
+                for idx, image in enumerate(data.images):
+                    series = node.zarr.create(str(idx))
+                    assert series.exists(), f"{series} is missing"
+                    _logger.info(f"found {series}")
+                    node.add(series)
             node.metadata["ome-xml"] = data
         except Exception as e:
             _logger.error(f"failed to parse metadata: {e}")
@@ -45,8 +48,32 @@ def fix_xml(self, ns, elem):
         """
         Note: elem.insert() was not updating the object correctly.
         """
+
         if elem.tag == f"{ns}Pixels":
-            elem.append(ET.Element(f"{ns}MetadataOnly"))
+
+            must_have = set([f"{ns}BinData", f"{ns}TiffData", f"{ns}MetadataOnly"])
+            children = set([x.tag for x in elem])
+
+            if not any(x in children for x in must_have):
+                # Needs fixing
+                metadata_only = ET.Element(f"{ns}MetadataOnly")
+
+                inserted = False
+                for idx, child in enumerate(elem):
+                    if child.tag == f"{ns}Channel":
+                        elem.insert(idx + 1, metadata_only)
+                        inserted = True
+
+                if not inserted:
+                    # Append to the beginning
+                    elem.insert(0, metadata_only)
+
+        elif elem.tag == f"{ns}Plane":
+            remove = None
+            for idx, child in enumerate(elem):
+                if child.tag == f"{ns}HashSHA1":
+                    remove = child
+            elem.remove(remove)
 
     def parse_xml(self, filename):
         # Parse the file and find the current schema