Preserve actual v2/v3 canonical input profiles

README.md

@@ -51,6 +51,13 @@ missing or false feature flags leave them disabled. Within enabled shallow
 storage, remote normalization is preferred; set `BIOMERO_REMOTE_SHALLOW_ZARR=false`
 to use importer-side normalization. NL-BIOMERO's demo enables these features.
 
+Canonical indexing records the backing store's actual OME-Zarr profile: 0.4/v2
+or 0.5/v3. Existing v2 stores are reused as v2, and importing an existing v3
+Image or Plate does not require conversion to v2. V3 indexing requires the
+generic semantic-guard API from the matching v3-capable shallower/importer;
+older installations retain v2-only indexing. Mixed-format Plate inventories
+are rejected rather than recorded under an incorrect profile.
+
 Result file attachments use the existing on-disk paths. Workflow-qualified
 attachment names are stored in OMERO metadata, so in-place image registrations
 and attachment links remain valid. Directory-backed Zarr stores are available

__workflows/SLURM_CellPose_Segmentation.py

@@ -51,7 +51,7 @@
 import logging
 
 # Version constant for easy version management
-VERSION = "2.9.0"
+VERSION = "2.9.0b15"
 
 logger = logging.getLogger(__name__)
 

__workflows/SLURM_Run_Workflow.py

@@ -102,7 +102,7 @@
                   constants.workflow.OUTPUT_CSV_TABLE,
                   constants.workflow.OUTPUT_ATTACH_FILE_OUTPUTS,
                   constants.workflow.OUTPUT_CREATE_ROIS]
-VERSION = "2.9.0"
+VERSION = "2.9.0b15"
 CANONICAL_INPUTS_OUTPUT = "Canonical_Inputs"
 
 

__workflows/SLURM_Run_Workflow_Batched.py

@@ -73,7 +73,7 @@
                   constants.workflow.OUTPUT_CREATE_ROIS]
 
 # Version constant for easy version management
-VERSION = "2.9.0"
+VERSION = "2.9.0b15"
 
 # Batched runs are queued the same way single runs are: this script resolves
 # the batches and records them in a launcher task, and the supervisor spawns

_data/SLURM_Get_Results.py

@@ -78,7 +78,7 @@
 from omero_metadata.populate import ParsingContext
 
 # Version constant for easy version management
-VERSION = "2.9.0"
+VERSION = "2.9.0b15"
 
 
 def get_images_by_ids(conn, image_ids):

_data/SLURM_Get_Update.py

@@ -54,7 +54,7 @@
 import sys
 
 # Version constant for easy version management
-VERSION = "2.9.0"
+VERSION = "2.9.0b15"
 
 logger = logging.getLogger(__name__)
 

_data/SLURM_Import_Results.py

@@ -318,7 +318,7 @@ def _mask_url(url): return url  # Fallback function if import fails
         )
 
 # Version constant for easy version management
-VERSION = "2.9.0"
+VERSION = "2.9.0b15"
 
 
 def load_canonical_input_snapshot(slurm_client, workflow_id):

_data/SLURM_Remote_Conversion.py

@@ -50,7 +50,7 @@
 CONV_OPTIONS_TARGET = ['tiff', 'zarr']
 
 # Version constant for easy version management
-VERSION = "2.9.0"
+VERSION = "2.9.0b15"
 
 
 def resolve_log_fallback_target(client, conn):

_data/_SLURM_File_Transfer.py

@@ -59,7 +59,7 @@
 
 logger = logging.getLogger(__name__)
 
-VERSION = "2.9.0"
+VERSION = "2.9.0b15"
 
 
 # ---------------------------------------------------------------------------

_data/_SLURM_Image_Transfer.py

@@ -128,6 +128,11 @@
             pixel_identities_match,
             read_zarr_v2_semantic_guard,
         )
+        try:
+            from biomero_importer.utils.pixel_identity import read_zarr_semantic_guard
+        except ImportError:
+            # Older deployments retain their v2-only behavior until upgraded.
+            read_zarr_semantic_guard = read_zarr_v2_semantic_guard
         from biomero_importer.utils.result_zarr import (
             discover_ngff_nodes,
         )
@@ -140,7 +145,7 @@
         )
 
 # Version constant for easy version management
-VERSION = "2.9.0"
+VERSION = "2.9.0b15"
 BIOMERO_CONFIG_FILE = os.getenv(
     "OMERO_BIOMERO_CONFIG_FILE",
     os.getenv("BIOMERO_CONFIG_FILE", "/opt/omero/server/biomero-config.json"),
@@ -684,6 +689,18 @@ def discover_canonical_inputs(objects, object_type):
     return sources, tuple(canonical_inputs) if complete else ()
 
 
+def canonical_interchange_profile(guard):
+    """Record the supported format actually backing this canonical node."""
+    profiles = {
+        ("0.4", 2): "ngff-0.4-zarr-v2",
+        ("0.5", 3): "ngff-0.5-zarr-v3",
+    }
+    try:
+        return profiles[(guard.ngff_version, guard.zarr_format)]
+    except KeyError as exc:
+        raise ValueError("Unsupported canonical OME-Zarr format") from exc
+
+
 def discover_canonical_label_components(
     source,
     storage_roots,
@@ -703,7 +720,7 @@ def discover_canonical_label_components(
             or node.parent_image_node_path != source.node_path
         ):
             continue
-        guard = read_zarr_v2_semantic_guard(root, node.node_path)
+        guard = read_zarr_semantic_guard(root, node.node_path)
         identity = provider.generate(
             root,
             node_path=node.node_path,
@@ -761,7 +778,8 @@ def build_canonical_plate_source(
         raise ValueError("Identity workers must be a positive integer")
 
     def generate_identity(node):
-        guard = read_zarr_v2_semantic_guard(root, node.node_path)
+        guard = read_zarr_semantic_guard(root, node.node_path)
+        profile = canonical_interchange_profile(guard)
         logger.info(
             "Calculating ISCC-BIO pixel identity for Plate %s %s node %s",
             plate.getId(),
@@ -787,18 +805,20 @@ def generate_identity(node):
             identity.data_code,
             identity.instance_code,
         )
-        return node.node_path, identity
+        return node.node_path, identity, profile
 
     identities = {}
+    profiles = set()
     last_keepalive = monotonic()
     with ThreadPoolExecutor(
         max_workers=min(identity_workers, len(nodes)),
         thread_name_prefix="biomero-iscc",
     ) as executor:
         # map preserves discovery order in the canonical manifest even though
         # the identity work and its diagnostic logging happen concurrently.
-        for node_path, identity in executor.map(generate_identity, nodes):
+        for node_path, identity, profile in executor.map(generate_identity, nodes):
             identities[node_path] = identity
+            profiles.add(profile)
             if (
                 keepalive is not None
                 and monotonic() - last_keepalive >= keepalive_interval
@@ -817,6 +837,9 @@ def generate_identity(node):
             "Lost the OMERO connection while indexing the canonical Plate Zarr"
         )
 
+    if len(profiles) != 1:
+        raise ValueError("Canonical Plate image/label nodes use different Zarr formats")
+    profile = profiles.pop()
     relative_path = Path(relative_path).as_posix()
     images = []
     for image_node in image_nodes:
@@ -827,7 +850,7 @@ def generate_identity(node):
             source_object_type="Plate",
             source_object_id=int(plate.getId()),
             source_generation=source_generation,
-            interchange_profile="ngff-0.4-zarr-v2",
+            interchange_profile=profile,
             pixel_identity=identities[image_node.node_path],
             pixel_identity_origin="canonical-bootstrap",
             canonical_pixel_verified=False,
@@ -858,7 +881,7 @@ def generate_identity(node):
         relative_path=relative_path,
         source_object_id=int(plate.getId()),
         source_generation=source_generation,
-        interchange_profile="ngff-0.4-zarr-v2",
+        interchange_profile=profile,
         images=tuple(images),
     )
 
@@ -1307,7 +1330,7 @@ def promote_exported_image_zarr(
         image, storage_roots)
     source_directory = derive_canonical_source_directory(image, storage_root)
     semantic_guard_reader = (
-        semantic_guard_reader or read_zarr_v2_semantic_guard
+        semantic_guard_reader or read_zarr_semantic_guard
     )
     guard = semantic_guard_reader(export_path, ".")
     validate_omero_image_semantics(image, guard)
@@ -1380,6 +1403,7 @@ def promote_exported_image_zarr(
         original_identity=original_identity,
         exported_identity=exported_identity,
         pixel_identity_origin="omero-pixels",
+        interchange_profile=canonical_interchange_profile(guard),
     )
     logger.info(
         "ISCC-BIO verification matched OMERO Pixels and exported Zarr for "
@@ -1428,7 +1452,7 @@ def index_existing_image_zarr(
         storage_roots,
     )
     semantic_guard_reader = (
-        semantic_guard_reader or read_zarr_v2_semantic_guard
+        semantic_guard_reader or read_zarr_semantic_guard
     )
     guard = semantic_guard_reader(existing_path, ".")
     validate_omero_image_semantics(image, guard)
@@ -1466,7 +1490,7 @@ def index_existing_image_zarr(
         source_object_id=int(image.getId()),
         source_generation=source_generation,
         node_path=".",
-        interchange_profile="ngff-0.4-zarr-v2",
+        interchange_profile=canonical_interchange_profile(guard),
         pixel_identity=existing_identity,
         pixel_identity_origin="canonical-bootstrap",
         canonical_pixel_verified=True,

admin/BIOMERO_Migrate_Shallow_Storage.py

@@ -47,7 +47,7 @@
 
 
 logger = logging.getLogger(__name__)
-VERSION = "2.9.0"
+VERSION = "2.9.0b15"
 
 OBJECT_TYPE = "Object Type"
 OBJECT_IDS = "Object IDs (optional)"

admin/Example_Minimal_Slurm_Script.py

@@ -66,7 +66,7 @@ def _check_command_safety(cmd: str) -> str | None:
 _SCMD = "Linux_Command"
 _DEFAULT_SCMD = "ls -la"
 
-VERSION = "2.9.0"
+VERSION = "2.9.0b15"
 
 
 def runScript():

admin/SLURM_Cownary.py

@@ -21,7 +21,7 @@
 
 logger = logging.getLogger(__name__)
 
-VERSION = "2.9.0"
+VERSION = "2.9.0b15"
 
 _LOLCOW_IMAGE = "docker://godlovedc/lolcow"
 _COWNARY_SBATCH_COMMAND = (

admin/SLURM_Init_environment.py

@@ -50,7 +50,7 @@
 from queue import Queue, Empty
 
 logger = logging.getLogger(__name__)
-VERSION = "2.9.0"
+VERSION = "2.9.0b15"
 
 
 def format_metadata_summary(report):

admin/SLURM_check_setup.py

@@ -60,7 +60,7 @@
 import pkg_resources
 
 # Version constant for easy version management
-VERSION = "2.9.0"
+VERSION = "2.9.0b15"
 
 logger = logging.getLogger(__name__)
 

admin/Tail_logs.py

@@ -26,7 +26,7 @@
 _DEFAULT_TAIL_LINES = 5000
 
 # Version constant for easy version management
-VERSION = "2.9.0"
+VERSION = "2.9.0b15"
 
 logger = logging.getLogger(__name__)