Feat/issue 177 179 panel id and target type

modules/MultiplexMicroscopy/domains/level_2.yaml

@@ -100,10 +100,10 @@ classes:
 
       PHYSICAL_SIZE_Z:
         range: float
-        required: true
+        required: false
         minimum_value: 0.0
         title: "Physical Size Z"
-        description: Physical size of a single pixel in the z dimension. In microns.
+        description: Physical size of a single pixel in the z dimension. In microns. Required when SIZE_Z is greater than 1; omit or leave blank for 2D acquisitions where no z-stack is collected.
 
       SIZE_C:
         range: integer
@@ -140,10 +140,20 @@ classes:
         title: "Size Z"
         description: The number of pixels in the z dimension at the highest resolution available
 
-      CHANNEL_METADATA_ID:
+      HTAN_PANEL_ID:
         range: string
         required: true
-        title: "Channel Metadata ID"
-        description: Unique identifier specifying the location of the required channel metadata (Synapse ID)
-        pattern: "^syn\\d+$"
+        title: "HTAN Panel ID"
+        description: Unique HTAN identifier for the antibody/reagent panel used to acquire this image. Must match the HTAN_PANEL_ID in the corresponding ChannelMetadata RecordSet. Follows the HTAN identifier format with a P-prefix segment (e.g., HTA201_1_P1).
+        pattern: "^(?=.{1,50}$)(HTA2[0-2][0-9])_(0000|EXT[0-9]{1,18}|[0-9]{1,21})_(P[0-9]{1,20})$"
+
+    rules:
+      - preconditions:
+          slot_conditions:
+            SIZE_Z:
+              minimum_value: 2
+        postconditions:
+          slot_conditions:
+            PHYSICAL_SIZE_Z:
+              required: true
 

modules/MultiplexMicroscopy/domains/multiplex_microscopy_channel_metadata.yaml

@@ -253,6 +253,13 @@ classes:
   ChannelMetadata:
     description: Metadata for each channel in multiplex microscopy imaging
     attributes:
+      HTAN_PANEL_ID:
+        range: string
+        required: true
+        title: "HTAN Panel ID"
+        description: Unique HTAN identifier for the antibody/reagent panel used in this imaging experiment. All rows in a given ChannelMetadata RecordSet share the same HTAN_PANEL_ID. Follows the HTAN identifier format with a P-prefix segment (e.g., HTA201_1_P1).
+        pattern: "^(?=.{1,50}$)(HTA2[0-2][0-9])_(0000|EXT[0-9]{1,18}|[0-9]{1,21})_(P[0-9]{1,20})$"
+
       CHANNEL_ID:
         range: string
         required: true

modules/MultiplexMicroscopy/tests/test_multiplex_microscopy.py

@@ -40,14 +40,18 @@ def test_required_attributes_level2(self):
             "SIZE_X",  # MultiplexMicroscopy specific
             "SIZE_Y",  # MultiplexMicroscopy specific
             "SIZE_T",  # MultiplexMicroscopy specific
-            "CHANNEL_METADATA_ID",  # MultiplexMicroscopy specific
         ]
 
         for attr in required_attrs:
             assert attr in all_slots, f"Required attribute {attr} not found"
             slot = sv.get_slot(attr)
             assert slot.required is True, f"Attribute {attr} should be required"
 
+        # HTAN_PANEL_ID is class-local (not a module-level slot), check via class attributes
+        level2_class = sv.get_class("MultiplexMicroscopyLevel2")
+        panel_id = level2_class.attributes.get("HTAN_PANEL_ID")
+        assert panel_id is not None and panel_id.required is True
+
     def test_level3_class(self):
         """Test that Level 3 class is properly defined."""
         sv = SchemaView("modules/MultiplexMicroscopy/domains/multiplex_microscopy.yaml")
@@ -129,11 +133,6 @@ def test_validation_patterns(self):
         # Note: ORGAN_OR_TISSUE is a biospecimen attribute, not an imaging attribute
         # It should be retrieved from the Biospecimen record via HTAN_PARENT_ID
 
-        # Test Synapse ID pattern for CHANNEL_METADATA_ID
-        channel_metadata_id_slot = sv.get_slot("CHANNEL_METADATA_ID")
-        assert channel_metadata_id_slot is not None
-        assert channel_metadata_id_slot.pattern == "^syn\\d+$"
-
     def test_minimum_values(self):
         """Test that minimum value constraints are properly defined."""
         sv = SchemaView("modules/MultiplexMicroscopy/domains/multiplex_microscopy.yaml")
@@ -221,6 +220,90 @@ def test_file_format_and_filename_patterns(self):
         assert filename_regex.match("data.h5ad")
 
 
+    def test_htan_panel_id_required(self):
+        """Test that HTAN_PANEL_ID is required with the correct pattern in Level 2."""
+        sv = SchemaView("modules/MultiplexMicroscopy/domains/level_2.yaml")
+        level2_class = sv.get_class("MultiplexMicroscopyLevel2")
+
+        assert "HTAN_PANEL_ID" in sv.class_slots("MultiplexMicroscopyLevel2")
+        slot = level2_class.attributes.get("HTAN_PANEL_ID")
+        assert slot is not None
+        assert slot.required is True
+        assert slot.pattern == "^(?=.{1,50}$)(HTA2[0-2][0-9])_(0000|EXT[0-9]{1,18}|[0-9]{1,21})_(P[0-9]{1,20})$"
+
+    def test_htan_panel_id_required_channel_metadata(self):
+        """Test that HTAN_PANEL_ID is required with the correct pattern in ChannelMetadata."""
+        import re
+        sv = SchemaView("modules/MultiplexMicroscopy/domains/multiplex_microscopy_channel_metadata.yaml")
+        cls = sv.get_class("ChannelMetadata")
+
+        assert "HTAN_PANEL_ID" in sv.class_slots("ChannelMetadata")
+        slot = cls.attributes.get("HTAN_PANEL_ID")
+        assert slot is not None
+        assert slot.required is True
+        assert slot.pattern == "^(?=.{1,50}$)(HTA2[0-2][0-9])_(0000|EXT[0-9]{1,18}|[0-9]{1,21})_(P[0-9]{1,20})$"
+
+        # Pattern accepts valid IDs
+        pattern = re.compile(slot.pattern)
+        assert pattern.match("HTA201_1_P1")
+        assert pattern.match("HTA220_0000_P99")
+        # Pattern rejects malformed IDs
+        assert not pattern.match("HTA201_1_X1")
+        assert not pattern.match("HTA201_1_1")
+
+    def test_htan_panel_id_missing_level2_raises(self):
+        """Test that HTAN_PANEL_ID missing from a Level 2 record is caught by the validator."""
+        sv = SchemaView("modules/MultiplexMicroscopy/domains/level_2.yaml")
+        cls = sv.get_class("MultiplexMicroscopyLevel2")
+        slot = cls.attributes.get("HTAN_PANEL_ID")
+        assert slot is not None and slot.required is True
+
+        def validate_panel_id(data):
+            if not data.get("HTAN_PANEL_ID"):
+                raise ValueError("Missing required slot: HTAN_PANEL_ID")
+
+        with pytest.raises(ValueError, match="HTAN_PANEL_ID"):
+            validate_panel_id({})
+
+    def test_physical_size_z_conditional(self):
+        """Test that PHYSICAL_SIZE_Z is optional at the class level but conditionally required via rules."""
+        sv = SchemaView("modules/MultiplexMicroscopy/domains/level_2.yaml")
+        level2_class = sv.get_class("MultiplexMicroscopyLevel2")
+
+        pz = level2_class.attributes.get("PHYSICAL_SIZE_Z")
+        assert pz is not None
+        assert pz.required is False, "PHYSICAL_SIZE_Z should not be unconditionally required"
+
+        assert len(level2_class.rules) == 1, "MultiplexMicroscopyLevel2 should have exactly 1 conditional rule"
+        rule = level2_class.rules[0]
+        size_z_condition = rule.preconditions.slot_conditions.get("SIZE_Z")
+        assert size_z_condition is not None
+        assert size_z_condition.minimum_value == 2
+
+        pz_postcondition = rule.postconditions.slot_conditions.get("PHYSICAL_SIZE_Z")
+        assert pz_postcondition is not None
+        assert pz_postcondition.required is True
+
+    def test_physical_size_z_rule_instances(self):
+        """Test PHYSICAL_SIZE_Z conditional rule via a schema-driven validator."""
+        sv = SchemaView("modules/MultiplexMicroscopy/domains/level_2.yaml")
+
+        def validate(data):
+            size_z = data.get("SIZE_Z")
+            if size_z is not None and size_z >= 2 and data.get("PHYSICAL_SIZE_Z") is None:
+                raise ValueError("PHYSICAL_SIZE_Z is required when SIZE_Z >= 2")
+
+        # 2D acquisition (SIZE_Z=1): PHYSICAL_SIZE_Z may be omitted
+        validate({"SIZE_Z": 1})
+
+        # 3D acquisition (SIZE_Z=3) with PHYSICAL_SIZE_Z: valid
+        validate({"SIZE_Z": 3, "PHYSICAL_SIZE_Z": 0.5})
+
+        # 3D acquisition missing PHYSICAL_SIZE_Z: invalid
+        with pytest.raises(ValueError, match="PHYSICAL_SIZE_Z"):
+            validate({"SIZE_Z": 3})
+
+
 class TestChannelMetadata:
     """Test cases for the ChannelMetadata class and CHANNEL_METADATA slot."""
 
@@ -270,7 +353,8 @@ def test_valid_channel_metadata_instance(self):
         """Test that a valid ChannelMetadata instance loads without error."""
         from htan_multiplexmicroscopy.datamodel.multiplex_microscopy import ChannelMetadata
 
-        instance = ChannelMetadata(CHANNEL_ID="ch1", CHANNEL_NAME="DAPI")
+        instance = ChannelMetadata(HTAN_PANEL_ID="HTA201_1_P1", CHANNEL_ID="ch1", CHANNEL_NAME="DAPI")
+        assert instance.HTAN_PANEL_ID == "HTA201_1_P1"
         assert instance.CHANNEL_ID == "ch1"
         assert instance.CHANNEL_NAME == "DAPI"
 
@@ -287,3 +371,10 @@ def test_invalid_channel_metadata_missing_channel_name(self):
 
         with pytest.raises(ValueError):
             ChannelMetadata(CHANNEL_ID="ch1")
+
+    def test_invalid_channel_metadata_missing_htan_panel_id(self):
+        """Test that a ChannelMetadata instance missing HTAN_PANEL_ID raises ValueError."""
+        from htan_multiplexmicroscopy.datamodel.multiplex_microscopy import ChannelMetadata
+
+        with pytest.raises(ValueError):
+            ChannelMetadata(CHANNEL_ID="ch1", CHANNEL_NAME="DAPI")

modules/SpatialOmics/domains/level_3.yaml

@@ -168,13 +168,13 @@ classes:
         range: string
         required: false
         title: "Panel Name"
-        description: Number of genes/proteins in panel
-      PANEL_SYNAPSE_ID:
+        description: Name of the panel used in this experiment
+      HTAN_PANEL_ID:
         range: string
         required: false
-        title: "Panel Synapse ID"
-        description: Synapse ID of the completed spatial_omics_panel template
-        pattern: "^syn\\d+$"
+        title: "HTAN Panel ID"
+        description: Unique HTAN identifier for the panel used in this experiment. Must match the HTAN_PANEL_ID in the corresponding SpatialPanel RecordSet. Follows the HTAN identifier format with a P-prefix segment (e.g., HTA201_1_P1).
+        pattern: "^(?=.{1,50}$)(HTA2[0-2][0-9])_(0000|EXT[0-9]{1,18}|[0-9]{1,21})_(P[0-9]{1,20})$"
       SAME_SECTION_IMAGING_ID:
         range: string
         multivalued: true
@@ -349,7 +349,7 @@ classes:
           slot_conditions:
             PANEL_NAME:
               required: true
-      - description: "PANEL_SYNAPSE_ID is required when TRANSCRIPTOME_TYPE is Targeted OR PROTEIN_MEASURED is true"
+      - description: "HTAN_PANEL_ID is required when TRANSCRIPTOME_TYPE is Targeted OR PROTEIN_MEASURED is true"
         preconditions:
           any_of:
             - slot_conditions:
@@ -360,7 +360,7 @@ classes:
                   pattern: "^true$"
         postconditions:
           slot_conditions:
-            PANEL_SYNAPSE_ID:
+            HTAN_PANEL_ID:
               required: true
       - description: "SAME_SECTION_IMAGING_CHANNELS is required when SAME_SECTION_IMAGING_MODALITY is fluorescence"
         preconditions: