Clev/model metadata v1 (#11)

* Add Model experiment type and refactor Experiment hierarchy

Split Experiment into abstract base class + InSituExperiment to separate
in-situ-specific fields (vertical_coverage, permits, meteorological data,
etc.) from fields shared with model experiments. Intervention and Tracer
now inherit from InSituExperiment.

New Model class (is_a: Experiment) with ModelComponent, ModelGrid, and
ModelInputDetails. Renamed model_simulation.yaml to model.yaml. Added
GridType and ModelComponentType enums.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* Add Dataset hierarchy: abstract Dataset, FieldDataset, and ModelSimulationDataset

Refactor Dataset into an abstract base class with two concrete subclasses,
mirroring the Experiment hierarchy pattern:

- Dataset (abstract): common fields shared by all dataset types (name,
  description, project_id, experiment_id, dataset_type, data_submitter,
  license, filenames, etc.)
- FieldDataset: field/observational-specific fields (temporal_coverage,
  platform_info, data_product_type, qc_flag_scheme, calibration_files,
  variables)
- ModelSimulationDataset: model-specific fields (simulation_type,
  start/end_datetime, spin_up_protocol, output_frequency,
  time_stepping_scheme, alkalinity_perturbation_description,
  hardware_configuration, model_output_variables) with a conditional
  rule requiring alkalinity_perturbation_description when
  simulation_type = "perturbation"

Also adds HardwareConfiguration class and two new enums: SimulationType
(counterfactual/perturbation) and ModelSimulationVariable (10 common
model output variables).

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* reset Dataset and Experiment to no longer be abstract classes

* experiment-level model metadata v1 feedback

* reset custom field from grid_type to model_component_type

* add conditional rendering rule for model_component_type_custom

Show and require model_component_type_custom only when
model_component_type is "other". Also fixes typo "Compoent" → "Component".

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* Fix 'Veritical' typo in ModelGrid vertical_coordinate_type title

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* updates for dataset level model metadata

---------

Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>

Author: clevinson

project/jsonschema/oae_data_protocol.schema.json

@@ -5,23 +5,27 @@ default_prefix: oae
 
 classes:
   Dataset:
+    # TODO: We may want to revert to set 'abstract: true' again once we set `include_range_class_descendents: true`
+    # As of right now, setting Dataset to abstract means we don't get it in the JSON Schema at all and it breaks
+    # downstream usage
+    # abstract: true
     description: >-
-      A dataset related to an OAE experiment. Generally following guidelines & best practices as outlined in
+      Abstract base class for all dataset types. Contains fields common to both field/observational and model simulation
+      datasets. Generally following guidelines & best practices as outlined in
       [science-on-schema.org](https://github.com/ESIPFed/science-on-schema.org/blob/main/guides/Dataset.md)
     slots:
       - name
       - description
       - project_id
       - experiment_id
-      - temporal_coverage
     slot_usage:
       - name:
           title: Dataset Title
           range: string
           required: true
           description: >-
             A brief descriptive sentence that summarizes the content of a dataset. Here is one example:
-            
+
             "Dissolved inorganic carbon, total alkalinity, pH, temperature, salinity and other variables collected from
             profile and discrete sample observations using CTD, Niskin bottle, and other instruments from R/V Wecoma in
             the U.S. West Coast California Current System during the 2011 West Coast Ocean Acidification Cruise
@@ -46,7 +50,7 @@ classes:
         # TODO: Add pre/post condition slots for _custom field rendering
         title: Dataset Type
         description: >-
-          Selected controlled vocabularies for data types relevant to mCDR have been referenced from NASA’s SeaBASS
+          Selected controlled vocabularies for data types relevant to mCDR have been referenced from NASA's SeaBASS
           metadata system and are provided below, for additional data types of optical characteristics see the [SeaBASS
           controlled definitions list](https://seabass.gsfc.nasa.gov/wiki/metadataheaders#data_type). Additional data
           types have been included to meet the needs of mCDR field projects.
@@ -82,6 +86,30 @@ classes:
         title: Fair Use Data Request
         description: A statement from the data producer regarding how this dataset should be used.
         range: string
+      filenames:
+        # TODO: Should be upgraded to be compatilbe with schema:distribution
+        # https://github.com/ESIPFed/science-on-schema.org/blob/main/guides/Dataset.md#distributions
+        title: Filenames
+        range: string
+        required: true
+        multivalued: true
+        # TODO: workaround since JSON Schema treats [] values as satisfying the "required" constraint
+        # It might be nice to fix this in a linkml PR to have minItems=1 automatically set for required lists in the
+        # JSONSchema generator
+        minimum_cardinality: 1
+
+    exact_mappings:
+      - "schema:Dataset"
+      - "dcat:Dataset"
+
+  FieldDataset:
+    is_a: Dataset
+    description: >-
+      A field or observational dataset related to an OAE experiment. Contains fields specific to in-situ data
+      collection such as platform information, calibration files, QC flags, and measured variables.
+    slots:
+      - temporal_coverage
+    attributes:
       data_product_type:
         title: Data Product Type
         description: >-
@@ -119,18 +147,93 @@ classes:
         slot_uri: schema:variableMeasured
         range: Variable
         multivalued: true
+
+  ModelOutputDataset:
+    is_a: Dataset
+    description: >-
+      A model simulation output dataset. Contains fields specific to computational model output including
+      simulation configuration, output variables, and hardware information.
+    slot_usage:
       filenames:
-        # TODO: Should be upgraded to be compatilbe with schema:distribution
-        # https://github.com/ESIPFed/science-on-schema.org/blob/main/guides/Dataset.md#distributions
-        title: Filenames
+        title: Model Output Filenames
+    attributes:
+      simulation_type:
+        title: Simulation Type
+        description: "Whether this is a counterfactual (control/baseline) or perturbation simulation."
+        range: SimulationType
+        required: true
+      spin_up_protocol:
+        title: Spin-up Protocol
+        description: "Description of the model spin-up process."
         range: string
+      start_datetime:
+        title: Start Date and Time
+        description: "Start date and time of the simulation in UTC ISO-8601."
+        range: datetime
+        required: true
+      end_datetime:
+        title: End Date and Time
+        description: "End date and time of the simulation in UTC ISO-8601."
+        range: datetime
         required: true
+      output_frequency:
+        title: Output Frequency
+        description: "Frequency of model output (e.g., 'hourly mean', 'daily mean')."
+        range: string
+      time_stepping_scheme:
+        title: Time-stepping Scheme
+        description: "Time-stepping method and time step used in the simulation."
+        range: string
+      alkalinity_perturbation_description:
+        title: Alkalinity Perturbation Description
+        description: >-
+          Description of the alkalinity perturbation applied in the simulation. Required when simulation_type
+          is "perturbation".
+        range: string
+      hardware_configuration:
+        title: Hardware Configuration
+        description: "Details about the computational hardware used for the simulation."
+        range: HardwareConfiguration
+        inlined: true
+      model_output_variables:
+        title: Key Model Output Variables
+        description: "Checklist of variables included in the model simulation output."
+        range: ModelOutputVariable
         multivalued: true
-        # TODO: workaround since JSON Schema treats [] values as satisfying the "required" constraint
-        # It might be nice to fix this in a linkml PR to have minItems=1 automatically set for required lists in the
-        # JSONSchema generator
-        minimum_cardinality: 1
+    rules:
+      - preconditions:
+          slot_conditions:
+            simulation_type:
+              equals_string: "perturbation"
+        postconditions:
+          slot_conditions:
+            alkalinity_perturbation_description:
+              required: true
 
-    exact_mappings:
-      - "schema:Dataset"
-      - "dcat:Dataset"
+  HardwareConfiguration:
+    description: "Details about the computational hardware used to run a model simulation."
+    attributes:
+      machine:
+        title: Machine
+        description: "Name of the machine or cluster (e.g., 'Perlmutter')."
+        range: string
+      operating_system:
+        title: Operating System
+        description: "Operating system used (e.g., 'Linux')."
+        range: string
+      cpu_gpu_details:
+        title: CPU/GPU Details
+        description: "Details about CPU/GPU hardware or link to specifications."
+        range: string
+      memory:
+        title: Memory
+        description: "Memory available (e.g., '512 GB DDR4')."
+        range: string
+      storage:
+        title: Storage
+        description: "Storage available (e.g., '44 PB')."
+        range: string
+      parallelization:
+        title: Parallelization
+        description: "Parallelization details (e.g., '3 nodes, 108 ntasks per node')."
+        range: string

src/oae_data_protocol/datamodel/oae_data_protocol.py

@@ -224,11 +224,75 @@ enums:
         description: "Nahcolite (NaHCO₃) used as an alkalinity source."
       other:
         description: "Enter a custom value in the field provided"
+  GridType:
+    description: "Type of grid in a multi-grid or nested model configuration"
+    permissible_values:
+      inner_grid:
+        description: "Inner (nested, higher-resolution) grid"
+      outer_grid:
+        description: "Outer (coarser-resolution) grid"
+      single_grid:
+        description: "Single grid (no nesting)"
+
+  ModelComponentType:
+    description: "Type of model component"
+    permissible_values:
+      physics:
+        title: "Physics"
+        description: "Physical model component (e.g., ocean circulation)"
+      bgc_ecosystem:
+        title: "BGC / Ecosystem"
+        description: "Biogeochemical or ecosystem model component"
+      sea_ice:
+        title: "Sea Ice"
+        description: "Sea Ice model component"
+      atmosphere:
+        title: "Atmosphere"
+        description: "Atmosphere model component"
+      other:
+        description: "Other model component (e.g., sea ice, sediment, atmosphere)"
+
   DataProductType:
     permissible_values:
       originally_collected_dataset:
         description: A dataset collected from a research cruise or laboratory experiment
       data_compilation_product:
         description: (e.g., SOCAT, GLODAP)
       derived_product:
-        description: (e.g. gridded products, or model output).
+        description: (e.g. gridded products, or model output).
+
+  SimulationType:
+    description: "Type of model simulation dataset"
+    permissible_values:
+      counterfactual:
+        description: "Control/baseline simulation without alkalinity perturbation"
+      perturbation:
+        description: "Simulation with alkalinity perturbation applied"
+
+  ModelOutputVariable:
+    description: "Variables commonly included in model simulation output datasets"
+    permissible_values:
+      air_sea_co2_flux:
+        title: "Air-sea CO2 flux"
+        description: "Air-sea exchange of carbon dioxide"
+      dissolved_inorganic_carbon:
+        title: "Dissolved Inorganic Carbon"
+        description: "Dissolved inorganic carbon (DIC)"
+      total_alkalinity:
+        title: "Total Alkalinity"
+        description: "Total alkalinity (TA)"
+      temperature:
+        description: "Temperature"
+      salinity:
+        description: "Salinity"
+      ph:
+        title: "pH"
+        description: "pH of seawater"
+      phytoplankton:
+        description: "Phytoplankton biomass or concentration"
+      horizontal_velocity:
+        title: "Horizontal velocity"
+        description: "Horizontal velocity components (u, v)"
+      vertical_velocity:
+        title: "Vertical velocity"
+        description: "Vertical velocity component (w)"

src/oae_data_protocol/schema/dataset.yaml

@@ -9,14 +9,16 @@ default_prefix: oae
 
 classes:
   Experiment:
+    # TODO: We may want to revert to set 'abstract: true' again once we set `include_range_class_descendents: true`
+    # As of right now, setting Experiment to abstract means we don't get it in the JSON Schema at all and it breaks
+    # downstream usage
+    # abstract: true
     description: >-
-      Experiment metadata applies to a specific study but remains consistent across datasets.
+      Abstract base class for all experiment types. Contains fields common to both in-situ and model experiments.
     slots:
       - name
       - description
       - spatial_coverage
-      - vertical_coverage
-      - permits
       - project_id
       - experiment_id
     slot_usage:
@@ -40,8 +42,6 @@ classes:
           Latitude/longitude bounds of observed data in experiment, provided in decimal degrees as westernmost
           longitude, southernmost latitude, easternmost longitude, northernmost latitude. [S, W, N, E]
         required: true
-      vertical_coverage:
-        description: Minimum and maximum depths of observations in meters.
     attributes:
       experiment_type:
         title: mCDR Experiment Type
@@ -60,15 +60,26 @@ classes:
         inlined_as_list: true
         required: true
       start_datetime:
-        title: Start Date and Time
+        title: Start Date and Time (UTC)
         description: "Start date and time of experiment in UTC ISO-8601"
         range: datetime
         required: true
       end_datetime:
-        title: End Date and Time
+        title: End Date and Time (UTC)
         description: "End date and time of experiment in UTC ISO-8601"
         range: datetime
-        required: true
+  InSituExperiment:
+    is_a: Experiment
+    description: >-
+      Experiment metadata for in-situ studies (interventions, tracer studies, etc.). Contains fields specific to
+      field-based experiments that don't apply to model experiments.
+    slots:
+      - vertical_coverage
+      - permits
+    slot_usage:
+      vertical_coverage:
+        description: Minimum and maximum depths of observations in meters.
+    attributes:
       data_conflicts_and_unreported_data:
         title: Data Conflicts and Unreported Data
         description: >-
@@ -91,7 +102,7 @@ classes:
           as digitized laboratory notebooks, blogs, etc., may be linked here.
         range: string
   Intervention:
-    is_a: Experiment
+    is_a: InSituExperiment
     mixins:
       - InterventionDetails
       - DosingDetails
@@ -118,7 +129,7 @@ classes:
 
 
   Tracer:
-    is_a: Experiment
+    is_a: InSituExperiment
     description: "Additional metadata that applies to experiments where a tracer study was conducted"
     mixins:
       - TracerDetails