potier_f/ro-crate-interoperability-profile
0
0
Fork 0
mirror of https://github.com/researchobjectschema/ro-crate-interoperability-profile.git synced 2026-03-07 17:32:44 +01:00
Code Issues Packages Projects Releases Wiki Activity
Files
main
ro-crate-interoperability-p…/0.2.x/lib/python/lib-ro-crate-schema/examples/full_example.py
Snowwpanda 60860ebbab Cleanup and adjustment to depreciated features 
Added Manifest for publishing
2025-11-09 23:30:51 +01:00

652 lines
26 KiB
Python
Raw Permalink Blame History

#!/usr/bin/env python3
"""
Comprehensive RO-Crate Schema Library Demonstration
This example showcases the full capabilities of the RO-Crate schema library through
a complex scientific workflow involving OpenBIS data management, chemical synthesis, object modification with round-trip persistence.
Features demonstrated:
- Complex nested object hierarchies (Project → Space → Collections/Equipment)
- Self-referential relationships (molecules containing other molecules)
- Mixed ontology namespaces (OpenBIS custom + schema.org)
- Dynamic experimental workflow simulation
- Large-scale RDF generation and serialization
- Round-trip fidelity with state modifications
- Real-world scientific data modeling
Run with: uv run python examples/full_example.py
"""
import json
from math import e
import sys
import csv
import tempfile
from pathlib import Path
from datetime import datetime
from tkinter import E
from typing import List, Optional, Dict, Any
# Add src to path for imports
sys.path.insert(0, str(Path(__file__).parent.parent / "src"))
from pydantic import BaseModel
from lib_ro_crate_schema.crate.decorators import ro_crate_schema, Field
from lib_ro_crate_schema.crate.schema_facade import SchemaFacade
# Removed print_section function - using direct print statements instead
# ============================================================================
# MODEL DEFINITIONS
# ============================================================================
@ro_crate_schema(ontology="http://openbis.org/Project")
class Project(BaseModel):
"""OpenBIS research project"""
code: str = Field(json_schema_extra={"comment": "Unique project identifier"})
name: str = Field(json_schema_extra={"ontology": "https://schema.org/name"})
description: str = Field(json_schema_extra={"ontology": "https://schema.org/description"})
created_date: datetime = Field(json_schema_extra={"ontology": "https://schema.org/dateCreated"})
space: Optional['Space'] = Field(default=None, json_schema_extra={"ontology": "http://openbis.org/hasSpace"})
@ro_crate_schema(ontology="http://openbis.org/Space")
class Space(BaseModel):
"""OpenBIS laboratory space"""
name: str = Field(json_schema_extra={"ontology": "https://schema.org/name"})
description: str = Field(json_schema_extra={"ontology": "https://schema.org/description"})
created_date: datetime = Field(json_schema_extra={"ontology": "https://schema.org/dateCreated"})
collections: List['Collection'] = Field(default=[], json_schema_extra={"ontology": "http://openbis.org/hasCollection"})
@ro_crate_schema(ontology="http://openbis.org/Collection")
class Collection(BaseModel):
"""OpenBIS sample/data collection"""
name: str = Field(json_schema_extra={"ontology": "https://schema.org/name"})
sample_type: str = Field(json_schema_extra={"comment": "Type of samples stored"})
storage_conditions: str = Field(json_schema_extra={"comment": "Storage requirements"})
created_date: datetime = Field(json_schema_extra={"ontology": "https://schema.org/dateCreated"})
contains: List[Any] = Field(default=[], json_schema_extra={"comment": "Entities contained in the collection"})
@ro_crate_schema(ontology="http://openbis.org/Equipment")
class Equipment(BaseModel):
"""Laboratory equipment with optional nesting"""
name: str = Field(json_schema_extra={"ontology": "https://schema.org/name"})
model: str = Field(json_schema_extra={"comment": "Equipment model/version"})
serial_number: str = Field(json_schema_extra={"ontology": "https://schema.org/serialNumber"})
created_date: datetime = Field(json_schema_extra={"ontology": "https://schema.org/dateCreated"})
parent_equipment: Optional['Equipment'] = Field(default=None, json_schema_extra={"ontology": "https://schema.org/isPartOf"})
configuration: Dict[str, Any] = Field(default={}, json_schema_extra={"comment": "Equipment configuration parameters"})
@ro_crate_schema(ontology="https://schema.org/ChemicalSubstance")
class Molecule(BaseModel):
"""Chemical compound with SMILES notation"""
name: str = Field(json_schema_extra={"ontology": "https://schema.org/name"})
smiles: str = Field(json_schema_extra={"comment": "SMILES notation for chemical structure"})
molecular_weight: float = Field(json_schema_extra={"comment": "Molecular weight in g/mol"})
contains_molecules: List['Molecule'] = Field(default=[], json_schema_extra={"ontology": "https://schema.org/hasPart"})
cas_number: Optional[str] = Field(default=None, json_schema_extra={"comment": "CAS Registry Number"})
created_date: datetime = Field(json_schema_extra={"ontology": "https://schema.org/dateCreated"})
experimental_notes: Optional[str] = Field(default=None, json_schema_extra={"comment": "Lab notes or modifications"})
@ro_crate_schema(ontology="https://schema.org/Person")
class Person(BaseModel):
"""Research author/scientist"""
name: str = Field(json_schema_extra={"ontology": "https://schema.org/name"})
orcid: str = Field(json_schema_extra={"ontology": "https://schema.org/identifier"})
email: str = Field(json_schema_extra={"ontology": "https://schema.org/email"})
affiliation: 'Organization' = Field(json_schema_extra={"ontology": "https://schema.org/affiliation"})
colleagues: List['Person'] = Field(default=[], json_schema_extra={"ontology": "https://schema.org/colleague"})
@ro_crate_schema(ontology="https://schema.org/Organization")
class Organization(BaseModel):
"""Research institution"""
name: str = Field(json_schema_extra={"ontology": "https://schema.org/name"})
country: str = Field(json_schema_extra={"ontology": "https://schema.org/addressCountry"})
website: str = Field(json_schema_extra={"ontology": "https://schema.org/url"})
@ro_crate_schema(ontology="https://schema.org/ScholarlyArticle")
class Publication(BaseModel):
"""Scientific publication"""
title: str = Field(json_schema_extra={"ontology": "https://schema.org/name"})
authors: List[Person] = Field(json_schema_extra={"ontology": "https://schema.org/author"})
molecules: List[Molecule] = Field(json_schema_extra={"ontology": "https://schema.org/mentions"})
equipment: List[Equipment] = Field(json_schema_extra={"ontology": "https://schema.org/instrument"})
organization: Organization = Field(json_schema_extra={"ontology": "https://schema.org/publisher"})
doi: str = Field(json_schema_extra={"ontology": "https://schema.org/identifier"})
publication_date: datetime = Field(json_schema_extra={"ontology": "https://schema.org/datePublished"})
def create_initial_data():
"""Create all initial model instances"""
print("\n🎯 PHASE 1: INITIAL DATA CREATION")
print("=" * 40)
# Organization
empa = Organization(
name="Swiss Federal Laboratories for Materials Science and Technology (Empa)",
country="Switzerland",
website="https://www.empa.ch"
)
# People (with circular colleague relationships)
# First create persons without colleagues
sarah = Person(
name="Dr. Sarah Chen",
orcid="0000-0002-1234-5678",
email="sarah.chen@empa.ch",
affiliation=empa,
colleagues=[]
)
marcus = Person(
name="Prof. Marcus Weber",
orcid="0000-0003-8765-4321",
email="marcus.weber@empa.ch",
affiliation=empa,
colleagues=[]
)
# Now establish circular colleague relationships
# This tests how the system handles circular imports in the schema
sarah = sarah.model_copy(update={'colleagues': [marcus]})
marcus = marcus.model_copy(update={'colleagues': [sarah]})
# Equipment (nested)
mass_spec = Equipment(
name="Agilent 7890A GC-MS",
model="7890A",
serial_number="DE43151234",
created_date=datetime(2023, 1, 15),
configuration={
"ionization_mode": "EI",
"mass_range_min": 50,
"mass_range_max": 500,
"resolution": "unit_mass",
"detector_voltage": 1200
}
)
reactor = Equipment(
name="FlowSyn Reactor",
model="v2.1",
serial_number="FSR-2024-001",
created_date=datetime(2023, 2, 1),
parent_equipment=mass_spec, # Mass spec is part of reactor system
configuration={
"max_temperature_celsius": 250,
"max_pressure_bar": 10,
"flow_rate_ml_per_min": 5,
"volume_ml": 50,
"heating_method": "microwave"
}
)
# Collections
molecules_collection = Collection(
name="Molecular Library",
sample_type="Chemical compounds",
storage_conditions="-20°C, inert atmosphere",
created_date=datetime(2023, 3, 1),
contains=[] # Will populate later
)
lab_equipment = Collection(
name="Laboratory Equipment",
sample_type="Analytical instruments",
storage_conditions="Room temperature, calibrated monthly",
created_date=datetime(2023, 2, 15),
contains=[reactor, mass_spec] # Equipment collection contains these items
)
# Molecules (with complex relationships)
benzene = Molecule(
name="Benzene",
smiles="c1ccccc1",
molecular_weight=78.11,
cas_number="71-43-2",
created_date=datetime(2024, 1, 10)
)
toluene = Molecule(
name="Toluene",
smiles="Cc1ccccc1",
molecular_weight=92.14,
cas_number="108-88-3",
created_date=datetime(2024, 1, 12)
)
phenol = Molecule(
name="Phenol",
smiles="c1ccc(cc1)O",
molecular_weight=94.11,
cas_number="108-95-2",
created_date=datetime(2024, 1, 15)
)
aniline = Molecule(
name="Aniline",
smiles="c1ccc(cc1)N",
molecular_weight=93.13,
cas_number="62-53-3",
created_date=datetime(2024, 1, 18)
)
# Complex polymer containing other molecules
complex_polymer = Molecule(
name="Benzene-Toluene Polymer",
smiles="[*]c1ccccc1[*].[*]Cc1ccccc1[*]", # Polymer SMILES
molecular_weight=340.45,
contains_molecules=[benzene, toluene], # Self-reference
created_date=datetime(2024, 2, 1)
)
# Add molecules to collection
molecules_collection.contains.extend([benzene, toluene, phenol, aniline, complex_polymer])
# OpenBIS hierarchy
science_space = Space(
name="Advanced Materials Laboratory",
description="State-of-the-art facility for nanomaterial synthesis and characterization",
created_date=datetime(2023, 1, 1),
collections=[molecules_collection, lab_equipment]
)
openbis_project = Project(
code="NANO-2024",
name="Nanocomposite Materials Research",
description="Development of advanced nanocomposite materials for industrial applications",
created_date=datetime(2024, 1, 1),
space=science_space
)
# Publication tying everything together
publication = Publication(
title="Advanced Nanocomposite Materials: From Molecular Design to Industrial Applications",
authors=[sarah, marcus],
molecules=[benzene, toluene, phenol, aniline, complex_polymer],
equipment=[reactor, mass_spec],
organization=empa,
doi="10.1021/acs.nanolett.2024.12345",
publication_date=datetime(2024, 6, 15)
)
return {
'openbis_project': openbis_project,
'science_space': science_space,
'molecules_collection': molecules_collection,
'lab_equipment': lab_equipment,
'reactor': reactor,
'mass_spec': mass_spec,
'benzene': benzene,
'toluene': toluene,
'phenol': phenol,
'aniline': aniline,
'complex_polymer': complex_polymer,
'sarah': sarah,
'marcus': marcus,
'empa': empa,
'publication': publication
}
class MoleculeModel: # Alias for sake of this example
pass
# EquipmentModel = Equipment # Alias for clarity
def experiment(reactant1, reactant2, catalyst, equipment) -> tuple[dict, Path]:
"""
Simulate chemical synthesis experiment and create observation file
Creates a new product molecule by combining reactants and modifies
the original reactants with experimental notes. Also generates a CSV
file with experimental observations.
Args:
reactant1: Primary reactant molecule
reactant2: Secondary reactant molecule
catalyst: Catalytic molecule (unchanged)
equipment: Equipment used for reaction
Returns:
Tuple of (new product molecule, path to observations CSV file)
"""
print("\n🔹 EXPERIMENTAL SYNTHESIS")
print(f" Reactants: {reactant1.name} + {reactant2.name}")
print(f" Catalyst: {catalyst.name}")
print(f" Equipment: {equipment.name}")
# Experimental parameters and observations
experiment_time = datetime.now()
# Create product molecule with combined SMILES
# Simple concatenation for demo (real chemistry would be more complex)
product_smiles = f"({reactant1.smiles}).({reactant2.smiles})"
product_mw = reactant1.molecular_weight + reactant2.molecular_weight
product_dict = {
"name": f"{reactant1.name}-{reactant2.name} Adduct",
"smiles": product_smiles,
"molecular_weight": product_mw,
"contains_molecules": [reactant1, reactant2], # Names instead of objects
"created_date": experiment_time.isoformat(),
"experimental_notes": f"Synthesized via {catalyst.name} catalysis using {equipment.name}"
}
# Get sample experimental observations CSV file (located in same folder as this scipt)
csv_path = Path(__file__).parent / "experimental_observations.csv"
# Check for file
if not csv_path.exists():
print(f" ⚠️ Warning: Observations CSV file not found at {csv_path}. Skipping file adding.")
else:
print(f" 📁 Found observations CSV file at: {csv_path}")
# Modify original reactants with experimental data
reactant1.experimental_notes = f"Consumed 0.5 mol in synthesis reaction at {experiment_time.strftime('%Y-%m-%d %H:%M')}"
reactant2.experimental_notes = f"Partially consumed, 0.3 mol remaining after reaction"
print(f" Product: {product_dict['name']}")
print(f" Product SMILES: {product_dict['smiles']}")
return product_dict, csv_path
def analyze_rocrate_changes(initial_path: Path, final_path: Path):
"""Compare initial and final RO-Crate files"""
print("\n🔹 RO-CRATE COMPARISON ANALYSIS")
with open(initial_path / "ro-crate-metadata.json", 'r') as f:
initial_data = json.load(f)
with open(final_path / "ro-crate-metadata.json", 'r') as f:
final_data = json.load(f)
initial_entities = len(initial_data["@graph"])
final_entities = len(final_data["@graph"])
print(f" 📊 Initial entities: {initial_entities}")
print(f" 📊 Final entities: {final_entities}")
print(f" 📈 Change: +{final_entities - initial_entities} entities")
# Count entity types
def count_types(data):
types = {}
for entity in data["@graph"]:
entity_type = entity.get("@type", "Unknown")
if isinstance(entity_type, list):
for t in entity_type:
types[t] = types.get(t, 0) + 1
else:
types[entity_type] = types.get(entity_type, 0) + 1
return types
initial_types = count_types(initial_data)
final_types = count_types(final_data)
print("\n 📋 Entity type changes:")
all_types = set(initial_types.keys()) | set(final_types.keys())
for entity_type in sorted(all_types):
initial_count = initial_types.get(entity_type, 0)
final_count = final_types.get(entity_type, 0)
if initial_count != final_count:
print(f" {entity_type}: {initial_count} → {final_count} ({final_count - initial_count:+d})")
else:
print(f" {entity_type}: {initial_count} (unchanged)")
def main():
"""Execute the complete workflow demonstration"""
print("🧪 COMPREHENSIVE RO-CRATE SCHEMA WORKFLOW DEMONSTRATION")
print("=" * 80)
print("This demo showcases complex scientific data modeling, experimental workflows,")
print("and dynamic object modification with full round-trip persistence.")
# ========================================================================
# PHASE 1: INITIAL SETUP
# ========================================================================
print("\n🎯 Creating Initial Schema and Data")
print("=" * 40)
# Create all instances
instances = create_initial_data()
print(f" ✅ Created {len(instances)} model instances")
print(" 📋 Instance types:")
type_counts = {}
for instance in instances.values():
type_name = type(instance).__name__
type_counts[type_name] = type_counts.get(type_name, 0) + 1
for type_name, count in sorted(type_counts.items()):
print(f" - {type_name}: {count}")
print(f"\n 🔄 Circular Relationship Test:")
sarah_instance = instances['sarah']
marcus_instance = instances['marcus']
print(f" - Sarah Chen has {len(sarah_instance.colleagues)} colleague(s): {[c.name for c in sarah_instance.colleagues]}")
print(f" - Marcus Weber has {len(marcus_instance.colleagues)} colleague(s): {[c.name for c in marcus_instance.colleagues]}")
# Build schema facade
facade = SchemaFacade()
facade.add_all_registered_models()
print(f"\n 📊 Schema: {len(facade.types)} types registered")
# Add all instances
for instance_id, instance in instances.items():
facade.add_model_instance(instance, instance_id)
print(f" 📦 Added {len(facade.metadata_entries)} metadata entries")
# Generate RDF
rdf_graph = facade.to_graph()
print(f" 🕸️ Generated {len(rdf_graph)} RDF triples")
# Export initial state
print("\n🔹 Exporting Initial RO-Crate")
import os
output_dir = "output_crates"
os.makedirs(output_dir, exist_ok=True)
initial_path = os.path.join(output_dir, "full_example_initial")
facade.write(
destination=initial_path,
name="Complex Scientific Workflow - Initial State",
description="Initial RO-Crate before experimental modifications",
license="MIT"
)
print(f" 💾 Saved initial state: {initial_path}")
initial_path = Path(initial_path)
# ========================================================================
# PHASE 2: IMPORT AND EXPERIMENT
# ========================================================================
print("\n🎯 Importing RO-Crate and Running Experiment")
print("=" * 40)
# Import the RO-Crate we just exported
print("\n🔹 Importing RO-Crate from exported files")
print(f" 📁 Loading RO-Crate from: {initial_path}")
imported_facade = SchemaFacade.from_ro_crate(initial_path)
print(f" ✅ Successfully imported RO-Crate!")
print(f" 📊 Imported {len(imported_facade.types)} types")
print(f" 📦 Imported {len(imported_facade.metadata_entries)} metadata entries")
# Show what was imported
print("\n 📋 Imported types:")
for imported_type in imported_facade.types:
props = len(imported_type.rdfs_property or [])
restrictions = len(imported_type.get_restrictions())
print(f" - {imported_type.id}: {props} properties, {restrictions} restrictions")
print("\n 📦 Imported metadata entries (first 5):")
for entry in imported_facade.metadata_entries[:5]:
print(f" - {entry.id} (type: {entry.class_id})")
# Import Molecule and Equipment Models
MoleculeModel = imported_facade.export_pydantic_model("Molecule")
EquipmentModel = imported_facade.export_pydantic_model("Equipment")
# Know we need molecules: benzene, toluene, aniline
# And equipment: reactor
benzene = imported_facade.get_entry_as("benzene", MoleculeModel)
toluene = imported_facade.get_entry_as("toluene", MoleculeModel)
aniline = imported_facade.get_entry_as("aniline", MoleculeModel)
reactor = imported_facade.get_entry_as("reactor", EquipmentModel)
print(f" ✅ Selected from imported data: {benzene.name}, {toluene.name}, {aniline.name}, {reactor.name}")
# Run experiment
product_dict, observations_csv = experiment(benzene, toluene, aniline, reactor)
# Create new product molecule instance
product = MoleculeModel(**product_dict)
print(f" 🧪 Experiment complete, product created: {product.name}")
# ========================================================================
# PHASE 3: UPDATE AND RE-EXPORT
# ========================================================================
print("\n🎯 Updating Schema with Experimental Results")
print("=" * 40)
# Create new facade with updated data
updated_facade = SchemaFacade()
updated_facade.add_all_registered_models()
# Add all original instances (now with modifications)
for instance_id, instance in instances.items():
updated_facade.add_model_instance(instance, instance_id)
# Add new product
updated_facade.add_model_instance(product, "synthesis_product")
print(f" 📊 Updated schema: {len(updated_facade.types)} types")
print(f" 📦 Updated entries: {len(updated_facade.metadata_entries)} metadata entries")
# Generate updated RDF
updated_rdf_graph = updated_facade.to_graph()
print(f" 🕸️ Updated RDF graph: {len(updated_rdf_graph)} triples")
print(f" 📈 RDF growth: +{len(updated_rdf_graph) - len(rdf_graph)} triples")
# Export final state
print("\n🔹 Exporting Final RO-Crate")
# Add experimental observations file to facade
updated_facade.add_file(
file_path=observations_csv,
name="Experimental Observations",
description="Detailed measurements from chemical synthesis experiment including temperature, pressure, yields and purity data"
)
final_path = os.path.join(output_dir, "full_example_final")
updated_facade.write(
destination=final_path,
name="Complex Scientific Workflow - Final State",
description="Final RO-Crate after experimental synthesis with observation data",
license="MIT"
)
print(f" 💾 Saved final state: {final_path}")
final_path = Path(final_path)
# ========================================================================
# PHASE 4: ANALYSIS
# ========================================================================
print("\n🎯 WORKFLOW ANALYSIS & RESULTS")
print("=" * 40)
# Compare facades (original vs imported)
print("\n🔹 Import Fidelity Analysis")
print(f" 📊 Original facade: {len(facade.types)} types, {len(facade.metadata_entries)} entries")
print(f" 📊 Imported facade: {len(imported_facade.types)} types, {len(imported_facade.metadata_entries)} entries")
# Check if all types were preserved
original_type_ids = {t.id for t in facade.types}
imported_type_ids = {t.id for t in imported_facade.types}
if original_type_ids == imported_type_ids:
print(f" ✅ All {len(original_type_ids)} types preserved in import")
else:
print(f" ⚠️ Type mismatch: original={len(original_type_ids)}, imported={len(imported_type_ids)}")
missing_types = original_type_ids - imported_type_ids
if missing_types:
print(f" Missing: {missing_types}")
extra_types = imported_type_ids - original_type_ids
if extra_types:
print(f" Extra: {extra_types}")
# Check if all metadata entries were preserved
original_entry_ids = {e.id for e in facade.metadata_entries}
imported_entry_ids = {e.id for e in imported_facade.metadata_entries}
if original_entry_ids == imported_entry_ids:
print(f" ✅ All {len(original_entry_ids)} metadata entries preserved in import")
else:
print(f" ⚠️ Metadata entry mismatch: original={len(original_entry_ids)}, imported={len(imported_entry_ids)}")
missing_entries = original_entry_ids - imported_entry_ids
if missing_entries:
print(f" Missing: {missing_entries}")
extra_entries = imported_entry_ids - original_entry_ids
if extra_entries:
print(f" Extra: {extra_entries}")
# Compare files
analyze_rocrate_changes(initial_path, final_path)
# Show experimental modifications
print("\n🔹 Experimental Modifications Detected")
print(f" 🧪 New molecule created: {product.name}")
print(f" SMILES: {product.smiles}")
print(f" Notes: {product.experimental_notes}")
print(f"\n 📝 Modified molecules:")
modified_molecules = [instances['benzene'], instances['toluene']]
for mol in modified_molecules:
if mol.experimental_notes:
print(f" - {mol.name}: {mol.experimental_notes}")
# Summary statistics
print("\n🔹 Final Statistics")
print(f" 📊 Original facade: {len(facade.types)} types, {len(facade.metadata_entries)} entries")
print(f" 📊 Imported facade: {len(imported_facade.types)} types, {len(imported_facade.metadata_entries)} entries")
print(f" <20> Final facade: {len(updated_facade.types)} types, {len(updated_facade.metadata_entries)} entries")
print(f" 🕸️ Final RDF triples: {len(updated_rdf_graph)}")
print(f" 🔄 Round-trip cycles: 3 (export → import → experiment → export)")
print(f" ⚗️ Experiments performed: 1")
print(f" 🆕 New entities created: 1")
print(f" ✏️ Entities modified: 2")
print("\n" + "="*80)
print("🎉 COMPREHENSIVE WORKFLOW WITH IMPORT DEMONSTRATION COMPLETE!")
print(" 📁 RO-Crates created:")
print(f" - Initial: {initial_path}")
print(f" - Final: {final_path}")
print("="*80)
return {
'initial_facade': facade,
'imported_facade': imported_facade,
'updated_facade': updated_facade,
'instances': instances,
'product': product,
'initial_path': initial_path,
'final_path': final_path
}
if __name__ == "__main__":
results = main()
Reference in New Issue View Git Blame Copy Permalink