forked from enviPath/enviPy
[Feature] Sync Features from Client Repo (#425)
- New PackageImporter - Fix persisting Molfile on Structure creation - Add NonPersistent Prediction - Pathway View Options - Edit Node Fix Co-authored-by: Tim Lorsbach <tim@lorsba.ch> Reviewed-on: enviPath/enviPy#425
This commit is contained in:
@ -9,32 +9,24 @@ from datetime import datetime
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from typing import Any, Dict, List, Optional, TYPE_CHECKING
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from django.conf import settings as s
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from django.db import transaction
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from ninja import Schema
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from pydantic import HttpUrl
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from pydantic import HttpUrl, ValidationError
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from epdb.exceptions import PackageImportException
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from epdb.models import (
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AdditionalInformation,
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Compound,
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CompoundStructure,
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Edge,
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EnviFormer,
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EPModel,
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ExternalDatabase,
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ExternalIdentifier,
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License,
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MLRelativeReasoning,
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Node,
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ParallelRule,
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Pathway,
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Reaction,
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Rule,
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RuleBasedRelativeReasoning,
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Scenario,
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Setting,
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SimpleAmbitRule,
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SimpleRDKitRule,
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SimpleRule,
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)
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from utilities.chem import FormatConverter
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@ -88,6 +80,9 @@ class RefPathwayExportSchema(RefExportSchema): ...
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class RefScenarioExportSchema(RefExportSchema): ...
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class RefEnzymeExportSchema(RefExportSchema): ...
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############
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# Compound #
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############
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@ -128,7 +123,28 @@ class ReactionExportSchema(RefReactionExportSchema):
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#########
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# Rules #
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#########
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class RuleExportSchema(RefRuleExportSchema):
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class EnzymeExportSchema(RefEnzymeExportSchema):
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ec_number: str
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classification_level: int
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linking_method: str
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reaction_evidence: List[RefReactionExportSchema]
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edge_evidence: List[RefEdgeExportSchema]
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class EnzymeRuleExportSchema(RefRuleExportSchema):
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enzymes: List[EnzymeExportSchema] | None = None
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@staticmethod
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def resolve_enzymes(obj):
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if isinstance(obj, dict):
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res = []
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for e in obj.get("enzymes", []):
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res.append(EnzymeExportSchema.model_validate(e))
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return res
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return obj.enzymelink_set.all()
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class RuleExportSchema(EnzymeRuleExportSchema):
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name: str
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description: str
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aliases: List[str]
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@ -138,7 +154,7 @@ class RuleExportSchema(RefRuleExportSchema):
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scenarios: List[RefScenarioExportSchema]
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class ParallelRuleExportSchema(RefRuleExportSchema):
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class ParallelRuleExportSchema(EnzymeRuleExportSchema):
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name: str
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description: str
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aliases: List[str]
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@ -210,7 +226,7 @@ class PackageExportSchema(Schema):
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description: str
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uuid: str
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reviewed: bool
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license: LicenseExportSchema | None
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license: LicenseExportSchema | None = None
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compounds: List[CompoundExportSchema]
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reactions: List[ReactionExportSchema]
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simple_rules: List[RuleExportSchema]
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@ -224,6 +240,15 @@ class PackageExportSchema(Schema):
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value = obj.get("uuid") if isinstance(obj, dict) else obj.uuid
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return str(value)
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@staticmethod
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def resolve_compounds(obj):
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res = []
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if isinstance(obj, dict):
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for c in obj.get("compounds", []):
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res.append(CompoundExportSchema.model_validate(c))
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return res
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return obj.compounds.all()
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@staticmethod
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def resolve_simple_rules(obj):
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if isinstance(obj, dict):
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@ -277,51 +302,239 @@ class PackageExporter:
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class PackageImporter:
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"""
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Imports package data from JSON export.
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Handles object creation, relationship mapping, and dependency resolution.
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"""
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def __init__(
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self,
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package: Dict[str, Any],
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preserve_uuids: bool = False,
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add_import_timestamp=True,
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trust_reviewed=False,
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):
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"""
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Initialize the importer.
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Args:
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preserve_uuids: If True, preserve original UUIDs. If False, generate new ones.
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"""
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def __init__(self, package: Dict[str, Any], preserve_uuids: bool = False):
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self.preserve_uuids = preserve_uuids
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self.add_import_timestamp = add_import_timestamp
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self.trust_reviewed = trust_reviewed
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self.uuid_mapping = {}
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self.object_cache = {}
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self._raw_package = package
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def _get_or_generate_uuid(self, original_uuid: str) -> str:
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"""Get mapped UUID or generate new one if not preserving UUIDs."""
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if self.preserve_uuids:
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return original_uuid
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if original_uuid not in self.uuid_mapping:
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self.uuid_mapping[original_uuid] = str(uuid.uuid4())
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return self.uuid_mapping[original_uuid]
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def _cache_object(self, model_name: str, uuid_str: str, obj):
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"""Cache a created object for later reference."""
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self.object_cache[(model_name, uuid_str)] = obj
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def _get_cached_object(self, model_name: str, uuid_str: str):
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"""Get a cached object by model name and UUID."""
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return self.object_cache.get((model_name, uuid_str))
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self._cache = {}
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def do_import(self) -> Package:
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return self._import_package_from_json(self._raw_package)
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return self._import_package_from_json()
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def _import_compounds(
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self,
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package: Package,
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compounds: List[CompoundExportSchema],
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):
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for c in compounds:
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new_c = Compound()
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new_c.uuid = str(uuid.uuid4()) if not self.preserve_uuids else c.uuid
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new_c.package = package
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new_c.name = c.name
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new_c.description = c.description
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new_c.aliases = c.aliases
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new_c.save()
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self._cache[c.uuid] = new_c
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for cs in c.structures:
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new_cs = CompoundStructure()
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new_cs.uuid = str(uuid.uuid4()) if not self.preserve_uuids else cs.uuid
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new_cs.compound = new_c
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new_cs.name = cs.name
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new_cs.description = cs.description
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new_cs.aliases = cs.aliases
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new_cs.smiles = cs.smiles
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new_cs.molfile = cs.molfile
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new_cs.normalized_structure = cs.normalized_structure
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new_cs.save()
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self._cache[cs.uuid] = new_cs
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# Now we can assigne the default_structure to the compound
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new_c.default_structure = self._cache[c.default_structure.uuid]
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new_c.save()
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def _import_simple_rules(self, package: Package, rules: List[RuleExportSchema]):
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for r in rules:
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new_r = SimpleAmbitRule()
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new_r.uuid = str(uuid.uuid4()) if not self.preserve_uuids else r.uuid
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new_r.package = package
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new_r.name = r.name
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new_r.description = r.description
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new_r.aliases = r.aliases
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new_r.smirks = r.smirks
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new_r.reactant_filter_smarts = r.reactant_filter_smarts
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new_r.product_filter_smarts = r.product_filter_smarts
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new_r.save()
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self._cache[r.uuid] = new_r
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def _import_composite_rules(self, package: Package, rules: List[ParallelRuleExportSchema]):
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for r in rules:
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new_r = ParallelRule()
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new_r.uuid = str(uuid.uuid4()) if not self.preserve_uuids else r.uuid
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new_r.package = package
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new_r.name = r.name
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new_r.description = r.description
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new_r.aliases = r.aliases
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new_r.save()
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for sr in r.simple_rules:
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new_r.simple_rules.add(self._cache[sr.uuid])
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self._cache[r.uuid] = new_r
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def _import_reactions(
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self,
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package: Package,
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reactions: List[ReactionExportSchema],
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):
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for r in reactions:
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new_r = Reaction()
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new_r.uuid = str(uuid.uuid4()) if not self.preserve_uuids else r.uuid
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new_r.package = package
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new_r.name = r.name
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new_r.description = r.description
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new_r.aliases = r.aliases
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new_r.multi_step = r.multi_step
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new_r.medline_references = r.medline_references
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new_r.save()
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for educt in r.educts:
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new_r.educts.add(self._cache[educt.uuid])
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for product in r.products:
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new_r.products.add(self._cache[product.uuid])
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for rule in r.rules:
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new_r.rules.add(self._cache[rule.uuid])
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self._cache[r.uuid] = new_r
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def _import_pathways(self, package: Package, pathways: List[PathwayExportSchema]):
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for pw in pathways:
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new_pw = Pathway()
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new_pw.uuid = str(uuid.uuid4()) if not self.preserve_uuids else pw.uuid
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new_pw.package = package
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new_pw.name = pw.name
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new_pw.description = pw.description
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new_pw.aliases = pw.aliases
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new_pw.predicted = pw.predicted
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new_pw.save()
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self._cache[pw.uuid] = new_pw
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for n in pw.nodes:
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new_n = Node()
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new_n.uuid = str(uuid.uuid4()) if not self.preserve_uuids else n.uuid
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new_n.pathway = new_pw
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new_n.name = n.name
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new_n.description = n.description
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new_n.aliases = n.aliases
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new_n.default_node_label = self._cache[n.default_node_label.uuid]
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new_n.depth = n.depth
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new_n.stereo_removed = n.stereo_removed
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new_n.save()
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for nl in n.node_labels:
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new_n.node_labels.add(self._cache[nl.uuid])
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self._cache[n.uuid] = new_n
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for e in pw.edges:
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new_e = Edge()
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new_e.uuid = str(uuid.uuid4()) if not self.preserve_uuids else e.uuid
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new_e.pathway = new_pw
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new_e.name = e.name
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new_e.description = e.description
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new_e.aliases = e.aliases
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new_e.edge_label = self._cache[e.edge_label.uuid]
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new_e.save()
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for sn in e.start_nodes:
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new_e.start_nodes.add(self._cache[sn.uuid])
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for en in e.end_nodes:
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new_e.end_nodes.add(self._cache[en.uuid])
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self._cache[e.uuid] = new_e
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def _import_scenarios(self, package: Package, scenarios: List[ScenarioExportSchema]):
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for scen in scenarios:
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new_s = Scenario()
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new_s.uuid = str(uuid.uuid4()) if not self.preserve_uuids else scen.uuid
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new_s.package = package
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new_s.name = scen.name
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new_s.description = scen.description
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new_s.scenario_date = scen.scenario_date
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new_s.scenario_type = scen.scenario_type
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new_s.save()
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self._cache[scen.uuid] = new_s
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def _import_additional_information(
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self, package: Package, additional_information: List[AdditionalInformationExportSchema]
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):
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for ai in additional_information:
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new_ai = AdditionalInformation()
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new_ai.uuid = str(uuid.uuid4()) if not self.preserve_uuids else ai.uuid
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new_ai.package = package
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new_ai.type = ai.type
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new_ai.data = ai.data
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if ai.scenario:
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new_ai.scenario = self._cache[ai.scenario.uuid]
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if ai.attach_object:
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new_ai.content_object = self._cache[ai.attach_object.uuid]
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new_ai.save()
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self._cache[ai.uuid] = new_ai
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def _link_scenarios_after_import(self, data: PackageExportSchema):
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collections = [
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data.compounds,
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data.simple_rules,
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data.composite_rules,
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data.reactions,
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data.pathways,
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[n for pw in data.pathways for n in pw.nodes],
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[e for pw in data.pathways for e in pw.edges],
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]
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for coll in collections:
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for elem in coll:
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elem_obj = self._cache[elem.uuid]
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for scen in elem.scenarios:
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elem_obj.scenarios.add(self._cache[scen.uuid])
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def _import_package_from_json(
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self,
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) -> Package:
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try:
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parsed = PackageExportSchema.model_validate(self._raw_package)
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except ValidationError as e:
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logger.error(f"Error validating package data: {e}")
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raise PackageImportException("Deserialization failed")
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package_uuid = str(uuid.uuid4())
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if self.preserve_uuids:
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package_uuid = parsed.uuid
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package_license = License.objects.get(link=parsed.license.link) if parsed.license else None
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package = Package()
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package.uuid = package_uuid
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package.name = f"{parsed.name} - Imported at {datetime.now()}"
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package.description = parsed.description
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package.reviewed = False
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package.license = package_license
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package.save()
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# Import Elements
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self._import_compounds(package, parsed.compounds)
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self._import_simple_rules(package, parsed.simple_rules)
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self._import_composite_rules(package, parsed.composite_rules)
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self._import_reactions(package, parsed.reactions)
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self._import_pathways(package, parsed.pathways)
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self._import_scenarios(package, parsed.scenarios)
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self._import_additional_information(package, parsed.additional_information)
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self._link_scenarios_after_import(parsed)
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return package
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@staticmethod
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def sign(data: Dict[str, Any], key: str) -> Dict[str, Any]:
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@ -339,510 +552,6 @@ class PackageImporter:
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expected = hmac.new(key.encode(), json_str.encode(), hashlib.sha256).digest()
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return hmac.compare_digest(signature, expected)
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@transaction.atomic
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def _import_package_from_json(self, package_data: Dict[str, Any]) -> Package:
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"""
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Import a complete package from JSON data.
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Args:
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package_data: Dictionary containing the package export data
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Returns:
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The created Package instance
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"""
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print(f"Starting import of package: {package_data['name']}")
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# Create the main package
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package = self._create_package(package_data)
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# Import in dependency order
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self._import_compounds(package, package_data.get("compounds", []))
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self._import_structures(package, package_data.get("structures", []))
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self._import_rules(package, package_data.get("rules", {}))
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self._import_reactions(package, package_data.get("reactions", []))
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self._import_pathways(package, package_data.get("pathways", []))
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self._import_nodes(package, package_data.get("nodes", []))
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self._import_edges(package, package_data.get("edges", []))
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self._import_scenarios(package, package_data.get("scenarios", []))
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if package_data.get("models"):
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self._import_models(package, package_data["models"])
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# Set default structures for compounds (after all structures are created)
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self._set_default_structures(package_data.get("compounds", []))
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print(f"Package import completed: {package.name}")
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return package
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def _create_package(self, package_data: Dict[str, Any]) -> Package:
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"""Create the main package object."""
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package_uuid = self._get_or_generate_uuid(package_data["uuid"])
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# Handle license
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license_obj = None
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if package_data.get("license"):
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license_data = package_data["license"]
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license_obj, _ = License.objects.get_or_create(
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name=license_data["name"],
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defaults={
|
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"cc_string": license_data.get("cc_string", ""),
|
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"link": license_data.get("link", ""),
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"image_link": license_data.get("image_link", ""),
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},
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)
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new_name = package_data.get("name")
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if self.add_import_timestamp:
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new_name = f"{new_name} - Imported at {datetime.now()}"
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new_reviewed = False
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if self.trust_reviewed:
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new_reviewed = package_data.get("reviewed", False)
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package = Package.objects.create(
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uuid=package_uuid,
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name=new_name,
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description=package_data["description"],
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kv=package_data.get("kv", {}),
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reviewed=new_reviewed,
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license=license_obj,
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)
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self._cache_object("Package", package_data["uuid"], package)
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print(f"Created package: {package.name}")
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return package
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def _import_compounds(self, package: Package, compounds_data: List[Dict[str, Any]]):
|
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"""Import compounds."""
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print(f"Importing {len(compounds_data)} compounds...")
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|
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for compound_data in compounds_data:
|
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compound_uuid = self._get_or_generate_uuid(compound_data["uuid"])
|
||||
|
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compound = Compound.objects.create(
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uuid=compound_uuid,
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package=package,
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||||
name=compound_data["name"],
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||||
description=compound_data["description"],
|
||||
kv=compound_data.get("kv", {}),
|
||||
# default_structure will be set later
|
||||
)
|
||||
|
||||
# Set aliases if present
|
||||
if compound_data.get("aliases"):
|
||||
compound.aliases = compound_data["aliases"]
|
||||
compound.save()
|
||||
|
||||
self._cache_object("Compound", compound_data["uuid"], compound)
|
||||
|
||||
# Handle external identifiers
|
||||
self._create_external_identifiers(
|
||||
compound, compound_data.get("external_identifiers", [])
|
||||
)
|
||||
|
||||
def _import_structures(self, package: Package, structures_data: List[Dict[str, Any]]):
|
||||
"""Import compound structures."""
|
||||
print(f"Importing {len(structures_data)} compound structures...")
|
||||
|
||||
for structure_data in structures_data:
|
||||
structure_uuid = self._get_or_generate_uuid(structure_data["uuid"])
|
||||
compound_uuid = structure_data["compound"]["uuid"]
|
||||
compound = self._get_cached_object("Compound", compound_uuid)
|
||||
|
||||
if not compound:
|
||||
print(f"Warning: Compound with UUID {compound_uuid} not found for structure")
|
||||
continue
|
||||
|
||||
structure = CompoundStructure.objects.create(
|
||||
uuid=structure_uuid,
|
||||
compound=compound,
|
||||
name=structure_data["name"],
|
||||
description=structure_data["description"],
|
||||
kv=structure_data.get("kv", {}),
|
||||
smiles=structure_data["smiles"],
|
||||
canonical_smiles=structure_data["canonical_smiles"],
|
||||
inchikey=structure_data["inchikey"],
|
||||
normalized_structure=structure_data.get("normalized_structure", False),
|
||||
)
|
||||
|
||||
# Set aliases if present
|
||||
if structure_data.get("aliases"):
|
||||
structure.aliases = structure_data["aliases"]
|
||||
structure.save()
|
||||
|
||||
self._cache_object("CompoundStructure", structure_data["uuid"], structure)
|
||||
|
||||
# Handle external identifiers
|
||||
self._create_external_identifiers(
|
||||
structure, structure_data.get("external_identifiers", [])
|
||||
)
|
||||
|
||||
def _import_rules(self, package: Package, rules_data: Dict[str, Any]):
|
||||
"""Import all types of rules."""
|
||||
print("Importing rules...")
|
||||
|
||||
# Import simple rules first
|
||||
simple_rules_data = rules_data.get("simple_rules", [])
|
||||
print(f"Importing {len(simple_rules_data)} simple rules...")
|
||||
|
||||
for rule_data in simple_rules_data:
|
||||
self._create_simple_rule(package, rule_data)
|
||||
|
||||
# Import parallel rules
|
||||
parallel_rules_data = rules_data.get("parallel_rules", [])
|
||||
print(f"Importing {len(parallel_rules_data)} parallel rules...")
|
||||
|
||||
for rule_data in parallel_rules_data:
|
||||
self._create_parallel_rule(package, rule_data)
|
||||
|
||||
def _create_simple_rule(self, package: Package, rule_data: Dict[str, Any]):
|
||||
"""Create a simple rule (SimpleAmbitRule or SimpleRDKitRule)."""
|
||||
rule_uuid = self._get_or_generate_uuid(rule_data["uuid"])
|
||||
rule_type = rule_data.get("rule_type", "SimpleRule")
|
||||
|
||||
common_fields = {
|
||||
"uuid": rule_uuid,
|
||||
"package": package,
|
||||
"name": rule_data["name"],
|
||||
"description": rule_data["description"],
|
||||
"kv": rule_data.get("kv", {}),
|
||||
}
|
||||
|
||||
if rule_type == "SimpleAmbitRule":
|
||||
rule = SimpleAmbitRule.objects.create(
|
||||
**common_fields,
|
||||
smirks=rule_data.get("smirks", ""),
|
||||
reactant_filter_smarts=rule_data.get("reactant_filter_smarts", ""),
|
||||
product_filter_smarts=rule_data.get("product_filter_smarts", ""),
|
||||
)
|
||||
elif rule_type == "SimpleRDKitRule":
|
||||
rule = SimpleRDKitRule.objects.create(
|
||||
**common_fields, reaction_smarts=rule_data.get("reaction_smarts", "")
|
||||
)
|
||||
else:
|
||||
rule = SimpleRule.objects.create(**common_fields)
|
||||
|
||||
# Set aliases if present
|
||||
if rule_data.get("aliases"):
|
||||
rule.aliases = rule_data["aliases"]
|
||||
rule.save()
|
||||
|
||||
self._cache_object("SimpleRule", rule_data["uuid"], rule)
|
||||
return rule
|
||||
|
||||
def _create_parallel_rule(self, package: Package, rule_data: Dict[str, Any]):
|
||||
"""Create a parallel rule."""
|
||||
rule_uuid = self._get_or_generate_uuid(rule_data["uuid"])
|
||||
|
||||
rule = ParallelRule.objects.create(
|
||||
uuid=rule_uuid,
|
||||
package=package,
|
||||
name=rule_data["name"],
|
||||
description=rule_data["description"],
|
||||
kv=rule_data.get("kv", {}),
|
||||
)
|
||||
|
||||
# Set aliases if present
|
||||
if rule_data.get("aliases"):
|
||||
rule.aliases = rule_data["aliases"]
|
||||
rule.save()
|
||||
|
||||
# Add simple rules
|
||||
for simple_rule_ref in rule_data.get("simple_rules", []):
|
||||
simple_rule = self._get_cached_object("SimpleRule", simple_rule_ref["uuid"])
|
||||
if simple_rule:
|
||||
rule.simple_rules.add(simple_rule)
|
||||
|
||||
self._cache_object("ParallelRule", rule_data["uuid"], rule)
|
||||
return rule
|
||||
|
||||
def _import_reactions(self, package: Package, reactions_data: List[Dict[str, Any]]):
|
||||
"""Import reactions."""
|
||||
print(f"Importing {len(reactions_data)} reactions...")
|
||||
|
||||
for reaction_data in reactions_data:
|
||||
reaction_uuid = self._get_or_generate_uuid(reaction_data["uuid"])
|
||||
|
||||
reaction = Reaction.objects.create(
|
||||
uuid=reaction_uuid,
|
||||
package=package,
|
||||
name=reaction_data["name"],
|
||||
description=reaction_data["description"],
|
||||
kv=reaction_data.get("kv", {}),
|
||||
multi_step=reaction_data.get("multi_step", False),
|
||||
medline_references=reaction_data.get("medline_references", []),
|
||||
)
|
||||
|
||||
# Set aliases if present
|
||||
if reaction_data.get("aliases"):
|
||||
reaction.aliases = reaction_data["aliases"]
|
||||
reaction.save()
|
||||
|
||||
# Add educts and products
|
||||
for educt_ref in reaction_data.get("educts", []):
|
||||
compound = self._get_cached_object("CompoundStructure", educt_ref["uuid"])
|
||||
if compound:
|
||||
reaction.educts.add(compound)
|
||||
|
||||
for product_ref in reaction_data.get("products", []):
|
||||
compound = self._get_cached_object("CompoundStructure", product_ref["uuid"])
|
||||
if compound:
|
||||
reaction.products.add(compound)
|
||||
|
||||
# Add rules
|
||||
for rule_ref in reaction_data.get("rules", []):
|
||||
# Try to find rule in different caches
|
||||
rule = self._get_cached_object(
|
||||
"SimpleRule", rule_ref["uuid"]
|
||||
) or self._get_cached_object("ParallelRule", rule_ref["uuid"])
|
||||
if rule:
|
||||
reaction.rules.add(rule)
|
||||
|
||||
self._cache_object("Reaction", reaction_data["uuid"], reaction)
|
||||
|
||||
# Handle external identifiers
|
||||
self._create_external_identifiers(
|
||||
reaction, reaction_data.get("external_identifiers", [])
|
||||
)
|
||||
|
||||
def _import_pathways(self, package: Package, pathways_data: List[Dict[str, Any]]):
|
||||
"""Import pathways."""
|
||||
print(f"Importing {len(pathways_data)} pathways...")
|
||||
|
||||
for pathway_data in pathways_data:
|
||||
pathway_uuid = self._get_or_generate_uuid(pathway_data["uuid"])
|
||||
|
||||
pathway = Pathway.objects.create(
|
||||
uuid=pathway_uuid,
|
||||
package=package,
|
||||
name=pathway_data["name"],
|
||||
description=pathway_data["description"],
|
||||
kv=pathway_data.get("kv", {}),
|
||||
# setting will be handled separately if needed
|
||||
)
|
||||
|
||||
# Set aliases if present
|
||||
if pathway_data.get("aliases"):
|
||||
pathway.aliases = pathway_data["aliases"]
|
||||
pathway.save()
|
||||
|
||||
self._cache_object("Pathway", pathway_data["uuid"], pathway)
|
||||
|
||||
def _import_nodes(self, package: Package, nodes_data: List[Dict[str, Any]]):
|
||||
"""Import pathway nodes."""
|
||||
print(f"Importing {len(nodes_data)} nodes...")
|
||||
|
||||
for node_data in nodes_data:
|
||||
node_uuid = self._get_or_generate_uuid(node_data["uuid"])
|
||||
pathway_uuid = node_data["pathway"]["uuid"]
|
||||
pathway = self._get_cached_object("Pathway", pathway_uuid)
|
||||
|
||||
if not pathway:
|
||||
print(f"Warning: Pathway with UUID {pathway_uuid} not found for node")
|
||||
continue
|
||||
|
||||
# For now, we'll set default_node_label to None and handle it later
|
||||
# as it requires compound structures to be fully imported
|
||||
node = Node.objects.create(
|
||||
uuid=node_uuid,
|
||||
pathway=pathway,
|
||||
name=node_data["name"],
|
||||
description=node_data["description"],
|
||||
kv=node_data.get("kv", {}),
|
||||
depth=node_data.get("depth", 0),
|
||||
default_node_label=self._get_cached_object(
|
||||
"CompoundStructure", node_data["default_node_label"]["uuid"]
|
||||
),
|
||||
)
|
||||
|
||||
# Set aliases if present
|
||||
if node_data.get("aliases"):
|
||||
node.aliases = node_data["aliases"]
|
||||
node.save()
|
||||
|
||||
self._cache_object("Node", node_data["uuid"], node)
|
||||
# Store node_data for later processing of relationships
|
||||
node._import_data = node_data
|
||||
|
||||
def _import_edges(self, package: Package, edges_data: List[Dict[str, Any]]):
|
||||
"""Import pathway edges."""
|
||||
print(f"Importing {len(edges_data)} edges...")
|
||||
|
||||
for edge_data in edges_data:
|
||||
edge_uuid = self._get_or_generate_uuid(edge_data["uuid"])
|
||||
pathway_uuid = edge_data["pathway"]["uuid"]
|
||||
pathway = self._get_cached_object("Pathway", pathway_uuid)
|
||||
|
||||
if not pathway:
|
||||
print(f"Warning: Pathway with UUID {pathway_uuid} not found for edge")
|
||||
continue
|
||||
|
||||
# For now, we'll set edge_label to None and handle it later
|
||||
edge = Edge.objects.create(
|
||||
uuid=edge_uuid,
|
||||
pathway=pathway,
|
||||
name=edge_data["name"],
|
||||
description=edge_data["description"],
|
||||
kv=edge_data.get("kv", {}),
|
||||
edge_label=self._get_cached_object("Reaction", edge_data["edge_label"]["uuid"]),
|
||||
)
|
||||
|
||||
# Set aliases if present
|
||||
if edge_data.get("aliases"):
|
||||
edge.aliases = edge_data["aliases"]
|
||||
edge.save()
|
||||
|
||||
# Add start and end nodes
|
||||
for start_node_ref in edge_data.get("start_nodes", []):
|
||||
node = self._get_cached_object("Node", start_node_ref["uuid"])
|
||||
if node:
|
||||
edge.start_nodes.add(node)
|
||||
|
||||
for end_node_ref in edge_data.get("end_nodes", []):
|
||||
node = self._get_cached_object("Node", end_node_ref["uuid"])
|
||||
if node:
|
||||
edge.end_nodes.add(node)
|
||||
|
||||
self._cache_object("Edge", edge_data["uuid"], edge)
|
||||
|
||||
def _import_scenarios(self, package: Package, scenarios_data: List[Dict[str, Any]]):
|
||||
"""Import scenarios."""
|
||||
print(f"Importing {len(scenarios_data)} scenarios...")
|
||||
|
||||
# First pass: create scenarios without parent relationships
|
||||
for scenario_data in scenarios_data:
|
||||
scenario_uuid = self._get_or_generate_uuid(scenario_data["uuid"])
|
||||
|
||||
scenario_date = None
|
||||
if scenario_data.get("scenario_date"):
|
||||
scenario_date = scenario_data["scenario_date"]
|
||||
|
||||
scenario = Scenario.objects.create(
|
||||
uuid=scenario_uuid,
|
||||
package=package,
|
||||
name=scenario_data["name"],
|
||||
description=scenario_data["description"],
|
||||
kv=scenario_data.get("kv", {}),
|
||||
scenario_date=scenario_date,
|
||||
scenario_type=scenario_data.get("scenario_type"),
|
||||
additional_information=scenario_data.get("additional_information", {}),
|
||||
)
|
||||
|
||||
self._cache_object("Scenario", scenario_data["uuid"], scenario)
|
||||
# Store scenario_data for later processing of parent relationships
|
||||
scenario._import_data = scenario_data
|
||||
|
||||
# Second pass: set parent relationships
|
||||
for scenario_data in scenarios_data:
|
||||
if scenario_data.get("parent"):
|
||||
scenario = self._get_cached_object("Scenario", scenario_data["uuid"])
|
||||
parent = self._get_cached_object("Scenario", scenario_data["parent"]["uuid"])
|
||||
if scenario and parent:
|
||||
scenario.parent = parent
|
||||
scenario.save()
|
||||
|
||||
def _import_models(self, package: Package, models_data: List[Dict[str, Any]]):
|
||||
"""Import EPModels."""
|
||||
print(f"Importing {len(models_data)} models...")
|
||||
|
||||
for model_data in models_data:
|
||||
model_uuid = self._get_or_generate_uuid(model_data["uuid"])
|
||||
model_type = model_data.get("model_type", "EPModel")
|
||||
|
||||
common_fields = {
|
||||
"uuid": model_uuid,
|
||||
"package": package,
|
||||
"name": model_data["name"],
|
||||
"description": model_data["description"],
|
||||
"kv": model_data.get("kv", {}),
|
||||
}
|
||||
|
||||
# Add PackageBasedModel fields if present
|
||||
if "threshold" in model_data:
|
||||
common_fields.update(
|
||||
{
|
||||
"threshold": model_data.get("threshold"),
|
||||
"eval_results": model_data.get("eval_results", {}),
|
||||
"model_status": model_data.get("model_status", "INITIAL"),
|
||||
}
|
||||
)
|
||||
|
||||
# Create the appropriate model type
|
||||
if model_type == "RuleBasedRelativeReasoning":
|
||||
model = RuleBasedRelativeReasoning.objects.create(
|
||||
**common_fields,
|
||||
min_count=model_data.get("min_count", 1),
|
||||
max_count=model_data.get("max_count", 10),
|
||||
)
|
||||
elif model_type == "MLRelativeReasoning":
|
||||
model = MLRelativeReasoning.objects.create(**common_fields)
|
||||
elif model_type == "EnviFormer":
|
||||
model = EnviFormer.objects.create(**common_fields)
|
||||
else:
|
||||
model = EPModel.objects.create(**common_fields)
|
||||
|
||||
# Set aliases if present
|
||||
if model_data.get("aliases"):
|
||||
model.aliases = model_data["aliases"]
|
||||
model.save()
|
||||
|
||||
# Add package relationships for PackageBasedModel
|
||||
if hasattr(model, "rule_packages"):
|
||||
for pkg_ref in model_data.get("rule_packages", []):
|
||||
pkg = self._get_cached_object("Package", pkg_ref["uuid"])
|
||||
if pkg:
|
||||
model.rule_packages.add(pkg)
|
||||
|
||||
for pkg_ref in model_data.get("data_packages", []):
|
||||
pkg = self._get_cached_object("Package", pkg_ref["uuid"])
|
||||
if pkg:
|
||||
model.data_packages.add(pkg)
|
||||
|
||||
for pkg_ref in model_data.get("eval_packages", []):
|
||||
pkg = self._get_cached_object("Package", pkg_ref["uuid"])
|
||||
if pkg:
|
||||
model.eval_packages.add(pkg)
|
||||
|
||||
self._cache_object("EPModel", model_data["uuid"], model)
|
||||
|
||||
def _set_default_structures(self, compounds_data: List[Dict[str, Any]]):
|
||||
"""Set default structures for compounds after all structures are created."""
|
||||
print("Setting default structures for compounds...")
|
||||
|
||||
for compound_data in compounds_data:
|
||||
if compound_data.get("default_structure"):
|
||||
compound = self._get_cached_object("Compound", compound_data["uuid"])
|
||||
structure = self._get_cached_object(
|
||||
"CompoundStructure", compound_data["default_structure"]["uuid"]
|
||||
)
|
||||
if compound and structure:
|
||||
compound.default_structure = structure
|
||||
compound.save()
|
||||
|
||||
def _create_external_identifiers(self, obj, identifiers_data: List[Dict[str, Any]]):
|
||||
"""Create external identifiers for an object."""
|
||||
for identifier_data in identifiers_data:
|
||||
# Get or create the external database
|
||||
db_data = identifier_data["database"]
|
||||
database, _ = ExternalDatabase.objects.get_or_create(
|
||||
name=db_data["name"],
|
||||
defaults={
|
||||
"base_url": db_data.get("base_url", ""),
|
||||
"full_name": db_data.get("name", ""),
|
||||
"description": "",
|
||||
"is_active": True,
|
||||
},
|
||||
)
|
||||
|
||||
# Create the external identifier
|
||||
ExternalIdentifier.objects.create(
|
||||
content_object=obj,
|
||||
database=database,
|
||||
identifier_value=identifier_data["identifier_value"],
|
||||
url=identifier_data.get("url", ""),
|
||||
is_primary=identifier_data.get("is_primary", False),
|
||||
)
|
||||
|
||||
|
||||
class PathwayUtils:
|
||||
def __init__(self, pathway: "Pathway"):
|
||||
|
||||
Reference in New Issue
Block a user