forked from enviPath/enviPy
feature/additional_information (#30)
Fixes #12 Co-authored-by: Tim Lorsbach <tim@lorsba.ch> Reviewed-on: enviPath/enviPy#30
This commit is contained in:
@ -1,6 +1,6 @@
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from django.contrib import admin
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from .models import User, Group, UserPackagePermission, GroupPackagePermission, Setting, SimpleAmbitRule
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from .models import User, Group, UserPackagePermission, GroupPackagePermission, Setting, SimpleAmbitRule, Scenario
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class UserAdmin(admin.ModelAdmin):
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@ -22,15 +22,19 @@ class GroupPackagePermissionAdmin(admin.ModelAdmin):
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class SettingAdmin(admin.ModelAdmin):
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pass
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admin.site.register(User, UserAdmin)
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admin.site.register(Group, GroupAdmin)
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admin.site.register(UserPackagePermission, UserPackagePermissionAdmin)
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admin.site.register(GroupPackagePermission, GroupPackagePermissionAdmin)
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admin.site.register(Setting, SettingAdmin)
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class SimpleAmbitRuleAdmin(admin.ModelAdmin):
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pass
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class ScenarioAdmin(admin.ModelAdmin):
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pass
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admin.site.register(User, UserAdmin)
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admin.site.register(Group, GroupAdmin)
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admin.site.register(UserPackagePermission, UserPackagePermissionAdmin)
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admin.site.register(GroupPackagePermission, GroupPackagePermissionAdmin)
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admin.site.register(Setting, SettingAdmin)
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admin.site.register(SimpleAmbitRule, SimpleAmbitRuleAdmin)
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admin.site.register(Scenario, ScenarioAdmin)
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376
epdb/logic.py
376
epdb/logic.py
@ -255,6 +255,382 @@ class PackageManager(object):
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else:
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_ = perm_cls.objects.update_or_create(defaults={'permission': new_perm}, **data)
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@staticmethod
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@transaction.atomic
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def import_package(data: dict, owner: User, keep_ids=False):
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from uuid import UUID, uuid4
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from datetime import datetime
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from collections import defaultdict
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from .models import Package, Compound, CompoundStructure, SimpleRule, SimpleAmbitRule, SimpleRDKitRule, \
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ParallelRule, SequentialRule, SequentialRuleOrdering, Reaction, Pathway, Node, Edge, Scenario
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from envipy_additional_information import AdditionalInformationConverter
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pack = Package()
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pack.uuid = UUID(data['id'].split('/')[-1]) if keep_ids else uuid4()
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pack.name = '{} - {}'.format(data['name'], datetime.now().strftime('%Y-%m-%d %H:%M'))
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pack.reviewed = True if data['reviewStatus'] == 'reviewed' else False
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pack.description = data['description']
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pack.save()
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up = UserPackagePermission()
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up.user = owner
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up.package = pack
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up.permission = up.ALL[0]
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up.save()
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# Stores old_id to new_id
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mapping = {}
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# Stores new_scen_id to old_parent_scen_id
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parent_mapping = {}
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# Mapping old scen_id to old_obj_id
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scen_mapping = defaultdict(list)
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# Store Scenarios
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for scenario in data['scenarios']:
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scen = Scenario()
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scen.package = pack
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scen.uuid = UUID(scenario['id'].split('/')[-1]) if keep_ids else uuid4()
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scen.name = scenario['name']
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scen.description = scenario['description']
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scen.scenario_type = scenario['type']
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scen.scenario_date = scenario['date']
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scen.additional_information = dict()
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scen.save()
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mapping[scenario['id']] = scen.uuid
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new_add_inf = defaultdict(list)
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# TODO Store AI...
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for ex in scenario.get('additionalInformationCollection', {}).get('additionalInformation', []):
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name = ex['name']
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addinf_data = ex['data']
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# park the parent scen id for now and link it later
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if name == 'referringscenario':
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parent_mapping[scen.uuid] = addinf_data
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continue
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# Broken eP Data
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if name == 'initialmasssediment' and addinf_data == 'missing data':
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continue
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# TODO Enzymes arent ready yet
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if name == 'enzyme':
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continue
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try:
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res = AdditionalInformationConverter.convert(name, addinf_data)
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except:
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logger.error(f"Failed to convert {name} with {addinf_data}")
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new_add_inf[name].append(res.model_dump_json())
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scen.additional_information = new_add_inf
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scen.save()
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print('Scenarios imported...')
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# Store compounds and its structures
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for compound in data['compounds']:
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comp = Compound()
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comp.package = pack
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comp.uuid = UUID(compound['id'].split('/')[-1]) if keep_ids else uuid4()
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comp.name = compound['name']
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comp.description = compound['description']
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comp.aliases = compound['aliases']
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comp.save()
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mapping[compound['id']] = comp.uuid
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for scen in compound['scenarios']:
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scen_mapping[scen['id']].append(comp)
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default_structure = None
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for structure in compound['structures']:
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struc = CompoundStructure()
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# struc.object_url = Command.get_id(structure, keep_ids)
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struc.compound = comp
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struc.uuid = UUID(structure['id'].split('/')[-1]) if keep_ids else uuid4()
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struc.name = structure['name']
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struc.description = structure['description']
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struc.smiles = structure['smiles']
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struc.save()
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for scen in structure['scenarios']:
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scen_mapping[scen['id']].append(struc)
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mapping[structure['id']] = struc.uuid
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if structure['id'] == compound['defaultStructure']['id']:
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default_structure = struc
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struc.save()
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if default_structure is None:
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raise ValueError('No default structure set')
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comp.default_structure = default_structure
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comp.save()
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print('Compounds imported...')
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# Store simple and parallel-rules
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par_rules = []
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seq_rules = []
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for rule in data['rules']:
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if rule['identifier'] == 'parallel-rule':
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par_rules.append(rule)
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continue
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if rule['identifier'] == 'sequential-rule':
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seq_rules.append(rule)
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continue
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r = SimpleAmbitRule()
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r.uuid = UUID(rule['id'].split('/')[-1]) if keep_ids else uuid4()
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r.package = pack
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r.name = rule['name']
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r.description = rule['description']
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r.smirks = rule['smirks']
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r.reactant_filter_smarts = rule.get('reactantFilterSmarts', None)
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r.product_filter_smarts = rule.get('productFilterSmarts', None)
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r.save()
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mapping[rule['id']] = r.uuid
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for scen in rule['scenarios']:
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scen_mapping[scen['id']].append(r)
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print("Par: ", len(par_rules))
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print("Seq: ", len(seq_rules))
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for par_rule in par_rules:
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r = ParallelRule()
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r.package = pack
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r.uuid = UUID(par_rule['id'].split('/')[-1]) if keep_ids else uuid4()
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r.name = par_rule['name']
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r.description = par_rule['description']
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r.save()
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mapping[par_rule['id']] = r.uuid
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for scen in par_rule['scenarios']:
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scen_mapping[scen['id']].append(r)
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for simple_rule in par_rule['simpleRules']:
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if simple_rule['id'] in mapping:
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r.simple_rules.add(SimpleRule.objects.get(uuid=mapping[simple_rule['id']]))
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r.save()
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for seq_rule in seq_rules:
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r = SequentialRule()
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r.package = pack
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r.uuid = UUID(seq_rule['id'].split('/')[-1]) if keep_ids else uuid4()
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r.name = seq_rule['name']
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r.description = seq_rule['description']
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r.save()
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mapping[seq_rule['id']] = r.uuid
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for scen in seq_rule['scenarios']:
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scen_mapping[scen['id']].append(r)
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for i, simple_rule in enumerate(seq_rule['simpleRules']):
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sro = SequentialRuleOrdering()
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sro.simple_rule = simple_rule
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sro.sequential_rule = r
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sro.order_index = i
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sro.save()
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# r.simple_rules.add(SimpleRule.objects.get(uuid=mapping[simple_rule['id']]))
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r.save()
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print('Rules imported...')
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for reaction in data['reactions']:
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r = Reaction()
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r.package = pack
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r.uuid = UUID(reaction['id'].split('/')[-1]) if keep_ids else uuid4()
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r.name = reaction['name']
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r.description = reaction['description']
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r.medlinereferences = reaction['medlinereferences'],
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r.multi_step = True if reaction['multistep'] == 'true' else False
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r.save()
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mapping[reaction['id']] = r.uuid
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for scen in reaction['scenarios']:
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scen_mapping[scen['id']].append(r)
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for educt in reaction['educts']:
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r.educts.add(CompoundStructure.objects.get(uuid=mapping[educt['id']]))
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for product in reaction['products']:
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r.products.add(CompoundStructure.objects.get(uuid=mapping[product['id']]))
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if 'rules' in reaction:
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for rule in reaction['rules']:
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try:
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r.rules.add(Rule.objects.get(uuid=mapping[rule['id']]))
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except Exception as e:
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print(f"Rule with id {rule['id']} not found!")
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print(e)
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r.save()
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print('Reactions imported...')
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for pathway in data['pathways']:
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pw = Pathway()
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pw.package = pack
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pw.uuid = UUID(pathway['id'].split('/')[-1]) if keep_ids else uuid4()
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pw.name = pathway['name']
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pw.description = pathway['description']
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pw.save()
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mapping[pathway['id']] = pw.uuid
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for scen in pathway['scenarios']:
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scen_mapping[scen['id']].append(pw)
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out_nodes_mapping = defaultdict(set)
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root_node = None
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for node in pathway['nodes']:
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n = Node()
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n.uuid = UUID(node['id'].split('/')[-1]) if keep_ids else uuid4()
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n.name = node['name']
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n.pathway = pw
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n.depth = node['depth']
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n.default_node_label = CompoundStructure.objects.get(uuid=mapping[node['defaultNodeLabel']['id']])
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n.save()
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mapping[node['id']] = n.uuid
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for scen in node['scenarios']:
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scen_mapping[scen['id']].append(n)
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for node_label in node['nodeLabels']:
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n.node_labels.add(CompoundStructure.objects.get(uuid=mapping[node_label['id']]))
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n.save()
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for out_edge in node['outEdges']:
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out_nodes_mapping[n.uuid].add(out_edge)
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for edge in pathway['edges']:
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e = Edge()
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e.uuid = UUID(edge['id'].split('/')[-1]) if keep_ids else uuid4()
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e.name = edge['name']
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e.pathway = pw
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e.description = edge['description']
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e.edge_label = Reaction.objects.get(uuid=mapping[edge['edgeLabel']['id']])
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e.save()
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mapping[edge['id']] = e.uuid
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for scen in edge['scenarios']:
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scen_mapping[scen['id']].append(e)
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for start_node in edge['startNodes']:
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e.start_nodes.add(Node.objects.get(uuid=mapping[start_node]))
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for end_node in edge['endNodes']:
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e.end_nodes.add(Node.objects.get(uuid=mapping[end_node]))
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e.save()
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for k, v in out_nodes_mapping.items():
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n = Node.objects.get(uuid=k)
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for v1 in v:
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n.out_edges.add(Edge.objects.get(uuid=mapping[v1]))
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n.save()
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print('Pathways imported...')
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# Linking Phase
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for child, parent in parent_mapping.items():
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child_obj = Scenario.objects.get(uuid=child)
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parent_obj = Scenario.objects.get(uuid=mapping[parent])
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child_obj.parent = parent_obj
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child_obj.save()
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for scen_id, objects in scen_mapping.items():
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scen = Scenario.objects.get(uuid=mapping[scen_id])
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for o in objects:
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o.scenarios.add(scen)
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o.save()
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print("Scenarios linked...")
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print('Import statistics:')
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print('Package {} stored'.format(pack.url))
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print('Imported {} compounds'.format(Compound.objects.filter(package=pack).count()))
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print('Imported {} rules'.format(Rule.objects.filter(package=pack).count()))
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print('Imported {} reactions'.format(Reaction.objects.filter(package=pack).count()))
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print('Imported {} pathways'.format(Pathway.objects.filter(package=pack).count()))
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print('Imported {} Scenarios'.format(Scenario.objects.filter(package=pack).count()))
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print("Fixing Node depths...")
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total_pws = Pathway.objects.filter(package=pack).count()
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for p, pw in enumerate(Pathway.objects.filter(package=pack)):
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print(pw.url)
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in_count = defaultdict(lambda: 0)
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out_count = defaultdict(lambda: 0)
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for e in pw.edges:
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# TODO check if this will remain
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for react in e.start_nodes.all():
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out_count[str(react.uuid)] += 1
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for prod in e.end_nodes.all():
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in_count[str(prod.uuid)] += 1
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root_nodes = []
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for n in pw.nodes:
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num_parents = in_count[str(n.uuid)]
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if num_parents == 0:
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# must be a root node or unconnected node
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if n.depth != 0:
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n.depth = 0
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n.save()
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# Only root node may have children
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if out_count[str(n.uuid)] > 0:
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root_nodes.append(n)
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levels = [root_nodes]
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seen = set()
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# Do a bfs to determine depths starting with level 0 a.k.a. root nodes
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for i, level_nodes in enumerate(levels):
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new_level = []
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for n in level_nodes:
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for e in n.out_edges.all():
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for prod in e.end_nodes.all():
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if str(prod.uuid) not in seen:
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old_depth = prod.depth
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if old_depth != i + 1:
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print(f'updating depth from {old_depth} to {i + 1}')
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prod.depth = i + 1
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prod.save()
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new_level.append(prod)
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seen.add(str(n.uuid))
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if new_level:
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levels.append(new_level)
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print(f'{p + 1}/{total_pws} fixed.')
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return pack
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class SettingManager(object):
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setting_pattern = re.compile(r".*/setting/[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}$")
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@ -1,11 +1,11 @@
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import json
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from collections import defaultdict
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from datetime import datetime
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from uuid import UUID
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from django.core.management.base import BaseCommand
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from django.conf import settings as s
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from epdb.models import *
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from django.core.management.base import BaseCommand
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from django.db import transaction
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from epdb.logic import UserManager, GroupManager, PackageManager, SettingManager
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from epdb.models import UserSettingPermission, MLRelativeReasoning, EnviFormer, Permission, User
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class Command(BaseCommand):
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@ -52,283 +52,7 @@ class Command(BaseCommand):
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return anon, admin, g, jebus
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def import_package(self, data, owner):
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# Start import
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pack = Package()
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pack.uuid = UUID(data['id'].split('/')[-1])
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pack.name = '{} - {}'.format(data['name'], datetime.now().strftime('%Y-%m-%d %H:%M'))
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pack.reviewed = True if data['reviewStatus'] == 'reviewed' else False
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pack.description = data['description']
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pack.save()
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up = UserPackagePermission()
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up.user = owner
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up.package = pack
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up.permission = up.ALL[0]
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up.save()
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# Stores old_id to new_id
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mapping = {}
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# Store compounds and its structures
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for compound in data['compounds']:
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comp = Compound()
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comp.package = pack
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comp.uuid = UUID(compound['id'].split('/')[-1])
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comp.name = compound['name']
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comp.description = compound['description']
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comp.aliases = compound['aliases']
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comp.save()
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mapping[compound['id']] = comp.uuid
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default_structure = None
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for structure in compound['structures']:
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struc = CompoundStructure()
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# struc.object_url = Command.get_id(structure, keep_ids)
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struc.compound = comp
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struc.uuid = UUID(structure['id'].split('/')[-1])
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struc.name = structure['name']
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struc.description = structure['description']
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struc.smiles = structure['smiles']
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struc.save()
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mapping[structure['id']] = struc.uuid
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if structure['id'] == compound['defaultStructure']['id']:
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default_structure = struc
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|
||||
struc.save()
|
||||
|
||||
if default_structure is None:
|
||||
raise ValueError('No default structure set')
|
||||
|
||||
comp.default_structure = default_structure
|
||||
comp.save()
|
||||
|
||||
print('Compounds imported...')
|
||||
|
||||
# Store simple and parallel-rules
|
||||
par_rules = []
|
||||
seq_rules = []
|
||||
|
||||
for rule in data['rules']:
|
||||
if rule['identifier'] == 'parallel-rule':
|
||||
par_rules.append(rule)
|
||||
continue
|
||||
if rule['identifier'] == 'sequential-rule':
|
||||
seq_rules.append(rule)
|
||||
continue
|
||||
r = SimpleAmbitRule()
|
||||
r.uuid = UUID(rule['id'].split('/')[-1])
|
||||
r.package = pack
|
||||
r.name = rule['name']
|
||||
r.description = rule['description']
|
||||
r.smirks = rule['smirks']
|
||||
r.reactant_filter_smarts = rule.get('reactantFilterSmarts', None)
|
||||
r.product_filter_smarts = rule.get('productFilterSmarts', None)
|
||||
r.save()
|
||||
|
||||
mapping[rule['id']] = r.uuid
|
||||
|
||||
print("Par: ", len(par_rules))
|
||||
print("Seq: ", len(seq_rules))
|
||||
|
||||
for par_rule in par_rules:
|
||||
r = ParallelRule()
|
||||
r.package = pack
|
||||
r.uuid = UUID(par_rule['id'].split('/')[-1])
|
||||
r.name = par_rule['name']
|
||||
r.description = par_rule['description']
|
||||
r.save()
|
||||
|
||||
mapping[par_rule['id']] = r.uuid
|
||||
|
||||
for simple_rule in par_rule['simpleRules']:
|
||||
if simple_rule['id'] in mapping:
|
||||
r.simple_rules.add(SimpleRule.objects.get(uuid=mapping[simple_rule['id']]))
|
||||
|
||||
r.save()
|
||||
|
||||
for seq_rule in seq_rules:
|
||||
r = SequentialRule()
|
||||
r.package = pack
|
||||
r.uuid = UUID(seq_rule['id'].split('/')[-1])
|
||||
r.name = seq_rule['name']
|
||||
r.description = seq_rule['description']
|
||||
r.save()
|
||||
|
||||
mapping[seq_rule['id']] = r.uuid
|
||||
|
||||
# m1 = Membership(
|
||||
# ... person=ringo,
|
||||
# ... group=beatles,
|
||||
# ... date_joined=date(1962, 8, 16),
|
||||
# ... invite_reason="Needed a new drummer.",
|
||||
# ... )
|
||||
# >>> m1.save()
|
||||
|
||||
for i, simple_rule in enumerate(seq_rule['simpleRules']):
|
||||
sro = SequentialRuleOrdering()
|
||||
sro.simple_rule = simple_rule
|
||||
sro.sequential_rule = r
|
||||
sro.order_index = i
|
||||
sro.save()
|
||||
# r.simple_rules.add(SimpleRule.objects.get(uuid=mapping[simple_rule['id']]))
|
||||
|
||||
r.save()
|
||||
|
||||
print('Rules imported...')
|
||||
|
||||
for reaction in data['reactions']:
|
||||
r = Reaction()
|
||||
r.package = pack
|
||||
r.uuid = UUID(reaction['id'].split('/')[-1])
|
||||
r.name = reaction['name']
|
||||
r.description = reaction['description']
|
||||
r.medlinereferences = reaction['medlinereferences'],
|
||||
r.multi_step = True if reaction['multistep'] == 'true' else False
|
||||
r.save()
|
||||
|
||||
mapping[reaction['id']] = r.uuid
|
||||
|
||||
for educt in reaction['educts']:
|
||||
r.educts.add(CompoundStructure.objects.get(uuid=mapping[educt['id']]))
|
||||
|
||||
for product in reaction['products']:
|
||||
r.products.add(CompoundStructure.objects.get(uuid=mapping[product['id']]))
|
||||
|
||||
if 'rules' in reaction:
|
||||
for rule in reaction['rules']:
|
||||
try:
|
||||
r.rules.add(Rule.objects.get(uuid=mapping[rule['id']]))
|
||||
except Exception as e:
|
||||
print(f"Rule with id {rule['id']} not found!")
|
||||
print(e)
|
||||
|
||||
r.save()
|
||||
|
||||
print('Reactions imported...')
|
||||
|
||||
for pathway in data['pathways']:
|
||||
pw = Pathway()
|
||||
pw.package = pack
|
||||
pw.uuid = UUID(pathway['id'].split('/')[-1])
|
||||
pw.name = pathway['name']
|
||||
pw.description = pathway['description']
|
||||
pw.save()
|
||||
|
||||
mapping[pathway['id']] = pw.uuid
|
||||
|
||||
out_nodes_mapping = defaultdict(set)
|
||||
|
||||
root_node = None
|
||||
|
||||
for node in pathway['nodes']:
|
||||
n = Node()
|
||||
n.uuid = UUID(node['id'].split('/')[-1])
|
||||
n.name = node['name']
|
||||
n.pathway = pw
|
||||
n.depth = node['depth']
|
||||
n.default_node_label = CompoundStructure.objects.get(uuid=mapping[node['defaultNodeLabel']['id']])
|
||||
n.save()
|
||||
|
||||
mapping[node['id']] = n.uuid
|
||||
|
||||
for node_label in node['nodeLabels']:
|
||||
n.node_labels.add(CompoundStructure.objects.get(uuid=mapping[node_label['id']]))
|
||||
|
||||
n.save()
|
||||
|
||||
for out_edge in node['outEdges']:
|
||||
out_nodes_mapping[n.uuid].add(out_edge)
|
||||
|
||||
for edge in pathway['edges']:
|
||||
e = Edge()
|
||||
e.uuid = UUID(edge['id'].split('/')[-1])
|
||||
e.name = edge['name']
|
||||
e.pathway = pw
|
||||
e.description = edge['description']
|
||||
e.edge_label = Reaction.objects.get(uuid=mapping[edge['edgeLabel']['id']])
|
||||
e.save()
|
||||
|
||||
mapping[edge['id']] = e.uuid
|
||||
|
||||
for start_node in edge['startNodes']:
|
||||
e.start_nodes.add(Node.objects.get(uuid=mapping[start_node]))
|
||||
|
||||
for end_node in edge['endNodes']:
|
||||
e.end_nodes.add(Node.objects.get(uuid=mapping[end_node]))
|
||||
|
||||
e.save()
|
||||
|
||||
for k, v in out_nodes_mapping.items():
|
||||
n = Node.objects.get(uuid=k)
|
||||
for v1 in v:
|
||||
n.out_edges.add(Edge.objects.get(uuid=mapping[v1]))
|
||||
n.save()
|
||||
|
||||
print('Pathways imported...')
|
||||
|
||||
print('Import statistics:')
|
||||
print('Package {} stored'.format(pack.url))
|
||||
print('Imported {} compounds'.format(Compound.objects.filter(package=pack).count()))
|
||||
print('Imported {} rules'.format(Rule.objects.filter(package=pack).count()))
|
||||
print('Imported {} reactions'.format(Reaction.objects.filter(package=pack).count()))
|
||||
print('Imported {} pathways'.format(Pathway.objects.filter(package=pack).count()))
|
||||
|
||||
print("Fixing Node depths...")
|
||||
total_pws = Pathway.objects.filter(package=pack).count()
|
||||
for p, pw in enumerate(Pathway.objects.filter(package=pack)):
|
||||
print(pw.url)
|
||||
in_count = defaultdict(lambda: 0)
|
||||
out_count = defaultdict(lambda: 0)
|
||||
|
||||
for e in pw.edges:
|
||||
# TODO check if this will remain
|
||||
for react in e.start_nodes.all():
|
||||
out_count[str(react.uuid)] += 1
|
||||
|
||||
for prod in e.end_nodes.all():
|
||||
in_count[str(prod.uuid)] += 1
|
||||
|
||||
root_nodes = []
|
||||
for n in pw.nodes:
|
||||
num_parents = in_count[str(n.uuid)]
|
||||
if num_parents == 0:
|
||||
# must be a root node or unconnected node
|
||||
if n.depth != 0:
|
||||
n.depth = 0
|
||||
n.save()
|
||||
|
||||
# Only root node may have children
|
||||
if out_count[str(n.uuid)] > 0:
|
||||
root_nodes.append(n)
|
||||
|
||||
levels = [root_nodes]
|
||||
seen = set()
|
||||
# Do a bfs to determine depths starting with level 0 a.k.a. root nodes
|
||||
for i, level_nodes in enumerate(levels):
|
||||
new_level = []
|
||||
for n in level_nodes:
|
||||
for e in n.out_edges.all():
|
||||
for prod in e.end_nodes.all():
|
||||
if str(prod.uuid) not in seen:
|
||||
old_depth = prod.depth
|
||||
if old_depth != i + 1:
|
||||
print(f'updating depth from {old_depth} to {i + 1}')
|
||||
prod.depth = i + 1
|
||||
prod.save()
|
||||
|
||||
new_level.append(prod)
|
||||
|
||||
seen.add(str(n.uuid))
|
||||
|
||||
if new_level:
|
||||
levels.append(new_level)
|
||||
|
||||
print(f'{p + 1}/{total_pws} fixed.')
|
||||
|
||||
return pack
|
||||
return PackageManager.import_package(data, owner, keep_ids=True)
|
||||
|
||||
def create_default_setting(self, owner, packages):
|
||||
s = SettingManager.create_setting(
|
||||
@ -344,8 +68,6 @@ class Command(BaseCommand):
|
||||
|
||||
return s
|
||||
|
||||
|
||||
|
||||
@transaction.atomic
|
||||
def handle(self, *args, **options):
|
||||
# Create users
|
||||
@ -356,12 +78,13 @@ class Command(BaseCommand):
|
||||
'EAWAG-BBD.json',
|
||||
'EAWAG-SOIL.json',
|
||||
'EAWAG-SLUDGE.json',
|
||||
'EAWAG-SEDIMENT.json',
|
||||
]
|
||||
|
||||
mapping = {}
|
||||
for p in packages:
|
||||
print(f"Importing {p}...")
|
||||
package_data = json.loads(open(s.BASE_DIR / 'fixtures' / p).read())
|
||||
package_data = json.loads(open(s.BASE_DIR / 'fixtures' / 'packages' / '2025-07-18' / p).read())
|
||||
imported_package = self.import_package(package_data, admin)
|
||||
mapping[p.replace('.json', '')] = imported_package
|
||||
|
||||
@ -378,7 +101,8 @@ class Command(BaseCommand):
|
||||
usp.save()
|
||||
|
||||
# Create Model Package
|
||||
pack = PackageManager.create_package(admin, "Public Prediction Models", "Package to make Prediction Models publicly available")
|
||||
pack = PackageManager.create_package(admin, "Public Prediction Models",
|
||||
"Package to make Prediction Models publicly available")
|
||||
pack.reviewed = True
|
||||
pack.save()
|
||||
|
||||
|
||||
27
epdb/management/commands/import_package.py
Normal file
27
epdb/management/commands/import_package.py
Normal file
@ -0,0 +1,27 @@
|
||||
from django.core.management.base import BaseCommand
|
||||
|
||||
from epdb.logic import PackageManager
|
||||
from epdb.models import *
|
||||
|
||||
|
||||
class Command(BaseCommand):
|
||||
|
||||
def add_arguments(self, parser):
|
||||
parser.add_argument(
|
||||
'--data',
|
||||
type=str,
|
||||
help='Path of the Package to import.',
|
||||
required=True,
|
||||
)
|
||||
parser.add_argument(
|
||||
'--owner',
|
||||
type=str,
|
||||
help='Username of the desired Owner.',
|
||||
required=True,
|
||||
)
|
||||
|
||||
@transaction.atomic
|
||||
def handle(self, *args, **options):
|
||||
owner = User.objects.get(username=options['owner'])
|
||||
package_data = json.load(open(options['data']))
|
||||
PackageManager.import_package(package_data, owner)
|
||||
@ -468,10 +468,10 @@ class Rule(PolymorphicModel, EnviPathModel, AliasMixin, ScenarioMixin):
|
||||
|
||||
# I think this only affects Django Admin which we are barely using
|
||||
# # https://github.com/django-polymorphic/django-polymorphic/issues/229
|
||||
_non_polymorphic = models.Manager()
|
||||
|
||||
class Meta:
|
||||
base_manager_name = '_non_polymorphic'
|
||||
# _non_polymorphic = models.Manager()
|
||||
#
|
||||
# class Meta:
|
||||
# base_manager_name = '_non_polymorphic'
|
||||
|
||||
@abc.abstractmethod
|
||||
def apply(self, *args, **kwargs):
|
||||
@ -1431,14 +1431,13 @@ class PluginModel(EPModel):
|
||||
pass
|
||||
|
||||
|
||||
# #
|
||||
# #
|
||||
# # # TODO fully implement AdditionalInformation
|
||||
# # # TODO consider Scenario, BaseScenario, RelatedScenario
|
||||
class Scenario(EnviPathModel):
|
||||
package = models.ForeignKey('epdb.Package', verbose_name='Package', on_delete=models.CASCADE, db_index=True)
|
||||
type = models.CharField(max_length=256, null=False, blank=False, default='No date')
|
||||
type = models.CharField(max_length=256, null=False, blank=False, default='Not specified')
|
||||
scenario_date = models.CharField(max_length=256, null=False, blank=False, default='No date')
|
||||
scenario_type = models.CharField(max_length=256, null=False, blank=False, default='Not specified')
|
||||
|
||||
# for Referring Scenarios this property will be filled
|
||||
parent = models.ForeignKey('self', on_delete=models.CASCADE, default=None, null=True)
|
||||
|
||||
additional_information = models.JSONField(verbose_name='Additional Information')
|
||||
|
||||
@ -1470,47 +1469,15 @@ class Scenario(EnviPathModel):
|
||||
def set_additional_information(self, data):
|
||||
pass
|
||||
|
||||
example = {
|
||||
"additionalInformationCollection": {
|
||||
"additionalInformation": [
|
||||
{
|
||||
"addInfoName": "referringscenario",
|
||||
"creationDate": "2017-12-15 11:46:07.993",
|
||||
"data": "http://localhost:8080/package/5882df9c-dae1-4d80-a40e-db4724271456/scenario/11482bc1-8a0c-44a0-ae8b-5a02ae732559",
|
||||
"id": "http://localhost:8080/package/5882df9c-dae1-4d80-a40e-db4724271456/infocollection/0f30d0ca-b2bd-4c85-a425-ed8b22d4fed6/referringscenario/41532eac-e04a-4474-937a-df1344c3dce7",
|
||||
"identifier": "referringscenario",
|
||||
"lastModified": "2017-12-15 11:46:07.993",
|
||||
"name": "referringscenario"
|
||||
},
|
||||
{
|
||||
"addInfoName": "halflife",
|
||||
"creationDate": "2017-12-15 11:46:07.934",
|
||||
"data": "First Order;;reported,no further information about the model;3690.0 - 3690.0;McCorquodale, G. & Wardrope, L. (2006)",
|
||||
"id": "http://localhost:8080/package/5882df9c-dae1-4d80-a40e-db4724271456/infocollection/0f30d0ca-b2bd-4c85-a425-ed8b22d4fed6/halflife/8f44fdd9-f453-4ab1-8509-2ee5826faad7",
|
||||
"identifier": "halflife",
|
||||
"lastModified": "2020-05-05 17:26:14.753",
|
||||
"name": "halflife"
|
||||
}
|
||||
],
|
||||
"creationDate": "2017-12-15 11:46:07.608",
|
||||
"id": "http://localhost:8080/package/5882df9c-dae1-4d80-a40e-db4724271456/infocollection/0f30d0ca-b2bd-4c85-a425-ed8b22d4fed6",
|
||||
"identifier": "infocollection",
|
||||
"lastModified": "2020-05-05 17:26:15.496",
|
||||
"name": "no name"
|
||||
},
|
||||
"aliases": [],
|
||||
"creationDate": "2017-12-15 11:46:08.221",
|
||||
"date": "no date",
|
||||
"description": "no description",
|
||||
"id": "http://localhost:8080/package/5882df9c-dae1-4d80-a40e-db4724271456/scenario/e7089e49-e07d-4a2d-8045-e144b7eb5a5e",
|
||||
"identifier": "scenario",
|
||||
"lastModified": "2020-05-05 17:26:15.065",
|
||||
"name": "McCorquodale, G. & Wardrope, L. (2006) - (00002) (Related Scenario) - (00000)",
|
||||
"reviewStatus": "reviewed",
|
||||
"scenarios": [],
|
||||
"type": "Not specified"
|
||||
}
|
||||
def get_additional_information(self):
|
||||
from envipy_additional_information import NAME_MAPPING
|
||||
|
||||
for k, vals in self.additional_information.items():
|
||||
if k == 'enzyme':
|
||||
continue
|
||||
|
||||
for v in vals:
|
||||
yield NAME_MAPPING[k](**json.loads(v))
|
||||
|
||||
class UserSettingPermission(Permission):
|
||||
uuid = models.UUIDField(null=False, blank=False, verbose_name='UUID of this object', primary_key=True,
|
||||
|
||||
@ -1141,7 +1141,24 @@ def package_scenarios(request, package_uuid):
|
||||
|
||||
# https://envipath.org/package/<id>/scenario/<id>
|
||||
def package_scenario(request, package_uuid, scenario_uuid):
|
||||
pass
|
||||
current_user = _anonymous_or_real(request)
|
||||
current_package = PackageManager.get_package_by_id(current_user, package_uuid)
|
||||
current_scenario = Scenario.objects.get(package=current_package, uuid=scenario_uuid)
|
||||
|
||||
if request.method == 'GET':
|
||||
context = get_base_context(request)
|
||||
context['title'] = f'enviPath - {current_package.name} - {current_scenario.name}'
|
||||
|
||||
context['meta']['current_package'] = current_package
|
||||
context['object_type'] = 'scenario'
|
||||
context['breadcrumbs'] = breadcrumbs(current_package, 'scenario', current_scenario)
|
||||
|
||||
context['scenario'] = current_scenario
|
||||
|
||||
return render(request, 'objects/scenario.html', context)
|
||||
|
||||
|
||||
|
||||
|
||||
### END UNTESTED
|
||||
|
||||
|
||||
@ -12,6 +12,7 @@ dependencies = [
|
||||
"django-ninja>=1.4.1",
|
||||
"django-polymorphic>=4.1.0",
|
||||
"enviformer",
|
||||
"envipy-additional-information",
|
||||
"envipy-plugins",
|
||||
"epam-indigo>=1.30.1",
|
||||
"gunicorn>=23.0.0",
|
||||
@ -28,3 +29,4 @@ dependencies = [
|
||||
[tool.uv.sources]
|
||||
enviformer = { git = "ssh://git@git.envipath.com/enviPath/enviformer.git", rev = "v0.1.0" }
|
||||
envipy-plugins = { git = "ssh://git@git.envipath.com/enviPath/enviPy-plugins.git", rev = "v0.1.0" }
|
||||
envipy-additional-information = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git" }
|
||||
|
||||
0
templates/actions/objects/scenario.html
Normal file
0
templates/actions/objects/scenario.html
Normal file
12
templates/errors/user_account_inactive.html
Normal file
12
templates/errors/user_account_inactive.html
Normal file
@ -0,0 +1,12 @@
|
||||
{% extends "framework.html" %}
|
||||
{% load static %}
|
||||
{% block content %}
|
||||
|
||||
<div class="alert alert-error" role="alert">
|
||||
<h4 class="alert-heading">Your account has not been activated yet!</h4>
|
||||
<p>Your account has not been activated yet. If you have question <a href="mailto:admin@envipath.org">contact
|
||||
us.</a>
|
||||
</p>
|
||||
</div>
|
||||
|
||||
{% endblock content %}
|
||||
51
templates/objects/scenario.html
Normal file
51
templates/objects/scenario.html
Normal file
@ -0,0 +1,51 @@
|
||||
{% extends "framework.html" %}
|
||||
|
||||
{% block content %}
|
||||
|
||||
{% block action_modals %}
|
||||
|
||||
{% endblock action_modals %}
|
||||
<div class="panel-group" id="scenario-detail">
|
||||
<div class="panel panel-default">
|
||||
<div class="panel-heading" id="headingPanel" style="font-size:2rem;height: 46px">
|
||||
{{ scenario.name }}
|
||||
<div id="actionsButton"
|
||||
style="float: right;font-weight: normal;font-size: medium;position: relative; top: 50%; transform: translateY(-50%);z-index:100;"
|
||||
class="dropdown"><a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button"
|
||||
aria-haspopup="true" aria-expanded="false"><span
|
||||
class="glyphicon glyphicon-wrench"></span> Actions <span class="caret"></span><span
|
||||
style="padding-right:1em"></span></a>
|
||||
<ul id="actionsList" class="dropdown-menu">
|
||||
{% block actions %}
|
||||
{% include "actions/objects/scenario.html" %}
|
||||
{% endblock %}
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="table-responsive">
|
||||
<table id="scenario-table" class="table table-bordered table-striped table-hover">
|
||||
<tbody>
|
||||
<tr>
|
||||
<th>Property</th>
|
||||
<th>Value</th>
|
||||
<th>Unit</th>
|
||||
<th>Remove</th>
|
||||
</tr>
|
||||
|
||||
{% for ai in scenario.get_additional_information %}
|
||||
<tr>
|
||||
<td>{{ ai.property_name|safe }} </td>
|
||||
<td> {{ ai.property_data|safe }} </td>
|
||||
<td> {{ ai.property_unit|safe }} </td>
|
||||
<td></td>
|
||||
</tr>
|
||||
{% endfor %}
|
||||
|
||||
</tbody>
|
||||
</table>
|
||||
</div>
|
||||
|
||||
|
||||
{% endblock content %}
|
||||
10
uv.lock
generated
10
uv.lock
generated
@ -403,6 +403,7 @@ dependencies = [
|
||||
{ name = "django-ninja" },
|
||||
{ name = "django-polymorphic" },
|
||||
{ name = "enviformer" },
|
||||
{ name = "envipy-additional-information" },
|
||||
{ name = "envipy-plugins" },
|
||||
{ name = "epam-indigo" },
|
||||
{ name = "gunicorn" },
|
||||
@ -425,6 +426,7 @@ requires-dist = [
|
||||
{ name = "django-ninja", specifier = ">=1.4.1" },
|
||||
{ name = "django-polymorphic", specifier = ">=4.1.0" },
|
||||
{ name = "enviformer", git = "ssh://git@git.envipath.com/enviPath/enviformer.git?rev=v0.1.0" },
|
||||
{ name = "envipy-additional-information", git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git" },
|
||||
{ name = "envipy-plugins", git = "ssh://git@git.envipath.com/enviPath/enviPy-plugins.git?rev=v0.1.0" },
|
||||
{ name = "epam-indigo", specifier = ">=1.30.1" },
|
||||
{ name = "gunicorn", specifier = ">=23.0.0" },
|
||||
@ -438,6 +440,14 @@ requires-dist = [
|
||||
{ name = "setuptools", specifier = ">=80.8.0" },
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "envipy-additional-information"
|
||||
version = "0.1.0"
|
||||
source = { git = "ssh://git@git.envipath.com/enviPath/enviPy-additional-information.git#4804b24b3479bed6108a49e4401bff8947c03cbd" }
|
||||
dependencies = [
|
||||
{ name = "pydantic" },
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "envipy-plugins"
|
||||
version = "0.1.0"
|
||||
|
||||
Reference in New Issue
Block a user