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Merge pull request #5 from linkml/material-process-data
added child process container slots and child process data
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# This file is public in git. No sensitive info allowed. | ||
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###### schema definition variables, used by makefile | ||
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LINKML_SCHEMA_NAME="cmdr" | ||
LINKML_SCHEMA_AUTHOR="LinkML Team <admin@linkml.org>" | ||
LINKML_SCHEMA_DESCRIPTION="Core Model for Clinical Data Collection" | ||
LINKML_SCHEMA_SOURCE_PATH="src/cmdr/schema/cmdr.yaml" | ||
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###### linkml generator variables, used by makefile | ||
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## gen-project configuration file | ||
LINKML_GENERATORS_CONFIG_YAML= --config-file config.yaml | ||
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## pass args if gendoc ignores config.yaml (i.e. --no-mergeimports) | ||
LINKML_GENERATORS_DOC_ARGS= | ||
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## pass args to workaround genowl rdfs config bug (linkml#1453) | ||
## (i.e. --no-type-objects --no-metaclasses --metadata-profile rdfs) | ||
LINKML_GENERATORS_OWL_ARGS= | ||
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## pass args to trigger experimental java/typescript generation | ||
LINKML_GENERATORS_JAVA_ARGS= | ||
LINKML_GENERATORS_TYPESCRIPT_ARGS= | ||
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LINKML_SCHEMA_GOOGLE_SHEET_ID="1wVoaiFg47aT9YWNeRfTZ8tYHN8s8PAuDx5i2HUcDpvQ" | ||
LINKML_SCHEMA_GOOGLE_SHEET_TABS="personinfo enums" |
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# Configuration of generators (defaults illustrated) | ||
--- | ||
generator_args: | ||
excel: | ||
mergeimports: true | ||
jsonschema: {} | ||
owl: | ||
mergeimports: true | ||
metaclasses: true | ||
type_objects: true | ||
# throws 'Cannot handle metadata profile: rdfs' | ||
# metadata_profile: rdfs | ||
markdown: | ||
mergeimports: true | ||
graphql: | ||
mergeimports: true | ||
java: | ||
mergeimports: true | ||
metadata: true | ||
jsonld: | ||
mergeimports: true | ||
jsonschema: | ||
mergeimports: true | ||
jsonldcontext: | ||
mergeimports: true | ||
python: | ||
mergeimports: true | ||
prefixmap: | ||
mergeimports: true | ||
proto: | ||
mergeimports: true | ||
shacl: | ||
mergeimports: true | ||
shex: | ||
mergeimports: true | ||
sqlddl: | ||
mergeimports: true | ||
typescript: | ||
mergeimports: true | ||
metadata: true | ||
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... | ||
includes: | ||
- jsonschema | ||
- python | ||
- owl | ||
- shex | ||
- shacl | ||
- prefixmap | ||
excludes: | ||
- graphql | ||
- sqlschema | ||
- protobuf |
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{ | ||
"comments": { | ||
"description": "Auto generated by LinkML jsonld context generator", | ||
"generation_date": "2023-03-07T15:56:42", | ||
"generation_date": "2024-08-05T13:47:38", | ||
"source": "cmdr.yaml" | ||
}, | ||
"@context": { | ||
"OBI": { | ||
"@id": "http://purl.obolibrary.org/obo/OBI_", | ||
"@prefix": true | ||
}, | ||
"OBI": "http://example.org/UNKNOWN/OBI/", | ||
"PATO": { | ||
"@id": "http://purl.obolibrary.org/obo/PATO_", | ||
"@prefix": true | ||
}, | ||
"TEMP": "https://example.org/TEMP/", | ||
"biolink": "https://w3id.org/biolink/", | ||
"cmdr": "https://w3id.org/linkml/cmdr/", | ||
"example": "https://example.org/", | ||
"linkml": "https://w3id.org/linkml/", | ||
"schema": "http://schema.org/", | ||
"@vocab": "https://w3id.org/linkml/cmdr/", | ||
"comparator": { | ||
"@id": "TEMP:comparator" | ||
}, | ||
"concentration": { | ||
"@id": "TEMP:concentration" | ||
}, | ||
"has_input": { | ||
"@id": "TEMP:has_input" | ||
}, | ||
"has_numeric_value": { | ||
"@id": "TEMP:has_numeric_value" | ||
}, | ||
"has_output": { | ||
"@id": "TEMP:has_output" | ||
}, | ||
"has_raw_value": { | ||
"@id": "TEMP:has_raw_value" | ||
}, | ||
"has_unit": { | ||
"@id": "TEMP:has_unit" | ||
}, | ||
"id": "@id", | ||
"includes": { | ||
"@id": "TEMP:includes" | ||
}, | ||
"investigations": { | ||
"@id": "TEMP:investigations" | ||
}, | ||
"involved_in": { | ||
"@id": "TEMP:involved_in" | ||
}, | ||
"material_processings": { | ||
"@id": "TEMP:material_processings" | ||
}, | ||
"materials": { | ||
"@id": "TEMP:materials" | ||
}, | ||
"name": { | ||
"@id": "TEMP:name" | ||
}, | ||
"part_of": { | ||
"@id": "TEMP:part_of" | ||
}, | ||
"participations": { | ||
"@id": "TEMP:participations" | ||
}, | ||
"source": { | ||
"@id": "TEMP:source" | ||
}, | ||
"specimen_collection_processes": { | ||
"@id": "TEMP:specimen_collection_processes" | ||
}, | ||
"subjects": { | ||
"@id": "TEMP:subjects" | ||
}, | ||
"used_in": { | ||
"@id": "TEMP:used_in" | ||
}, | ||
"volume": { | ||
"@id": "TEMP:volume" | ||
}, | ||
"Container": { | ||
"@id": "TEMP:Container" | ||
}, | ||
"DataObject": { | ||
"@id": "TEMP:DataObject" | ||
}, | ||
"Investigation": { | ||
"@id": "TEMP:Investigation" | ||
}, | ||
"MaterialEntity": { | ||
"@id": "TEMP:MaterialEntity" | ||
}, | ||
"MaterialProcessing": { | ||
"@id": "OBI:0000094" | ||
}, | ||
"Participation": { | ||
"@id": "TEMP:Participation" | ||
}, | ||
"Process": { | ||
"@id": "TEMP:Process" | ||
}, | ||
"Quantity": { | ||
"@id": "TEMP:Quantity" | ||
}, | ||
"SpecimenCollectionProcess": { | ||
"@id": "OBI:0000659" | ||
}, | ||
"Subject": { | ||
"@id": "TEMP:Subject" | ||
} | ||
} | ||
} |
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{ | ||
"OBI": "http://purl.obolibrary.org/obo/OBI_", | ||
"OBI": "http://example.org/UNKNOWN/OBI/", | ||
"PATO": "http://purl.obolibrary.org/obo/PATO_", | ||
"TEMP": "https://example.org/TEMP/", | ||
"biolink": "https://w3id.org/biolink/", | ||
"cmdr": "https://w3id.org/linkml/cmdr/", | ||
"example": "https://example.org/", | ||
"linkml": "https://w3id.org/linkml/", | ||
"schema": "http://schema.org/", | ||
"Container": { | ||
"@id": "TEMP:Container" | ||
}, | ||
"DataObject": { | ||
"@id": "TEMP:DataObject" | ||
}, | ||
"Investigation": { | ||
"@id": "TEMP:Investigation" | ||
}, | ||
"MaterialEntity": { | ||
"@id": "TEMP:MaterialEntity" | ||
}, | ||
"MaterialProcessing": { | ||
"@id": "OBI:0000094" | ||
}, | ||
"Participation": { | ||
"@id": "TEMP:Participation" | ||
}, | ||
"Process": { | ||
"@id": "TEMP:Process" | ||
}, | ||
"Quantity": { | ||
"@id": "TEMP:Quantity" | ||
}, | ||
"SpecimenCollectionProcess": { | ||
"@id": "OBI:0000659" | ||
}, | ||
"Subject": { | ||
"@id": "TEMP:Subject" | ||
} | ||
} |
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@prefix cmdr: <https://w3id.org/linkml/cmdr/> . | ||
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . | ||
@prefix sh: <http://www.w3.org/ns/shacl#> . | ||
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> . | ||
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<https://example.org/TEMP/Container> a sh:NodeShape ; | ||
cmdr:Container a sh:NodeShape ; | ||
sh:closed true ; | ||
sh:ignoredProperties ( rdf:type ) ; | ||
sh:property [ sh:class <https://example.org/TEMP/Subject> ; | ||
sh:property [ sh:class cmdr:MaterialEntity ; | ||
sh:nodeKind sh:IRI ; | ||
sh:order 5 ; | ||
sh:path <https://example.org/TEMP/subjects> ], | ||
[ sh:class <https://example.org/TEMP/Investigation> ; | ||
sh:order 0 ; | ||
sh:path cmdr:materials ], | ||
[ sh:class cmdr:Investigation ; | ||
sh:nodeKind sh:IRI ; | ||
sh:order 4 ; | ||
sh:path <https://example.org/TEMP/investigations> ], | ||
[ sh:class <https://example.org/TEMP/MaterialEntity> ; | ||
sh:path cmdr:investigations ], | ||
[ sh:class cmdr:Participation ; | ||
sh:nodeKind sh:IRI ; | ||
sh:order 0 ; | ||
sh:path <https://example.org/TEMP/materials> ], | ||
[ sh:class <http://purl.obolibrary.org/obo/OBI_0000094> ; | ||
sh:order 1 ; | ||
sh:path cmdr:participations ], | ||
[ sh:class cmdr:Subject ; | ||
sh:nodeKind sh:IRI ; | ||
sh:order 2 ; | ||
sh:path <https://example.org/TEMP/material_processings> ], | ||
[ sh:class <https://example.org/TEMP/Participation> ; | ||
sh:order 5 ; | ||
sh:path cmdr:subjects ], | ||
[ sh:class <OBI:0000094> ; | ||
sh:nodeKind sh:IRI ; | ||
sh:order 1 ; | ||
sh:path <https://example.org/TEMP/participations> ], | ||
[ sh:class <http://purl.obolibrary.org/obo/OBI_0000659> ; | ||
sh:order 2 ; | ||
sh:path cmdr:material_processings ], | ||
[ sh:class <OBI:0000659> ; | ||
sh:nodeKind sh:IRI ; | ||
sh:order 3 ; | ||
sh:path <https://example.org/TEMP/specimen_collection_processes> ] ; | ||
sh:targetClass <https://example.org/TEMP/Container> . | ||
sh:path cmdr:specimen_collection_processes ] ; | ||
sh:targetClass cmdr:Container . | ||
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<https://example.org/TEMP/DataObject> a sh:NodeShape ; | ||
cmdr:DataObject a sh:NodeShape ; | ||
sh:closed true ; | ||
sh:description "A DataFile Associated with a Subject or Investigation or MaterialEntity" ; | ||
sh:ignoredProperties ( rdf:type ) ; | ||
sh:targetClass <https://example.org/TEMP/DataObject> . | ||
sh:targetClass cmdr:DataObject . | ||
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<https://example.org/TEMP/Process> a sh:NodeShape ; | ||
cmdr:Process a sh:NodeShape ; | ||
sh:closed false ; | ||
sh:description "A planned process resulting in a material or data" ; | ||
sh:ignoredProperties ( rdf:type ) ; | ||
sh:property [ sh:order 3 ; | ||
sh:path <https://example.org/TEMP/has_output> ], | ||
sh:path cmdr:has_output ], | ||
[ sh:order 2 ; | ||
sh:path <https://example.org/TEMP/has_input> ], | ||
sh:path cmdr:has_input ], | ||
[ sh:maxCount 1 ; | ||
sh:order 0 ; | ||
sh:path <https://example.org/TEMP/id> ], | ||
sh:path cmdr:id ], | ||
[ sh:maxCount 1 ; | ||
sh:order 1 ; | ||
sh:path <https://example.org/TEMP/name> ] ; | ||
sh:targetClass <https://example.org/TEMP/Process> . | ||
sh:path cmdr:name ] ; | ||
sh:targetClass cmdr:Process . | ||
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<http://purl.obolibrary.org/obo/OBI_0000094> a sh:NodeShape ; | ||
<OBI:0000094> a sh:NodeShape ; | ||
sh:closed true ; | ||
sh:description "A planned process which results in physical changes in a specified input material" ; | ||
sh:ignoredProperties ( rdf:type ) ; | ||
sh:property [ sh:maxCount 1 ; | ||
sh:order 3 ; | ||
sh:path <https://example.org/TEMP/name> ], | ||
[ sh:class <https://example.org/TEMP/MaterialEntity> ; | ||
sh:property [ sh:class cmdr:MaterialEntity ; | ||
sh:nodeKind sh:IRI ; | ||
sh:order 0 ; | ||
sh:path <https://example.org/TEMP/has_input> ], | ||
[ sh:class <https://example.org/TEMP/MaterialEntity> ; | ||
sh:path cmdr:has_input ], | ||
[ sh:class cmdr:MaterialEntity ; | ||
sh:nodeKind sh:IRI ; | ||
sh:order 1 ; | ||
sh:path <https://example.org/TEMP/has_output> ], | ||
sh:path cmdr:has_output ], | ||
[ sh:maxCount 1 ; | ||
sh:order 2 ; | ||
sh:path <https://example.org/TEMP/id> ] ; | ||
sh:targetClass <http://purl.obolibrary.org/obo/OBI_0000094> . | ||
sh:path cmdr:id ], | ||
[ sh:maxCount 1 ; | ||
sh:order 3 ; | ||
sh:path cmdr:name ] ; | ||
sh:targetClass <OBI:0000094> . | ||
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<http://purl.obolibrary.org/obo/OBI_0000659> a sh:NodeShape ; | ||
<OBI:0000659> a sh:NodeShape ; | ||
sh:closed true ; | ||
sh:description "A planned process with the objective of collecting a specimen" ; | ||
sh:ignoredProperties ( rdf:type ) ; | ||
sh:property [ sh:class <https://example.org/TEMP/Subject> ; | ||
sh:property [ sh:class cmdr:MaterialEntity ; | ||
sh:nodeKind sh:IRI ; | ||
sh:order 1 ; | ||
sh:path cmdr:has_output ], | ||
[ sh:class cmdr:Subject ; | ||
sh:nodeKind sh:IRI ; | ||
sh:order 0 ; | ||
sh:path <https://example.org/TEMP/has_input> ], | ||
[ sh:maxCount 1 ; | ||
sh:order 3 ; | ||
sh:path <https://example.org/TEMP/name> ], | ||
sh:path cmdr:has_input ], | ||
[ sh:maxCount 1 ; | ||
sh:order 2 ; | ||
sh:path <https://example.org/TEMP/id> ], | ||
[ sh:class <https://example.org/TEMP/MaterialEntity> ; | ||
sh:nodeKind sh:IRI ; | ||
sh:order 1 ; | ||
sh:path <https://example.org/TEMP/has_output> ] ; | ||
sh:targetClass <http://purl.obolibrary.org/obo/OBI_0000659> . | ||
sh:path cmdr:id ], | ||
[ sh:maxCount 1 ; | ||
sh:order 3 ; | ||
sh:path cmdr:name ] ; | ||
sh:targetClass <OBI:0000659> . | ||
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<https://example.org/TEMP/Participation> a sh:NodeShape ; | ||
cmdr:Participation a sh:NodeShape ; | ||
sh:closed true ; | ||
sh:description "Subject/Study participation information" ; | ||
sh:ignoredProperties ( rdf:type ) ; | ||
sh:property [ sh:maxCount 1 ; | ||
sh:order 1 ; | ||
sh:path cmdr:name ], | ||
[ sh:maxCount 1 ; | ||
sh:order 0 ; | ||
sh:path <https://example.org/TEMP/id> ], | ||
[ sh:class <https://example.org/TEMP/Subject> ; | ||
sh:path cmdr:id ], | ||
[ sh:class cmdr:Subject ; | ||
sh:maxCount 1 ; | ||
sh:nodeKind sh:IRI ; | ||
sh:order 3 ; | ||
sh:path <https://example.org/TEMP/includes> ], | ||
[ sh:class <https://example.org/TEMP/Investigation> ; | ||
sh:path cmdr:includes ], | ||
[ sh:class cmdr:Investigation ; | ||
sh:nodeKind sh:IRI ; | ||
sh:order 2 ; | ||
sh:path <https://example.org/TEMP/involved_in> ], | ||
[ sh:maxCount 1 ; | ||
sh:order 1 ; | ||
sh:path <https://example.org/TEMP/name> ] ; | ||
sh:targetClass <https://example.org/TEMP/Participation> . | ||
sh:path cmdr:involved_in ] ; | ||
sh:targetClass cmdr:Participation . | ||
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<https://example.org/TEMP/Quantity> a sh:NodeShape ; | ||
cmdr:Quantity a sh:NodeShape ; | ||
sh:closed true ; | ||
sh:ignoredProperties ( rdf:type ) ; | ||
sh:property [ sh:maxCount 1 ; | ||
sh:order 1 ; | ||
sh:path <https://example.org/TEMP/has_numeric_value> ], | ||
sh:order 0 ; | ||
sh:path cmdr:has_raw_value ], | ||
[ sh:maxCount 1 ; | ||
sh:order 3 ; | ||
sh:path <https://example.org/TEMP/comparator> ], | ||
sh:order 1 ; | ||
sh:path cmdr:has_numeric_value ], | ||
[ sh:maxCount 1 ; | ||
sh:order 2 ; | ||
sh:path <https://example.org/TEMP/has_unit> ], | ||
sh:path cmdr:has_unit ], | ||
[ sh:maxCount 1 ; | ||
sh:order 0 ; | ||
sh:path <https://example.org/TEMP/has_raw_value> ] ; | ||
sh:targetClass <https://example.org/TEMP/Quantity> . | ||
sh:order 3 ; | ||
sh:path cmdr:comparator ] ; | ||
sh:targetClass cmdr:Quantity . | ||
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<https://example.org/TEMP/Investigation> a sh:NodeShape ; | ||
cmdr:Investigation a sh:NodeShape ; | ||
sh:closed true ; | ||
sh:description "General information about the Investigation" ; | ||
sh:ignoredProperties ( rdf:type ) ; | ||
sh:property [ sh:maxCount 1 ; | ||
sh:order 0 ; | ||
sh:path <https://example.org/TEMP/id> ], | ||
[ sh:maxCount 1 ; | ||
sh:order 1 ; | ||
sh:path <https://example.org/TEMP/name> ], | ||
[ sh:class <https://example.org/TEMP/Investigation> ; | ||
sh:path cmdr:id ], | ||
[ sh:class cmdr:Investigation ; | ||
sh:maxCount 1 ; | ||
sh:nodeKind sh:IRI ; | ||
sh:order 2 ; | ||
sh:path <https://example.org/TEMP/part_of> ] ; | ||
sh:targetClass <https://example.org/TEMP/Investigation> . | ||
sh:path cmdr:part_of ], | ||
[ sh:maxCount 1 ; | ||
sh:order 1 ; | ||
sh:path cmdr:name ] ; | ||
sh:targetClass cmdr:Investigation . | ||
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<https://example.org/TEMP/MaterialEntity> a sh:NodeShape ; | ||
cmdr:MaterialEntity a sh:NodeShape ; | ||
sh:closed true ; | ||
sh:description "Physical entity that is an input our output of a process from a Subject" ; | ||
sh:ignoredProperties ( rdf:type ) ; | ||
sh:property [ sh:class <https://example.org/TEMP/Investigation> ; | ||
sh:nodeKind sh:IRI ; | ||
sh:order 2 ; | ||
sh:path <https://example.org/TEMP/used_in> ], | ||
[ sh:class <https://example.org/TEMP/Quantity> ; | ||
sh:property [ sh:maxCount 1 ; | ||
sh:order 1 ; | ||
sh:path cmdr:name ], | ||
[ sh:class cmdr:Subject ; | ||
sh:maxCount 1 ; | ||
sh:nodeKind sh:BlankNode ; | ||
sh:order 5 ; | ||
sh:path <https://example.org/TEMP/concentration> ], | ||
[ sh:class <https://example.org/TEMP/Quantity> ; | ||
sh:nodeKind sh:IRI ; | ||
sh:order 3 ; | ||
sh:path cmdr:source ], | ||
[ sh:class cmdr:Quantity ; | ||
sh:maxCount 1 ; | ||
sh:nodeKind sh:BlankNode ; | ||
sh:order 4 ; | ||
sh:path <https://example.org/TEMP/volume> ], | ||
[ sh:maxCount 1 ; | ||
sh:order 1 ; | ||
sh:path <https://example.org/TEMP/name> ], | ||
sh:path cmdr:volume ], | ||
[ sh:maxCount 1 ; | ||
sh:order 0 ; | ||
sh:path <https://example.org/TEMP/id> ], | ||
[ sh:class <https://example.org/TEMP/Subject> ; | ||
sh:maxCount 1 ; | ||
sh:path cmdr:id ], | ||
[ sh:class cmdr:Investigation ; | ||
sh:nodeKind sh:IRI ; | ||
sh:order 3 ; | ||
sh:path <https://example.org/TEMP/source> ] ; | ||
sh:targetClass <https://example.org/TEMP/MaterialEntity> . | ||
sh:order 2 ; | ||
sh:path cmdr:used_in ], | ||
[ sh:class cmdr:Quantity ; | ||
sh:maxCount 1 ; | ||
sh:nodeKind sh:BlankNode ; | ||
sh:order 5 ; | ||
sh:path cmdr:concentration ] ; | ||
sh:targetClass cmdr:MaterialEntity . | ||
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<https://example.org/TEMP/Subject> a sh:NodeShape ; | ||
cmdr:Subject a sh:NodeShape ; | ||
sh:closed true ; | ||
sh:description "Demographic and clinical information about the subject" ; | ||
sh:ignoredProperties ( rdf:type ) ; | ||
sh:property [ sh:maxCount 1 ; | ||
sh:order 0 ; | ||
sh:path <https://example.org/TEMP/id> ], | ||
[ sh:maxCount 1 ; | ||
sh:order 1 ; | ||
sh:path <https://example.org/TEMP/name> ] ; | ||
sh:targetClass <https://example.org/TEMP/Subject> . | ||
sh:path cmdr:name ], | ||
[ sh:maxCount 1 ; | ||
sh:order 0 ; | ||
sh:path cmdr:id ] ; | ||
sh:targetClass cmdr:Subject . | ||
|
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