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‎README.md‎

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Extension to linkml-runtime for converting between instances of LinkML models and CSVs. This may involve selective normalization/denormalization, plus serialization of selected elements as JSON/YAML
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This builds on [json-flattener](https://github.com/cmungall/json-flattener)
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## Command Line Usage
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Denormalizing conversion from YAML instance data to TSV
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```
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link-convert \
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-s examples/bookshop.schema.yaml \
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-C Shop \
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-S all_book_series \
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-o examples/shop1.instance.tsv \
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examples/shop1.instance.yaml
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```
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Converting back to YAML/JSON:
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```
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link-convert \
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-s examples/bookshop.schema.yaml \
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-C Shop \
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-S all_book_series \
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-o examples/shop1-troundtrip.instance.json \
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examples/shop1.instance.tsv
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```

‎examples/bookshop.schema.yaml‎

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id: https://w3id.org/example
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name: example
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description: example
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imports:
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- linkml:types
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prefixes:
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linkml: https://w3id.org/linkml/
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example: https://w3id.org/example
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default_prefix: example
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types: {}
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classes:
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creative work:
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slots:
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- id
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- name
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- genres
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- creator
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- genres
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- summary
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- reviews
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book:
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is_a: creative work
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slots:
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- price
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- inStock
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book series:
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is_a: creative work
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slots:
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- books
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- genres
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- price
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author:
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slots:
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- name
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- genres
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- from_country
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shop:
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slots:
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- all_book_series
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country:
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slots:
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- name
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slot_usage:
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name:
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identifier: true
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review:
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slots:
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- creator
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- rating
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- review_text
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slots:
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id:
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range: string
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identifier: true
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examples:
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- value: '123'
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book_category:
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range: string
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examples:
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- value: book
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multivalued: true
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name:
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range: string
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examples:
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- value: Consider Phlebas
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price:
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range: float
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examples:
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- value: '7.99'
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inStock:
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range: string
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examples:
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- value: 'true'
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creator:
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range: author
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examples:
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- value: Ian M Banks
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genres:
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#range: genre_enum
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range: string
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multivalued: true
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from_country:
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range: country
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books:
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range: book
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multivalued: true
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inlined: true
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inlined_as_list: true
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all_book_series:
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range: book series
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multivalued: true
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inlined: true
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inlined_as_list: true
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summary:
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reviews:
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multivalued: true
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range: review
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rating:
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range: integer
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review_text:
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enums:
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genre_enum:
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permissible_values:
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scifi:
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fantasy:
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western:
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romance:
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modern:
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‎examples/shop1-troundtrip.instance.json‎

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{
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"all_book_series": [
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{
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"id": "S001",
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"name": "Lord of the Rings",
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"genres": [
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"fantasy"
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],
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"creator": {
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"name": "JRR Tolkein",
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"from_country": "England"
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},
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"books": [
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{
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"id": "S001.1",
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"name": "Fellowship of the Ring",
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"summary": "Hobbits",
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"price": 5.99
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},
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{
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"id": "S001.2",
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"name": "The Two Towers",
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"summary": "More hobbits",
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"price": 5.99
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},
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{
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"id": "S001.3",
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"name": "Return of the King",
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"summary": "Yet more hobbits",
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"price": 6.99
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}
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]
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},
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{
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"id": "S002",
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"name": "The Culture Series",
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"genres": [
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"scifi"
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],
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"creator": {
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"name": "Ian M Banks",
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"from_country": "Scotland"
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},
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"books": [
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{
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"id": "S002.1",
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"name": "Consider Phlebas",
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"price": 5.99
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},
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{
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"id": "S002.2",
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"name": "Player of Games",
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"price": 5.99
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}
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]
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},
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{
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"id": "S003",
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"name": "Book of the New Sun",
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"genres": [
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"scifi",
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"fantasy"
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],
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"creator": {
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"name": "Gene Wolfe",
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"genres": [
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"scifi",
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"fantasy"
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],
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"from_country": "USA"
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},
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"books": [
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{
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"id": "S003.1",
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"name": "Shadow of the Torturer"
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},
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{
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"id": "S003.2",
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"name": "Claw of the Conciliator",
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"price": 6.99
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}
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]
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},
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{
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"id": "S004",
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"name": "Example with single book",
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"creator": {
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"name": "Ms Writer",
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"genres": [
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"romance"
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],
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"from_country": "USA"
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},
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"books": [
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{
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"id": "S004.1",
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"name": "Blah"
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}
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]
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},
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{
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"id": "S005",
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"name": "Example with no books",
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"creator": {
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"name": "Mr Unproductive",
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"genres": [
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"romance",
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"scifi",
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"fantasy"
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],
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"from_country": "USA"
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}
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}
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],
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"@type": "Shop"
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}

‎examples/shop1.instance.tsv‎

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id name genres creator_json creator_name creator_from_country books_json books_summary books_price books_name books_id creator_genres
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S001 Lord of the Rings [fantasy] {\"name\": \"JRR Tolkein\", \"from_country\": \"England\"} JRR Tolkein England [{\"id\": \"S001.1\", \"name\": \"Fellowship of the Ring\", \"summary\": \"Hobbits\", \"price\": 5.99}, {\"id\": \"S001.2\", \"name\": \"The Two Towers\", \"summary\": \"More hobbits\", \"price\": 5.99}, {\"id\": \"S001.3\", \"name\": \"Return of the King\", \"summary\": \"Yet more hobbits\", \"price\": 6.99}] [Hobbits|More hobbits|Yet more hobbits] [5.99|5.99|6.99] [Fellowship of the Ring|The Two Towers|Return of the King] [S001.1|S001.2|S001.3]
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S002 The Culture Series [scifi] {\"name\": \"Ian M Banks\", \"from_country\": \"Scotland\"} Ian M Banks Scotland [{\"id\": \"S002.1\", \"name\": \"Consider Phlebas\", \"price\": 5.99}, {\"id\": \"S002.2\", \"name\": \"Player of Games\", \"price\": 5.99}] [5.99|5.99] [Consider Phlebas|Player of Games] [S002.1|S002.2]
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S003 Book of the New Sun [scifi|fantasy] {\"name\": \"Gene Wolfe\", \"genres\": [\"scifi\", \"fantasy\"], \"from_country\": \"USA\"} Gene Wolfe USA [{\"id\": \"S003.1\", \"name\": \"Shadow of the Torturer\"}, {\"id\": \"S003.2\", \"name\": \"Claw of the Conciliator\", \"price\": 6.99}] [|6.99] [Shadow of the Torturer|Claw of the Conciliator] [S003.1|S003.2] [scifi|fantasy]
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S004 Example with single book {\"name\": \"Ms Writer\", \"genres\": [\"romance\"], \"from_country\": \"USA\"} Ms Writer USA [{\"id\": \"S004.1\", \"name\": \"Blah\"}] [Blah] [S004.1] [romance]
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S005 Example with no books {\"name\": \"Mr Unproductive\", \"genres\": [\"romance\", \"scifi\", \"fantasy\"], \"from_country\": \"USA\"} Mr Unproductive USA [romance|scifi|fantasy]

‎examples/shop1.instance.yaml‎

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all_book_series:
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- id: S001
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name: Lord of the Rings
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genres:
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- fantasy
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creator:
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name: JRR Tolkein
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from_country: England
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books:
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- id: S001.1
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name: Fellowship of the Ring
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price: 5.99
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summary: Hobbits
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- id: S001.2
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name: The Two Towers
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price: 5.99
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summary: More hobbits
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- id: S001.3
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name: Return of the King
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price: 6.99
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summary: Yet more hobbits
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- id: S002
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name: The Culture Series
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genres:
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- scifi
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creator:
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name: Ian M Banks
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from_country: Scotland
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books:
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- id: S002.1
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name: Consider Phlebas
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price: 5.99
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- id: S002.2
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name: Player of Games
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price: 5.99
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- id: S003
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name: Book of the New Sun
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genres:
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- scifi
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- fantasy
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creator:
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name: Gene Wolfe
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from_country: USA
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genres:
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- scifi
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- fantasy
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books:
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- id: S003.1
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name: Shadow of the Torturer
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# deliberately omit price information
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- id: S003.2
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name: Claw of the Conciliator
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price: 6.99
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- id: S004
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name: Example with single book
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creator:
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name: Ms Writer
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from_country: USA
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genres:
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- romance
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books:
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- id: S004.1
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name: Blah
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- id: S005
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name: Example with no books
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creator:
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name: Mr Unproductive
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from_country: USA
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genres:
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- romance
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- scifi
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- fantasy
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