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linkml · Jul 30, 2021 · d69690c · d69690c
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diff --git a/README.md b/README.md
@@ -3,3 +3,27 @@
 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
 
 This builds on [json-flattener](https://github.com/cmungall/json-flattener)
+
+## Command Line Usage
+
+Denormalizing conversion from YAML instance data to TSV
+
+```
+link-convert \
+  -s examples/bookshop.schema.yaml \
+  -C Shop \
+  -S all_book_series \
+  -o examples/shop1.instance.tsv \
+  examples/shop1.instance.yaml
+```
+
+Converting back to YAML/JSON:
+
+```
+link-convert \
+  -s examples/bookshop.schema.yaml \
+  -C Shop \
+  -S all_book_series \
+  -o examples/shop1-troundtrip.instance.json \
+  examples/shop1.instance.tsv
+```
diff --git a/examples/bookshop.schema.yaml b/examples/bookshop.schema.yaml
@@ -0,0 +1,112 @@
+id: https://w3id.org/example
+name: example
+description: example
+imports:
+- linkml:types
+prefixes:
+  linkml: https://w3id.org/linkml/
+  example: https://w3id.org/example
+default_prefix: example
+types: {}
+classes:
+  creative work:
+    slots:
+      - id
+      - name
+      - genres
+      - creator
+      - genres
+      - summary
+      - reviews
+  book:
+    is_a: creative work
+    slots:
+      - price
+      - inStock
+  book series:
+    is_a: creative work
+    slots:
+      - books
+      - genres
+      - price
+  author:
+    slots:
+      - name
+      - genres
+      - from_country
+  shop:
+    slots:
+      - all_book_series
+  country:
+    slots:
+      - name
+    slot_usage:
+      name:
+        identifier: true
+  review:
+    slots:
+      - creator
+      - rating
+      - review_text
+
+
+slots:
+  id:
+    range: string
+    identifier: true
+    examples:
+    - value: '123'
+  book_category:
+    range: string
+    examples:
+    - value: book
+    multivalued: true
+  name:
+    range: string
+    examples:
+    - value: Consider Phlebas
+  price:
+    range: float
+    examples:
+    - value: '7.99'
+  inStock:
+    range: string
+    examples:
+    - value: 'true'
+  creator:
+    range: author
+    examples:
+    - value: Ian M Banks
+  genres:
+    #range: genre_enum
+    range: string
+    multivalued: true
+  from_country:
+    range: country
+  books:
+    range: book
+    multivalued: true
+    inlined: true
+    inlined_as_list: true
+  all_book_series:
+    range: book series
+    multivalued: true
+    inlined: true
+    inlined_as_list: true
+  summary:
+  reviews:
+    multivalued: true
+    range: review
+  rating:
+    range: integer
+  review_text:
+
+enums:
+  genre_enum:
+    permissible_values:
+      scifi:
+      fantasy:
+      western:
+      romance:
+      modern:
+
diff --git a/examples/shop1-troundtrip.instance.json b/examples/shop1-troundtrip.instance.json
@@ -0,0 +1,116 @@
+{
+  "all_book_series": [
+    {
+      "id": "S001",
+      "name": "Lord of the Rings",
+      "genres": [
+        "fantasy"
+      ],
+      "creator": {
+        "name": "JRR Tolkein",
+        "from_country": "England"
+      },
+      "books": [
+        {
+          "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
+        }
+      ]
+    },
+    {
+      "id": "S002",
+      "name": "The Culture Series",
+      "genres": [
+        "scifi"
+      ],
+      "creator": {
+        "name": "Ian M Banks",
+        "from_country": "Scotland"
+      },
+      "books": [
+        {
+          "id": "S002.1",
+          "name": "Consider Phlebas",
+          "price": 5.99
+        },
+        {
+          "id": "S002.2",
+          "name": "Player of Games",
+          "price": 5.99
+        }
+      ]
+    },
+    {
+      "id": "S003",
+      "name": "Book of the New Sun",
+      "genres": [
+        "scifi",
+        "fantasy"
+      ],
+      "creator": {
+        "name": "Gene Wolfe",
+        "genres": [
+          "scifi",
+          "fantasy"
+        ],
+        "from_country": "USA"
+      },
+      "books": [
+        {
+          "id": "S003.1",
+          "name": "Shadow of the Torturer"
+        },
+        {
+          "id": "S003.2",
+          "name": "Claw of the Conciliator",
+          "price": 6.99
+        }
+      ]
+    },
+    {
+      "id": "S004",
+      "name": "Example with single book",
+      "creator": {
+        "name": "Ms Writer",
+        "genres": [
+          "romance"
+        ],
+        "from_country": "USA"
+      },
+      "books": [
+        {
+          "id": "S004.1",
+          "name": "Blah"
+        }
+      ]
+    },
+    {
+      "id": "S005",
+      "name": "Example with no books",
+      "creator": {
+        "name": "Mr Unproductive",
+        "genres": [
+          "romance",
+          "scifi",
+          "fantasy"
+        ],
+        "from_country": "USA"
+      }
+    }
+  ],
+  "@type": "Shop"
+}
diff --git a/examples/shop1.instance.tsv b/examples/shop1.instance.tsv
@@ -0,0 +1,6 @@
+id	name	genres	creator_json	creator_name	creator_from_country	books_json	books_summary	books_price	books_name	books_id	creator_genres
+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]	
+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]	
+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]
+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]
+S005	Example with no books		{\"name\": \"Mr Unproductive\", \"genres\": [\"romance\", \"scifi\", \"fantasy\"], \"from_country\": \"USA\"}	Mr Unproductive	USA						[romance|scifi|fantasy]
diff --git a/examples/shop1.instance.yaml b/examples/shop1.instance.yaml
@@ -0,0 +1,73 @@
+all_book_series:
+- id: S001
+  name: Lord of the Rings
+  genres:
+    - fantasy
+  creator:
+    name: JRR Tolkein
+    from_country: England
+  books:
+    - id: S001.1
+      name: Fellowship of the Ring
+      price: 5.99
+      summary: Hobbits
+    - id: S001.2
+      name: The Two Towers
+      price: 5.99
+      summary: More hobbits
+    - id: S001.3
+      name: Return of the King
+      price: 6.99
+      summary: Yet more hobbits
+- id: S002
+  name: The Culture Series
+  genres:
+    - scifi
+  creator:
+    name: Ian M Banks
+    from_country: Scotland
+  books:
+    - id: S002.1
+      name: Consider Phlebas
+      price: 5.99
+    - id: S002.2
+      name: Player of Games
+      price: 5.99
+- id: S003
+  name: Book of the New Sun
+  genres:
+    - scifi
+    - fantasy
+  creator:
+    name: Gene Wolfe
+    from_country: USA
+    genres:
+      - scifi
+      - fantasy
+  books:
+    - id: S003.1
+      name: Shadow of the Torturer
+      # deliberately omit price information
+    - id: S003.2
+      name: Claw of the Conciliator
+      price: 6.99
+- id: S004
+  name: Example with single book
+  creator:
+    name: Ms Writer
+    from_country: USA
+    genres:
+      - romance
+  books:
+    - id: S004.1
+      name: Blah
+- id: S005
+  name: Example with no books
+  creator:
+    name: Mr Unproductive
+    from_country: USA
+    genres:
+      - romance
+      - scifi
+      - fantasy
+