Merge pull request linkml#3272 from dalito/validate-tutorial

Validate tutorial as part of standard tests

Author: dalito

docs/intro/tutorial03.md

@@ -71,9 +71,8 @@ linkml-validate -s personinfo.yaml bad-data.yaml
 
 Output:
 
-```text
-[ERROR] [bad-data.yaml/0] '1-800-kryptonite' does not match '^[\\d\\(\\)\\-]+$' in /persons/0/phone
-[ERROR] [bad-data.yaml/0] 'full_name' is a required property in /persons/1
+```{literalinclude} ../../examples/tutorial/tutorial03/validate-bad-data-errors.txt
+:language: text
 ```
 
 This indicates there are two issues with our data. The first says that the phone number of the first entry in the persons list (`/persons/0/phone`) doesn’t conform to the regular expression syntax we stated. The second says that we are missing the required `full_name` slot on the second entry in the person list (`/persons/1`).
@@ -93,8 +92,8 @@ linkml-validate -s personinfo.yaml better-data.yaml
 
 Output:
 
-```text
-[ERROR] [better-data.yaml/0] '1-800-kryptonite' does not match '^[\\d\\(\\)\\-]+$' in /persons/0/phone
+```{literalinclude} ../../examples/tutorial/tutorial03/validate-better-data-errors.txt
+:language: text
 ```
 
 We have successfully fixed one of the issues with the data!

docs/intro/tutorial04.md

@@ -44,23 +44,8 @@ linkml-convert -s personinfo.yaml -t rdf data.yaml
 
 Outputs:
 
-```turtle
-@prefix ORCID: <https://orcid.org/> .
-@prefix personinfo: <https://w3id.org/linkml/examples/personinfo/> .
-@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
-
-ORCID:1234 a personinfo:Person ;
-    personinfo:age 33 ;
-    personinfo:full_name "Clark Kent" ;
-    personinfo:phone "555-555-5555" .
-
-ORCID:4567 a personinfo:Person ;
-    personinfo:age 34 ;
-    personinfo:full_name "Lois Lane" .
-
-[] a personinfo:Container ;
-    personinfo:persons ORCID:1234,
-        ORCID:4567 .
+```{literalinclude} ../../examples/tutorial/tutorial04/data.ttl
+:language: turtle
 ```
 
 Note that each person is now represented by an ORCID URI. This is a
@@ -90,25 +75,8 @@ linkml-convert -s personinfo-semantic.yaml -t rdf data.yaml
 
 Outputs:
 
-```turtle
-@prefix ORCID: <https://orcid.org/> .
-@prefix personinfo: <https://w3id.org/linkml/examples/personinfo/> .
-@prefix schema1: <http://schema.org/> .
-@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
-
-ORCID:1234 a schema1:Person ;
-    schema1:name "Clark Kent" ;
-    schema1:telephone "555-555-5555" ;
-    personinfo:age 33 .
-
-ORCID:4567 a schema1:Person ;
-    schema1:name "Lois Lane" ;
-    personinfo:age 34 .
-
-[] a personinfo:Container ;
-    personinfo:persons ORCID:1234,
-        ORCID:4567 .
-
+```{literalinclude} ../../examples/tutorial/tutorial04/data-semantic.ttl
+:language: turtle
 ```
 
 Note that the prefixes are hidden but the effect is to reuse URIs such as [schema:telephone](http://schema.org/telephone)
@@ -127,41 +95,8 @@ gen-jsonld-context --no-metadata personinfo-semantic.yaml
 
 Outputs:
 
-```json
-{
-   "@context": {
-      "xsd": "http://www.w3.org/2001/XMLSchema#",
-      "ORCID": "https://orcid.org/",
-      "linkml": "https://w3id.org/linkml/",
-      "personinfo": "https://w3id.org/linkml/examples/personinfo/",
-      "schema": "http://schema.org/",
-      "@vocab": "https://w3id.org/linkml/examples/personinfo/",
-      "persons": {
-         "@type": "schema:Person",
-         "@id": "persons"
-      },
-      "age": {
-         "@type": "xsd:integer",
-         "@id": "age"
-      },
-      "aliases": {
-         "@id": "aliases"
-      },
-      "full_name": {
-         "@id": "schema:name"
-      },
-      "id": "@id",
-      "phone": {
-         "@id": "schema:telephone"
-      },
-      "Container": {
-         "@id": "Container"
-      },
-      "Person": {
-         "@id": "schema:Person"
-      }
-   }
-}
+```{literalinclude} ../../examples/tutorial/tutorial04/personinfo-semantic.context.jsonld
+:language: json
 ```
 
 NOTE: currently you need to declare your own type object and map this to `rdf:type` for typing information to be shown
@@ -177,68 +112,8 @@ gen-shex --no-metadata personinfo-semantic.yaml
 
 Outputs:
 
-```shex
-# metamodel_version: 1.7.0
-BASE <https://w3id.org/linkml/examples/personinfo/>
-PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
-PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
-PREFIX linkml: <https://w3id.org/linkml/>
-PREFIX schema1: <http://schema.org/>
-
-
-linkml:String xsd:string
-
-linkml:Integer xsd:integer
-
-linkml:Boolean xsd:boolean
-
-linkml:Float xsd:float
-
-linkml:Double xsd:double
-
-linkml:Decimal xsd:decimal
-
-linkml:Time xsd:time
-
-linkml:Date xsd:date
-
-linkml:Datetime xsd:dateTime
-
-linkml:DateOrDatetime linkml:DateOrDatetime
-
-linkml:Uriorcurie IRI
-
-linkml:Curie xsd:string
-
-linkml:Uri IRI
-
-linkml:Ncname xsd:string
-
-linkml:Objectidentifier IRI
-
-linkml:Nodeidentifier NONLITERAL
-
-linkml:Jsonpointer xsd:string
-
-linkml:Jsonpath xsd:string
-
-linkml:Sparqlpath xsd:string
-
-<Container> CLOSED {
-    (  $<Container_tes> <persons> @<Person> * ;
-       rdf:type [ <Container> ] ?
-    )
-}
-
-<Person> CLOSED {
-    (  $<Person_tes> (  schema1:name @linkml:String ;
-          <aliases> @linkml:String * ;
-          schema1:telephone @linkml:String ? ;
-          <age> @linkml:Integer ?
-       ) ;
-       rdf:type [ schema1:Person ]
-    )
-}
+```{literalinclude} ../../examples/tutorial/tutorial04/personinfo-semantic.shex
+:language: shex
 ```
 
 
@@ -250,46 +125,8 @@ Outputs:
 
 <!-- compare_rdf -->
 <!-- NOTE: the order of properties is non-deterministic so we cannot compare string directly>
-```turtle
-@prefix personinfo: <https://w3id.org/linkml/examples/personinfo/> .
-@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
-@prefix schema1: <http://schema.org/> .
-@prefix sh: <http://www.w3.org/ns/shacl#> .
-@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
-
-personinfo:Container a sh:NodeShape ;
-    sh:closed true ;
-    sh:ignoredProperties ( rdf:type ) ;
-    sh:property [ sh:class schema1:Person ;
-            sh:nodeKind sh:IRI ;
-            sh:order 0 ;
-            sh:path personinfo:persons ] ;
-    sh:targetClass personinfo:Container .
-
-schema1:Person a sh:NodeShape ;
-    sh:closed true ;
-    sh:ignoredProperties ( rdf:type ) ;
-    sh:property [ sh:maxCount 1 ;
-            sh:maxInclusive 200 ;
-            sh:minInclusive 0 ;
-            sh:order 4 ;
-            sh:path personinfo:age ],
-        [ sh:description "name of the person" ;
-            sh:maxCount 1 ;
-            sh:minCount 1 ;
-            sh:order 1 ;
-            sh:path schema1:name ],
-        [ sh:maxCount 1 ;
-            sh:order 0 ;
-            sh:path personinfo:id ],
-        [ sh:description "other names for the person" ;
-            sh:order 2 ;
-            sh:path personinfo:aliases ],
-        [ sh:maxCount 1 ;
-            sh:order 3 ;
-            sh:path schema1:telephone ;
-            sh:pattern "^[\\d\\(\\)\\-]+$" ] ;
-    sh:targetClass schema1:Person .
+```{literalinclude} ../../examples/tutorial/tutorial04/personinfo-semantic.shacl.ttl
+:language: turtle
 ```
 
 <!-- TODO: SPARQL -->

docs/intro/tutorial05.md

@@ -13,48 +13,8 @@ For illustration, we will take the schema we developed in the last section:
 
 personinfo.yaml:
 
-```yaml
-id: https://w3id.org/linkml/examples/personinfo
-name: personinfo
-prefixes:                                  ## Note are adding 3 new ones here
-  linkml: https://w3id.org/linkml/
-  schema: http://schema.org/
-  personinfo: https://w3id.org/linkml/examples/personinfo/
-  ORCID: https://orcid.org/
-imports:
-  - linkml:types
-default_range: string
-
-classes:
-  Person:
-    class_uri: schema:Person              ## reuse schema.org vocabulary
-    attributes:
-      id:
-        identifier: true
-      full_name:
-        required: true
-        description:
-          name of the person
-        slot_uri: schema:name             ## reuse schema.org vocabulary
-      aliases:
-        multivalued: true
-        description:
-          other names for the person
-      phone:
-        pattern: "^[\\d\\(\\)\\-]+$"
-        slot_uri: schema:telephone       ## reuse schema.org vocabulary
-      age:
-        range: integer
-        minimum_value: 0
-        maximum_value: 200
-    id_prefixes:
-      - ORCID
-  Container:
-    attributes:
-      persons:
-        multivalued: true
-        inlined_as_list: true
-        range: Person
+```{literalinclude} ../../examples/tutorial/tutorial05/personinfo.yaml
+:language: yaml
 ```
 
 We can use a script that is distributed with LinkML to generate a python dataclasses model:
@@ -82,11 +42,8 @@ You can now write code like:
 
 test.py:
 
-```python
-from personinfo import Person
-
-p1 = Person(id='ORCID:9876', full_name='Lex Luthor')
-print(p1)
+```{literalinclude} ../../examples/tutorial/tutorial05/test.py
+:language: python
 ```
 
 run this:
@@ -97,8 +54,8 @@ python test.py
 
 Outputs:
 
-```text
-Person(id='ORCID:9876', full_name='Lex Luthor', aliases=[], phone=None, age=None)
+```{literalinclude} ../../examples/tutorial/tutorial05/test-output.txt
+:language: text
 ```
 
 Hurray! Perhaps this is not very impressive in itself,
@@ -111,12 +68,8 @@ The LinkML runtime is a separate python library that provides methods needed by
 
 test_runtime.py:
 
-```python
-from linkml_runtime.dumpers import json_dumper
-from personinfo import Person
-
-p1 = Person(id='ORCID:9876', full_name='Lex Luthor', aliases=["Bad Guy"])
-print(json_dumper.dumps(p1))
+```{literalinclude} ../../examples/tutorial/tutorial05/test_runtime.py
+:language: python
 ```
 
 ```bash
@@ -125,15 +78,8 @@ python test_runtime.py
 
 Outputs:
 
-```text
-{
-  "id": "ORCID:9876",
-  "full_name": "Lex Luthor",
-  "aliases": [
-    "Bad Guy"
-  ],
-  "@type": "Person"
-}
+```{literalinclude} ../../examples/tutorial/tutorial05/test-runtime-output.txt
+:language: text
 ```
 
 ## Alternatives