tests

linkml · Jul 30, 2021 · 100357f · 100357f
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diff --git a/tests/inputs/books.csv b/tests/inputs/books.csv
@@ -0,0 +1,12 @@
+id,book_category,name,price,inStock,author,series_t,sequence_i,genre_s,yesno,blah_b
+0553573403,book|game,A Game of Thrones,7.99,true,George R.R. Martin,"A Song of Ice and Fire",1,fantasy,true,false
+0553579908,book,A Clash of Kings,7.99,true,George R.R. Martin,"A Song of Ice and Fire",2,fantasy,true,false
+055357342X,book,A Storm of Swords,7.99,true,George R.R. Martin,"A Song of Ice and Fire",3,fantasy,true,false
+0553293354,book,Foundation,7.99,true,Isaac Asimov,Foundation Novels,1,scifi,true,false
+0812521390,book,The Black Company,6.99,false,Glen Cook,The Chronicles of The Black Company,1,fantasy,true,false
+0812550706,book,Ender's Game,6.99,true,Orson Scott Card,Ender,1,scifi,true,false
+0441385532,book,Jhereg,7.95,false,Steven Brust,Vlad Taltos,1,fantasy,true,false
+0380014300,book,Nine Princes In Amber,6.99,true,Roger Zelazny,the Chronicles of Amber,1,fantasy,true,false
+0805080481,book,The Book of Three,5.99,true,Lloyd Alexander,The Chronicles of Prydain,1,fantasy,true,false
+080508049X,book|film,The Black Cauldron,5.99,true,Lloyd Alexander,The Chronicles of Prydain,2,fantasy,false,true
+123,book,Consider Phlebas,7.99,true,Ian M Banks,"",1,scifi,true,false
diff --git a/tests/inputs/books.json b/tests/inputs/books.json
@@ -0,0 +1,4 @@
+[{"id": "X:1", "name": "mytestname"}]
+[{"id": "X:2", "name": "deep",
+  "xyz": 1
+ }]
diff --git a/tests/inputs/books.tsv b/tests/inputs/books.tsv
@@ -0,0 +1,13 @@
+id	book_category	name	price	inStock	author	series_t	sequence_i	genre_s	yesno	blah_b
+0553573403	book|game	A Game of Thrones	7.99	true	George R.R. Martin	A Song of Ice and Fire	1	fantasy	true	false
+0553579908	book	A Clash of Kings	7.99	true	George R.R. Martin	A Song of Ice and Fire	2	fantasy	true	false
+055357342X	book	A Storm of Swords	7.99	true	George R.R. Martin	A Song of Ice and Fire	3	fantasy	true	false
+0553293354	book	Foundation	7.99	true	Isaac Asimov	Foundation Novels	1	scifi	true	false
+0812521390	book	The Black Company	6.99	false	Glen Cook	The Chronicles of The Black Company	1	fantasy	true	false
+0812550706	book	Ender's Game	6.99	true	Orson Scott Card	Ender	1	scifi	true	false
+0441385532	book	Jhereg	7.95	false	Steven Brust	Vlad Taltos	1	fantasy	true	false
+0380014300	book	Nine Princes In Amber	6.99	true	Roger Zelazny	the Chronicles of Amber	1	fantasy	true	false
+0805080481	book	The Book of Three	5.99	true	Lloyd Alexander	The Chronicles of Prydain	1	fantasy	true	false
+080508049X	book|film	The Black Cauldron	5.99	true	Lloyd Alexander	The Chronicles of Prydain	2	fantasy	false	true
+123	book	Consider Phlebas	7.99	true	Ian M Banks		1	scifi	true	false
+456	book	Warlord of the Air	5.99	true	Michael Moorcock	Oswald Bastable Trilogy	1	steambunk	true	false
diff --git a/tests/inputs/books2.csv b/tests/inputs/books2.csv
@@ -0,0 +1,12 @@
+id,book_category,name,price,inStock,author,series,sequence,genre,yesno,blah
+0553573403,book|game,A Game of Thrones,7.99,true,George R.R. Martin,"A Song of Ice and Fire",1,fantasy,true,false
+0553579908,book,A Clash of Kings,7.99,true,George R.R. Martin,"A Song of Ice and Fire",2,fantasy,true,false
+055357342X,book,A Storm of Swords,7.99,true,George R.R. Martin,"A Song of Ice and Fire",3,fantasy,true,false
+0553293354,book,Foundation,7.99,true,Isaac Asimov,Foundation Novels,1,scifi,true,false
+0812521390,book,The Black Company,6.99,false,Glen Cook,The Chronicles of The Black Company,1,fantasy,true,false
+0812550706,book,Ender's Game,6.99,true,Orson Scott Card,Ender,1,scifi,true,false
+0441385532,book,Jhereg,7.95,false,Steven Brust,Vlad Taltos,1,fantasy,true,false
+0380014300,book,Nine Princes In Amber,6.99,true,Roger Zelazny,the Chronicles of Amber,1,fantasy,true,false
+0805080481,book,The Book of Three,5.99,true,Lloyd Alexander,The Chronicles of Prydain,1,fantasy,true,false
+080508049X,book|film,The Black Cauldron,5.99,true,Lloyd Alexander,The Chronicles of Prydain,2,fantasy,false,true
+123,book,Consider Phlebas,7.99,true,Ian M Banks,"",1,scifi,true,false
diff --git a/tests/inputs/books_normalized_01.yaml b/tests/inputs/books_normalized_01.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
+
diff --git a/tests/inputs/books_normalized_02.yaml b/tests/inputs/books_normalized_02.yaml
@@ -0,0 +1,84 @@
+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
+      genres:
+        - fantasy
+      reviews:
+        - creator:
+            name: Alexa Fan
+          rating: 5
+          review_text: loved it
+        - creator:
+            name: Bob Hater
+          rating: 0
+          review_text: too many 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
+
diff --git a/tests/inputs/kitchen_sink_inst_01.yaml b/tests/inputs/kitchen_sink_inst_01.yaml
@@ -0,0 +1,25 @@
+persons:
+  - id: P:001
+    name: fred bloggs
+    age_in_years: 33
+  - id: P:002
+    name: joe schmoe
+    has_employment_history:
+      - employed_at: ROR:1
+        started_at_time: 2019-01-01
+        is_current: true
+    has_familial_relationships:
+      - related_to: P:001
+        type: SIBLING_OF
+    has_medical_history:
+      - started_at_time: 2019-01-01
+    addresses:
+      - street: 1 foo street
+        city: foo city
+companies:
+  - id: ROR:1
+    name: foo
+activities:
+  - id: A:1
+    started_at_time: 2019-01-01
+    was_associated_with: Agent:987
diff --git a/tests/test_amigo.py b/tests/test_amigo.py
@@ -0,0 +1,44 @@
+import os
+import unittest
+
+from linkml_runtime.dumpers import json_dumper, rdf_dumper
+from linkml_runtime.loaders import yaml_loader
+from linkml.generators.yamlgen import YAMLGenerator
+from tests.test_models.amigo import *
+import tests.test_models.amigo as amigo
+
+from tests import INPUT_DIR, MODEL_DIR
+
+from linkml_solr import SolrQueryEngine, SolrEndpoint
+from SPARQLWrapper import SPARQLWrapper, N3
+from rdflib import Graph
+
+DATA = os.path.join(INPUT_DIR, 'kitchen_sink_inst_01.yaml')
+CONTEXT = os.path.join(MODEL_DIR, 'kitchen_sink.context.jsonld')
+SCHEMA = os.path.join(MODEL_DIR, 'amigo.yaml')
+
+class QueryTestCase(unittest.TestCase):
+
+    def test_query(self):
+        """ solr """
+        # TODO: use mock server
+        schema = YAMLGenerator(SCHEMA).schema
+        qe = SolrQueryEngine(schema=schema,
+                             discriminator_field=amigo.slots.document_category.name,
+                             endpoint=SolrEndpoint(url='http://golr.geneontology.org/solr/'))
+
+        sq = qe.generate_query(document_category=OntologyClass.class_name, synonym='apoptosis')
+        print(sq)
+        print(sq.http_params())
+
+        result = qe.search(target_class=OntologyClass, isa_partof_closure='GO:0031965') ## nuclear membrane
+        #print(f'Result={result}')
+        for oc in result.items:
+            oc: OntologyClass
+            print(f'Term: {oc.id} {oc.annotation_class_label}')
+
+
+
+
+if __name__ == '__main__':
+    unittest.main()