test_remote_sparql.py

from ontobio import OntologyFactory
from ontobio import GraphRenderer
import logging

HAS_PART = 'BFO:0000051'
PART_OF = 'BFO:0000050'

QUALITY = 'PATO:0000001'
PLOIDY = 'PATO:0001374'
EUPLOID = 'PATO:0001393'
SHAPE = 'PATO:0000052'
Y_SHAPED = 'PATO:0001201'
PENTAPLOID = 'PATO:0001383'
SWOLLEN = 'PATO:0001851'
DILATED = 'PATO:0001571'
INCREASED_SIZE = 'PATO:0000586'
PROTRUDING = 'PATO:0001598'
MORPHOLOGY = 'PATO:0000051'
ABSENT = 'PATO:0000462'
CONICAL = 'PATO:0002021'
APOPTOTIC = 'PATO:0000638'

def test_remote_sparql_pato():
    """
    Load ontology from remote SPARQL endpoint
    """
    factory = OntologyFactory()
    print("Creating ont")
    ont = factory.create('pato')

    ont_id = ont.id
    assert 'pato' in ont_id.lower()
    
    ploidy = ont.node(PLOIDY)
    print("PLOIDY: {}".format(ploidy))
    assert ont.label(PLOIDY) == 'ploidy'

    # exact match
    search_results = ont.search('shape')
    print("SEARCH (exact): {}".format(search_results))
    assert [SHAPE] == search_results

    # implicit regexp
    search_results = ont.search('%shape%')
    print("SEARCH (re, implicit): {}".format(search_results))
    assert SHAPE in search_results
    assert len(search_results)>10

    # explicit regexp
    search_results = ont.search('.*shape.*', is_regex=True)
    print("SEARCH (re, explicit): {}".format(search_results))
    assert SHAPE in search_results
    assert len(search_results)>10
    
    # syns
    syn = 'cone-shaped'
    search_results = ont.search(syn, synonyms=False)
    print("SEARCH (no syns): {}".format(search_results))
    assert [] == search_results
    #search_results = ont.search(syn, synonyms=True)
    #print("SEARCH (with syns): {}".format(search_results))
    #assert [CONICAL] == search_results
    
    num_nodes = 0
    for n in ont.nodes():
        num_nodes = num_nodes+1
    assert num_nodes > 100

    ancs = ont.ancestors(PLOIDY)
    print("ANCS ploidy (all): {}".format(ancs))
    assert QUALITY in ancs
    assert PENTAPLOID not in ancs

    ancs = ont.ancestors(PLOIDY, relations=['subClassOf'])
    print("ANCS ploidy (subClassOf): {}".format(ancs))
    assert QUALITY in ancs
    assert PENTAPLOID not in ancs

    # this is a non-use case
    ancs = ont.ancestors(SWOLLEN, relations=[HAS_PART])
    print("ANCS swollen (has_part): {}".format(ancs))
    assert INCREASED_SIZE in ancs
    assert PROTRUDING in ancs
    assert len(ancs) == 2

    ancs = ont.ancestors(SWOLLEN, relations=['subClassOf'])
    print("ANCS swollen (has_part): {}".format(ancs))
    assert MORPHOLOGY in ancs
    assert QUALITY in ancs
    assert PROTRUDING not in ancs
    
    decs = ont.descendants(PLOIDY)
    print("DECS ploidy (all): {}".format(decs))
    assert QUALITY not in decs
    assert EUPLOID in decs
    assert PENTAPLOID in decs

    # this is a non-use case
    ancs = ont.descendants(INCREASED_SIZE, relations=[HAS_PART])
    print("ANCS increased size (has part): {}".format(ancs))
    assert SWOLLEN in ancs
    assert len(ancs) == 1

    subsets = ont.subsets()
    print("SUBSETS: {}".format(subsets))

    slim = ont.extract_subset('absent_slim')
    print("SLIM: {}".format(slim))
    assert ABSENT in slim
    assert QUALITY not in slim

    syns = ont.synonyms(INCREASED_SIZE)
    print("SYNS: {}".format(syns))
    syn_vals = [syn.val for syn in syns]
    assert 'big' in syn_vals
    [bigsyn] = [syn for syn in syns if syn.val=='big']
    # TODO xrefs
    assert not bigsyn.exact_or_label()
    assert bigsyn.scope() == 'RELATED'

    defn = ont.text_definition(INCREASED_SIZE)
    assert defn is not None

    assert ont.is_obsolete('PATO:0000000') == True
    
    w = GraphRenderer.create('obo')
    w.write_subgraph(ont, [INCREASED_SIZE])

    assert len(ont.xref_graph.nodes()) > 1
    assert 'GO:0006915' in ont.xrefs(APOPTOTIC)
    w = GraphRenderer.create('obo')
    w.write_subgraph(ont, [APOPTOTIC])
    
def test_dynamic_query():
    """
    Dynamic query
    """
    factory = OntologyFactory()
    print("Creating ont")
    ont = factory.create('pato')

    ids = ont.sparql(body="{?x rdfs:subClassOf+ "+SHAPE+"}",
                     inject_prefixes = ont.prefixes(),
                     single_column=True)
    assert Y_SHAPED in ids
    assert ABSENT not in ids

def test_subontology():
    """
    subontology
    """
    factory = OntologyFactory()
    print("Creating ont")
    ont = factory.create('go')
    assert ont.is_obsolete('GO:0000267') == True
    print("ONT NODES: {}".format(ont.nodes()))
    subont = ont.subontology(relations=['subClassOf'])
    PERM = 'GO:1990578'
    print("NODES: {}".format(subont.nodes()))
    ancs = subont.ancestors(PERM, reflexive=True)
    print(str(ancs))
    for a in ancs:
        print(" ANC: {} '{}'".format(a,subont.label(a)))
    assert len(ancs) > 0

    assert subont.is_obsolete('GO:0000267') == True
    
    w = GraphRenderer.create('tree')
    w.write_subgraph(ont, ancs)

    # TODO: sub-ontology does not create
    # full metadata
    w = GraphRenderer.create('obo')
    w.write_subgraph(ont, ancs)