示例#1
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def _make_queries_in_results(result_iter):
    # Each element of result_iter: (model_id, query_json, result_json, date)
    # Replace query_json with Query object
    results = []
    for res in result_iter:
        query = QueryObject._from_json(res[1])
        results.append((res[0], query, res[2], res[3], res[4]))
    return results
示例#2
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def test_intervention_query_from_json():
    query_file = join(dirname(abspath(__file__)), 'intervention_query.json')
    with open(query_file, 'r') as f:
        json_dict = json.load(f)
    query = Query._from_json(json_dict)
    assert query
    assert isinstance(query, SimpleInterventionProperty)
    assert isinstance(query.condition_entity, Agent)
    assert query.condition_entity.name == 'EGF'
    assert isinstance(query.target_entity, Agent)
    assert query.target_entity.name == 'ERK'
    assert query.direction == 'up'
示例#3
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def test_open_query_to_json():
    ag = Agent('EGFR', db_refs={'HGNC': '3236'})
    query = OpenSearchQuery(ag, 'Inhibition', 'object', ['chebi'])
    assert query
    json = query.to_json()
    assert json.get('type') == 'open_search_query'
    assert json.get('stmt_type') == 'Inhibition'
    assert json.get('entity_role') == 'object'
    assert json.get('terminal_ns') == ['chebi']
    deserialize_query = Query._from_json(json)
    json2 = deserialize_query.to_json()
    assert json == json2, {'json': json, 'json2': json2}
示例#4
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def test_path_property_to_json():
    stmt = Phosphorylation(enz=Agent('EGFR', db_refs={'HGNC': '3236'}),
                           sub=Agent('ERK', db_refs={'FPLX': 'ERK'}))
    entity_constraints = {'exclude': [Agent('PI3K', db_refs={'FPLX': 'PI3K'})]}
    relationship_contraints = {'exclude': ['IncreaseAmount', 'DecreaseAmount']}
    query = PathProperty(stmt, entity_constraints, relationship_contraints)
    assert query
    json = query.to_json()
    assert json.get('type') == 'path_property'
    path = json.get('path')
    assert path.get('type') == 'Phosphorylation'
    deserialize_query = Query._from_json(json)
    json2 = deserialize_query.to_json()
    assert json == json2, {'json': json, 'json2': json2}
示例#5
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def test_open_query_from_json():
    query_file = join(dirname(abspath(__file__)), 'open_query.json')
    with open(query_file, 'r') as f:
        json_dict = json.load(f)
    query = Query._from_json(json_dict)
    assert query
    assert isinstance(query, OpenSearchQuery)
    assert isinstance(query.entity, Agent)
    assert query.entity.name == 'EGFR'
    assert query.entity_role == 'object'
    assert query.stmt_type == 'Inhibition'
    assert isinstance(query.path_stmt, Inhibition)
    assert query.path_stmt.subj is None
    assert query.terminal_ns == ['chebi']
示例#6
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def test_path_property_from_json():
    query_file = join(dirname(abspath(__file__)), 'path_property_query.json')
    with open(query_file, 'r') as f:
        json_dict = json.load(f)
    query = Query._from_json(json_dict)
    assert query
    assert isinstance(query, PathProperty)
    assert isinstance(query.path_stmt, Phosphorylation), query.path_stmt
    assert query.path_stmt.enz.name == 'EGFR', query.path_stmt
    assert query.path_stmt.sub.name == 'ERK', query.path_stmt
    assert isinstance(query.exclude_entities[0], Agent)
    assert query.exclude_entities[0].name == 'PI3K'
    assert isinstance(query.include_entities[0], Agent)
    assert query.include_entities[0].name == 'MAPK1'
    assert set(query.exclude_rels) == set(['IncreaseAmount', 'DecreaseAmount'])
    assert query.include_rels[0] == 'Inhibition'
示例#7
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def test_dynamic_property_from_json():
    query_file = join(dirname(abspath(__file__)),
                      'dynamic_property_query.json')
    with open(query_file, 'r') as f:
        json_dict = json.load(f)
    query = Query._from_json(json_dict)
    assert query
    assert isinstance(query, DynamicProperty)
    assert isinstance(query.entity, Agent)
    assert query.entity.name == 'EGFR'
    assert isinstance(query.pattern_type, str)
    assert query.pattern_type == 'always_value'
    assert isinstance(query.quant_value, str)
    assert query.quant_value == 'low'
    assert isinstance(query.quant_type, str)
    assert query.quant_type == 'qualitative'
示例#8
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    def get_queries(self, model_id):
        """Get queries that refer to the given model_id.

        Parameters
        ----------
        model_id : str
            The short, standard model ID.

        Returns
        -------
        queries : list[emmaa.queries.Query]
            A list of queries retrieved from the database.
        """
        # TODO: check whether a query is registered or not.
        with self.get_session() as sess:
            q = sess.query(Query.json).filter(Query.model_id == model_id)
            queries = [QueryObject._from_json(q) for q, in q.all()]
        return queries
示例#9
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文件: manager.py 项目: kolusask/emmaa
    def get_queries(self, model_id):
        """Get queries that refer to the given model_id.

        Parameters
        ----------
        model_id : str
            The short, standard model ID.

        Returns
        -------
        queries : list[emmaa.queries.Query]
            A list of queries retrieved from the database.
        """
        with self.get_session() as sess:
            q = sess.query(Query.json).filter(
                Query.model_id == model_id, Query.hash == UserQuery.query_hash,
                UserQuery.subscription).distinct()
            queries = [QueryObject._from_json(q) for q, in q.all()]
        return queries
示例#10
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文件: manager.py 项目: kolusask/emmaa
    def get_subscribed_queries(self, email):
        """Get a list of (query object, model id, query hash) for a user

        Parameters
        ----------
        email : str
            The email address to check subscribed queries for

        Returns
        -------
        list(tuple(emmaa.queries.Query, str, query_hash))
        """
        logger.info(f"Got request to list user queries for {email}")
        # Get the query json for which email is subscribed
        with self.get_session() as sess:
            q = sess.query(Query.json, Query.model_id, Query.hash).filter(
                Query.hash == UserQuery.query_hash,
                UserQuery.user_id == User.id, User.email == email,
                UserQuery.subscription)
            # Returns list of (query json, query hash) tuples
        return [(QueryObject._from_json(qj), mid, qh)
                for qj, mid, qh in q.all()]
示例#11
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            'db_refs': {
                'HGNC': '1097'
            }
        },
        'obj': {
            'type': 'Agent',
            'name': 'MAPK1',
            'db_refs': {
                'HGNC': '6871'
            }
        },
        'obj_activity': 'activity'
    }
}
simple_query = 'BRAF activates MAPK1.'
query_object = Query._from_json(test_query)
dyn_ag = get_agent_from_trips('active MAP2K1')
dyn_query = DynamicProperty(dyn_ag, 'eventual_value', 'high')
open_qj = {
    'type': 'open_search_query',
    'entity': {
        'type': 'Agent',
        'name': 'BRAF',
        'db_refs': {
            'HGNC': '1097'
        }
    },
    'entity_role': 'subject',
    'stmt_type': 'Activation'
}
open_query = Query._from_json(open_qj)
示例#12
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        },
        'obj': {
            'type': 'Agent',
            'name': 'MAPK1',
            'db_refs': {
                'HGNC': '6871'
            }
        }
    }
}
simple_query = {
    'typeSelection': 'Activation',
    'subjectSelection': 'BRAF',
    'objectSelection': 'MAPK1'
}
query_object = Query._from_json(test_query)

test_response = {
    3801854542:
    [('BRAF activates MAP2K1.',
      'https://db.indra.bio/statements/from_agents?subject=1097@HGNC&object='
      '6840@HGNC&type=Activation&format=html'),
     ('Active MAP2K1 activates MAPK1.',
      'https://db.indra.bio/statements/from_agents?subject=6840@HGNC&object='
      '6871@HGNC&type=Activation&format=html')]
}
processed_link = '<a href="https://db.indra.bio/statements/from_agents?'\
    'subject=1097@HGNC&object=6840@HGNC&type=Activation&format=html" '\
                 'target="_blank" class="status-link">'\
                 'BRAF activates MAP2K1.</a>'
query_not_appl = {
示例#13
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文件: test_db.py 项目: indralab/emmaa
}, {
    'type': 'path_property',
    'path': {
        'type': 'Phosphorylation',
        'enz': {
            'type': 'Agent',
            'name': 'ERK'
        },
        'sub': {
            'type': 'Agent',
            'name': 'MEK'
        }
    }
}]

test_queries = [QueryObject._from_json(qj) for qj in test_query_jsons]


@with_setup(setup_query_db, teardown_query_db)
@attr('nonpublic')
def test_instantiation():
    db = _get_test_db()
    assert db
    return


@with_setup(setup_query_db, teardown_query_db)
@attr('nonpublic')
def test_put_queries():
    db = _get_test_db()
    db.put_queries('joshua', 1, test_queries[0], ['aml', 'luad'])