Coverage for src/python/ensembl/ncbi_taxonomy/models.py: 100%

1# See the NOTICE file distributed with this work for additional information 

2# regarding copyright ownership. 

3# 

4# Licensed under the Apache License, Version 2.0 (the "License"); 

5# you may not use this file except in compliance with the License. 

6# You may obtain a copy of the License at 

7# http://www.apache.org/licenses/LICENSE-2.0 

8# 

9# Unless required by applicable law or agreed to in writing, software 

10# distributed under the License is distributed on an "AS IS" BASIS, 

11# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 

12# See the License for the specific language governing permissions and 

13# limitations under the License. 

14"""NCBI Taxonomy database ORM.""" 

15# Ignore some pylint and mypy checks due to the nature of SQLAlchemy ORMs 

16# pylint: disable=missing-class-docstring 

17# mypy: disable-error-code="misc, valid-type" 

18 

19from sqlalchemy import ( 

20 Column, 

21 ForeignKey, 

22 join, 

23) 

24from sqlalchemy.dialects.mysql import ( 

25 INTEGER, 

26 TINYINT, 

27 VARCHAR, 

28 CHAR, 

29) 

30from sqlalchemy.orm import ( 

31 relationship, 

32 column_property, 

33) 

34from sqlalchemy.orm import declarative_base 

35 

36Base = declarative_base() 

37 

38 

39class NCBITaxaNode(Base): 

40 __tablename__ = "ncbi_taxa_node" 

41 

42 taxon_id = Column(INTEGER(10), primary_key=True) 

43 parent_id = Column(INTEGER(10), ForeignKey("ncbi_taxa_node.taxon_id"), nullable=False, index=True) 

44 rank = Column(CHAR(32), nullable=False, index=True) 

45 genbank_hidden_flag = Column(TINYINT(1), nullable=False, default=0) 

46 left_index = Column(INTEGER(10), nullable=False, default=0, index=True) 

47 right_index = Column(INTEGER(10), nullable=False, default=0, index=True) 

48 root_id = Column(INTEGER(10), nullable=False, default=1) 

49 

50 parent = relationship("NCBITaxaNode", remote_side=[taxon_id]) 

51 children = relationship("NCBITaxaName") 

52 

53 

54class NCBITaxaName(Base): 

55 __tablename__ = "ncbi_taxa_name" 

56 

57 taxon_id = Column(INTEGER(10), ForeignKey("ncbi_taxa_node.taxon_id"), index=True, primary_key=True) 

58 name = Column(VARCHAR(500), index=True, primary_key=True) 

59 name_class = Column(VARCHAR(50), nullable=False, index=True) 

60 

61 

62class NCBITaxonomy(Base): 

63 ncbi_taxa_name_table = NCBITaxaName.__table__ 

64 ncbi_taxa_node_table = NCBITaxaNode.__table__ 

65 

66 name_node_join = join(ncbi_taxa_name_table, ncbi_taxa_node_table) 

67 

68 __table__ = name_node_join 

69 

70 taxon_id = column_property(ncbi_taxa_name_table.c.taxon_id, ncbi_taxa_node_table.c.taxon_id)