NaturalHistoryMuseum/ukbol | Build 13897929404 | api/ukbol/model.py | Coveralls

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from datetime import datetime

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from typing import Any, List, Self

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from sqlalchemy import DateTime, ForeignKey

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from sqlalchemy.orm import Mapped, mapped_column, relationship

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from ukbol.extensions import db

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class Taxon(db.Model):

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    id: Mapped[str] = mapped_column(primary_key=True)

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    name: Mapped[str]

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    authorship: Mapped[str | None]

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    rank: Mapped[str] = mapped_column(index=True)

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    parent_id: Mapped[int | None] = mapped_column(ForeignKey("taxon.id"), index=True)

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    parent: Mapped["Taxon"] = relationship(back_populates="children", remote_side=[id])

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    children: Mapped[List["Taxon"]] = relationship(back_populates="parent")

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    synonyms: Mapped[List["Synonym"]] = relationship(back_populates="taxon")

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    @classmethod

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    def get(cls, ident: Any) -> Self | None:

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        return db.session.get(cls, ident)

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class Synonym(db.Model):

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    id: Mapped[str] = mapped_column(primary_key=True)

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    name: Mapped[str]

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    authorship: Mapped[str | None]

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    rank: Mapped[str]

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    taxon_id: Mapped[str] = mapped_column(ForeignKey(Taxon.id), index=True)

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    taxon: Mapped["Taxon"] = relationship(back_populates="synonyms")

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    @classmethod

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    def get(cls, ident: Any) -> Self | None:

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        return db.session.get(cls, ident)

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class Specimen(db.Model):

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    id: Mapped[int] = mapped_column(primary_key=True)

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    processid: Mapped[str | None]

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    sampleid: Mapped[str | None]

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    fieldid: Mapped[str | None]

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    museumid: Mapped[str | None]

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    record_id: Mapped[str | None]

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    specimenid: Mapped[str | None]

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    processid_minted_date: Mapped[str | None]

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    bin_uri: Mapped[str | None] = mapped_column(index=True)

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    bin_created_date: Mapped[str | None]

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    collection_code: Mapped[str | None]

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    inst: Mapped[str | None]

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    taxid: Mapped[str | None]

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    kingdom: Mapped[str | None]

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    phylum: Mapped[str | None]

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    cls: Mapped[str | None]

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    order: Mapped[str | None]

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    family: Mapped[str | None]

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    subfamily: Mapped[str | None]

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    tribe: Mapped[str | None]

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    genus: Mapped[str | None]

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    species: Mapped[str | None]

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    subspecies: Mapped[str | None]

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    species_reference: Mapped[str | None]

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    identification: Mapped[str | None] = mapped_column(index=True)

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    identification_method: Mapped[str | None]

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    identification_rank: Mapped[str | None] = mapped_column(index=True)

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    identified_by: Mapped[str | None]

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    identifier_email: Mapped[str | None]

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    taxonomy_notes: Mapped[str | None]

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    sex: Mapped[str | None]

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    reproduction: Mapped[str | None]

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    life_stage: Mapped[str | None]

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    short_note: Mapped[str | None]

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    notes: Mapped[str | None]

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    voucher_type: Mapped[str | None]

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    tissue_type: Mapped[str | None]

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    specimen_linkout: Mapped[str | None]

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    associated_specimens: Mapped[str | None]

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    associated_taxa: Mapped[str | None]

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    collectors: Mapped[str | None]

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    collection_date_start: Mapped[str | None]

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    collection_date_end: Mapped[str | None]

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    collection_event_id: Mapped[str | None]

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    collection_time: Mapped[str | None]

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    collection_notes: Mapped[str | None]

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    geoid: Mapped[str | None]

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    country_ocean: Mapped[str | None]

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    country_iso: Mapped[str | None] = mapped_column(index=True)

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    province_state: Mapped[str | None]

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    region: Mapped[str | None]

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    sector: Mapped[str | None]

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    site: Mapped[str | None]

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    site_code: Mapped[str | None]

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    coord: Mapped[str | None]

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    coord_accuracy: Mapped[str | None]

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    coord_source: Mapped[str | None]

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    elev: Mapped[str | None]

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    elev_accuracy: Mapped[str | None]

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    depth: Mapped[str | None]

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    depth_accuracy: Mapped[str | None]

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    habitat: Mapped[str | None]

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    sampling_protocol: Mapped[str | None]

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    nuc: Mapped[str | None]

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    nuc_basecount: Mapped[str | None]

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    insdc_acs: Mapped[str | None]

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    funding_src: Mapped[str | None]

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    marker_code: Mapped[str | None]

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    primers_forward: Mapped[str | None]

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    primers_reverse: Mapped[str | None]

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    sequence_run_site: Mapped[str | None]

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    sequence_upload_date: Mapped[str | None]

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    bold_recordset_code_arr: Mapped[str | None]

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    ecoregion: Mapped[str | None]

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    biome: Mapped[str | None]

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    realm: Mapped[str | None]

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    sovereign_inst: Mapped[str | None]

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    @classmethod

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    def get(cls, ident: Any) -> Self | None:

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class PantheonSpecies(db.Model):

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    id: Mapped[int] = mapped_column(primary_key=True)

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    species: Mapped[str | None] = mapped_column(index=True)

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    family: Mapped[str | None]

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    order: Mapped[str | None]

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    sqs: Mapped[str | None]

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    conservation_status: Mapped[str | None]

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    larval_feeding_guild: Mapped[str | None]

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    adult_feeding_guild: Mapped[str | None]

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    broad_biotope: Mapped[str | None]

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    habitat: Mapped[str | None]

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    resources: Mapped[str | None]

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    specific_assemblage_type: Mapped[str | None] = mapped_column(index=True)

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    habitat_score: Mapped[str | None]

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    associations: Mapped[str | None]

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    common_name: Mapped[str | None]

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    notes: Mapped[str | None]

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class DataSourceStatus(db.Model):

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    name: Mapped[str] = mapped_column(primary_key=True)

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    updated_at: Mapped[datetime] = mapped_column(DateTime(timezone=True))

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    version: Mapped[str | None]

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    total: Mapped[int]

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    @classmethod

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    def get(cls, name: str) -> Self | None:

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        return db.session.get(cls, name)

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NaturalHistoryMuseum / ukbol / 13897929404

Source File
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1	from datetime import datetime	1✔
2	from typing import Any, List, Self	1✔
3
4	from sqlalchemy import DateTime, ForeignKey	1✔
5	from sqlalchemy.orm import Mapped, mapped_column, relationship	1✔
6
7	from ukbol.extensions import db	1✔
8
9
10	# imported from uksi
11	class Taxon(db.Model):	1✔
12	id: Mapped[str] = mapped_column(primary_key=True)	1✔
13	name: Mapped[str]	1✔
14	authorship: Mapped[str \| None]	1✔
15	rank: Mapped[str] = mapped_column(index=True)	1✔
16	parent_id: Mapped[int \| None] = mapped_column(ForeignKey("taxon.id"), index=True)	1✔
17
18	# relationships
19	parent: Mapped["Taxon"] = relationship(back_populates="children", remote_side=[id])	1✔
20	children: Mapped[List["Taxon"]] = relationship(back_populates="parent")	1✔
21	synonyms: Mapped[List["Synonym"]] = relationship(back_populates="taxon")	1✔
22
23	@classmethod	1✔
24	def get(cls, ident: Any) -> Self \| None:	1✔
25	return db.session.get(cls, ident)	1✔
26
27
28	# imported from uksi
29	class Synonym(db.Model):	1✔
30	id: Mapped[str] = mapped_column(primary_key=True)	1✔
31	name: Mapped[str]	1✔
32	authorship: Mapped[str \| None]	1✔
33	rank: Mapped[str]	1✔
34	taxon_id: Mapped[str] = mapped_column(ForeignKey(Taxon.id), index=True)	1✔
35
36	# relationships
37	taxon: Mapped["Taxon"] = relationship(back_populates="synonyms")	1✔
38
39	@classmethod	1✔
40	def get(cls, ident: Any) -> Self \| None:	1✔
41	return db.session.get(cls, ident)	1✔
42
43
44	# imported from BOLD
45	class Specimen(db.Model):	1✔
46	id: Mapped[int] = mapped_column(primary_key=True)	1✔
47	processid: Mapped[str \| None]	1✔
48	sampleid: Mapped[str \| None]	1✔
49	fieldid: Mapped[str \| None]	1✔
50	museumid: Mapped[str \| None]	1✔
51	record_id: Mapped[str \| None]	1✔
52	specimenid: Mapped[str \| None]	1✔
53	processid_minted_date: Mapped[str \| None]	1✔
54	bin_uri: Mapped[str \| None] = mapped_column(index=True)	1✔
55	bin_created_date: Mapped[str \| None]	1✔
56	collection_code: Mapped[str \| None]	1✔
57	inst: Mapped[str \| None]	1✔
58	taxid: Mapped[str \| None]	1✔
59	kingdom: Mapped[str \| None]	1✔
60	phylum: Mapped[str \| None]	1✔
61	cls: Mapped[str \| None]	1✔
62	order: Mapped[str \| None]	1✔
63	family: Mapped[str \| None]	1✔
64	subfamily: Mapped[str \| None]	1✔
65	tribe: Mapped[str \| None]	1✔
66	genus: Mapped[str \| None]	1✔
67	species: Mapped[str \| None]	1✔
68	subspecies: Mapped[str \| None]	1✔
69	species_reference: Mapped[str \| None]	1✔
70	identification: Mapped[str \| None] = mapped_column(index=True)	1✔
71	identification_method: Mapped[str \| None]	1✔
72	identification_rank: Mapped[str \| None] = mapped_column(index=True)	1✔
73	identified_by: Mapped[str \| None]	1✔
74	identifier_email: Mapped[str \| None]	1✔
75	taxonomy_notes: Mapped[str \| None]	1✔
76	sex: Mapped[str \| None]	1✔
77	reproduction: Mapped[str \| None]	1✔
78	life_stage: Mapped[str \| None]	1✔
79	short_note: Mapped[str \| None]	1✔
80	notes: Mapped[str \| None]	1✔
81	voucher_type: Mapped[str \| None]	1✔
82	tissue_type: Mapped[str \| None]	1✔
83	specimen_linkout: Mapped[str \| None]	1✔
84	associated_specimens: Mapped[str \| None]	1✔
85	associated_taxa: Mapped[str \| None]	1✔
86	collectors: Mapped[str \| None]	1✔
87	collection_date_start: Mapped[str \| None]	1✔
88	collection_date_end: Mapped[str \| None]	1✔
89	collection_event_id: Mapped[str \| None]	1✔
90	collection_time: Mapped[str \| None]	1✔
91	collection_notes: Mapped[str \| None]	1✔
92	geoid: Mapped[str \| None]	1✔
93	country_ocean: Mapped[str \| None]	1✔
94	country_iso: Mapped[str \| None] = mapped_column(index=True)	1✔
95	province_state: Mapped[str \| None]	1✔
96	region: Mapped[str \| None]	1✔
97	sector: Mapped[str \| None]	1✔
98	site: Mapped[str \| None]	1✔
99	site_code: Mapped[str \| None]	1✔
100	coord: Mapped[str \| None]	1✔
101	coord_accuracy: Mapped[str \| None]	1✔
102	coord_source: Mapped[str \| None]	1✔
103	elev: Mapped[str \| None]	1✔
104	elev_accuracy: Mapped[str \| None]	1✔
105	depth: Mapped[str \| None]	1✔
106	depth_accuracy: Mapped[str \| None]	1✔
107	habitat: Mapped[str \| None]	1✔
108	sampling_protocol: Mapped[str \| None]	1✔
109	nuc: Mapped[str \| None]	1✔
110	nuc_basecount: Mapped[str \| None]	1✔
111	insdc_acs: Mapped[str \| None]	1✔
112	funding_src: Mapped[str \| None]	1✔
113	marker_code: Mapped[str \| None]	1✔
114	primers_forward: Mapped[str \| None]	1✔
115	primers_reverse: Mapped[str \| None]	1✔
116	sequence_run_site: Mapped[str \| None]	1✔
117	sequence_upload_date: Mapped[str \| None]	1✔
118	bold_recordset_code_arr: Mapped[str \| None]	1✔
119	ecoregion: Mapped[str \| None]	1✔
120	biome: Mapped[str \| None]	1✔
121	realm: Mapped[str \| None]	1✔
122	sovereign_inst: Mapped[str \| None]	1✔
123
124	@classmethod	1✔
125	def get(cls, ident: Any) -> Self \| None:	1✔
126	return db.session.get(cls, ident)	×
127
128
129	# imported from PANTHEON
130	class PantheonSpecies(db.Model):	1✔
131	id: Mapped[int] = mapped_column(primary_key=True)	1✔
132	species: Mapped[str \| None] = mapped_column(index=True)	1✔
133	family: Mapped[str \| None]	1✔
134	order: Mapped[str \| None]	1✔
135	sqs: Mapped[str \| None]	1✔
136	conservation_status: Mapped[str \| None]	1✔
137	larval_feeding_guild: Mapped[str \| None]	1✔
138	adult_feeding_guild: Mapped[str \| None]	1✔
139	broad_biotope: Mapped[str \| None]	1✔
140	habitat: Mapped[str \| None]	1✔
141	resources: Mapped[str \| None]	1✔
142	specific_assemblage_type: Mapped[str \| None] = mapped_column(index=True)	1✔
143	habitat_score: Mapped[str \| None]	1✔
144	associations: Mapped[str \| None]	1✔
145	common_name: Mapped[str \| None]	1✔
146	notes: Mapped[str \| None]	1✔
147
148
149	# information about when the data was imported from each source
150	class DataSourceStatus(db.Model):	1✔
151	name: Mapped[str] = mapped_column(primary_key=True)	1✔
152	updated_at: Mapped[datetime] = mapped_column(DateTime(timezone=True))	1✔
153	version: Mapped[str \| None]	1✔
154	total: Mapped[int]	1✔
155
156	@classmethod	1✔
157	def get(cls, name: str) -> Self \| None:	1✔
158	return db.session.get(cls, name)	1✔

NaturalHistoryMuseum / ukbol / 13897929404

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