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Merged
merged 2 commits into from
Nov 20, 2024
Merged

chore: bump dependencies #226

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d10d344
chore: bump dependency
holtgrewe Nov 20, 2024
a8e3e3a
adjust schema
holtgrewe Nov 20, 2024
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1,846 changes: 725 additions & 1,121 deletions Cargo.lock
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14 changes: 7 additions & 7 deletions Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -15,12 +15,12 @@ clap-verbosity-flag = "2.2"
clap = { version = "4.5", features = ["derive", "help", "env"] }
console = "0.15"
csv = "1.3"
derive_more = "0.99"
env_logger = "0.10"
derive_more = { version = "1.0", features = ["full"] }
env_logger = "0.11"
fastobo = "0.15.2"
fastrand = "2.1"
flate2 = "1.0"
hpo = "0.8"
hpo = "0.11"
indexmap = { version = "2.6", features = ["serde"] }
indicatif = { version = "0.17", features = ["rayon"] }
itertools = "0.13"
Expand All @@ -36,13 +36,13 @@ serde_with = { version = "3.9", features=["alloc", "macros", "indexmap_2"], defa
shellexpand = "3.0"
strum_macros = "0.26"
strum = { version = "0.26", features = ["strum_macros", "derive"] }
tantivy = "0.21.1"
tempdir = "0.3.7"
tantivy = "0.22"
tempdir = "0.3"
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⚠️ Potential issue

Verify tempdir version change

The tempdir version change from 0.3.7 to 0.3 appears to be a downgrade. Please verify if this is intentional or if it should be 0.3.x where x ≥ 7.

thiserror = "2.0"
tracing = "0.1"
tracing-subscriber = "0.3"
utoipa-swagger-ui = { version = "7.1.0", features = ["actix-web"] }
utoipa = { version = "4.2", features = ["actix_extras", "chrono", "indexmap", "preserve_order", "yaml"] }
utoipa-swagger-ui = { version = "8.0", features = ["actix-web"] }
utoipa = { version = "5.2", features = ["actix_extras", "chrono", "indexmap", "preserve_order", "yaml"] }

[build-dependencies]
anyhow = "1.0"
Expand Down
169 changes: 99 additions & 70 deletions openapi.yaml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
openapi: 3.0.3
openapi: 3.1.0
info:
title: viguno
description: Phenotype/disease for VarFish
Expand All @@ -7,7 +7,7 @@ info:
email: manuel.holtgrewe@bih-charite.de
license:
name: Apache-2.0
version: 0.2.1
version: 0.3.2
paths:
/hpo/genes:
get:
Expand All @@ -21,23 +21,25 @@ paths:
description: The gene ID to search for.
required: false
schema:
type: string
nullable: true
type:
- string
- 'null'
- name: gene_symbol
in: query
description: The gene symbol to search for.
required: false
schema:
type: string
nullable: true
type:
- string
- 'null'
- name: match_
in: query
description: The match mode.
required: false
schema:
allOf:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/Match'
nullable: true
- name: max_results
in: query
description: Maximal number of results to return.
Expand Down Expand Up @@ -70,30 +72,33 @@ paths:
description: The OMIM ID to search for.
required: false
schema:
type: string
nullable: true
type:
- string
- 'null'
- name: name
in: query
description: The disease name to search for.
required: false
schema:
type: string
nullable: true
type:
- string
- 'null'
- name: match_
in: query
description: The match mode, default is `Match::Exact`.
required: false
schema:
allOf:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/Match'
nullable: true
- name: ignore_case
in: query
description: Whether case is insentivie, default is `false`.
required: false
schema:
type: boolean
nullable: true
type:
- boolean
- 'null'
- name: max_results
in: query
description: Maximal number of results to return.
Expand All @@ -118,8 +123,9 @@ paths:
get:
tags:
- hpo_sim::term_gene
summary: Query for similarity between a set of terms to each entry in a
description: list of genes.
summary: |-
Query for similarity between a set of terms to each entry in a
list of genes.
operationId: hpo_sim_term_gene
parameters:
- name: terms
Expand All @@ -135,19 +141,21 @@ paths:
description: The set of ids for genes to use as "database".
required: false
schema:
type: array
type:
- array
- 'null'
items:
type: string
nullable: true
- name: gene_symbols
in: query
description: The set of symbols for genes to use as "database".
required: false
schema:
type: array
type:
- array
- 'null'
items:
type: string
nullable: true
responses:
'200':
description: The query was successful.
Expand Down Expand Up @@ -225,15 +233,17 @@ paths:
description: The term ID to search for.
required: false
schema:
type: string
nullable: true
type:
- string
- 'null'
- name: name
in: query
description: The term name to search for.
required: false
schema:
type: string
nullable: true
type:
- string
- 'null'
- name: max_results
in: query
description: Maximal number of results to return.
Expand All @@ -253,9 +263,29 @@ paths:
content:
application/json:
schema:
$ref: '#/components/schemas/Result'
$ref: '#/components/schemas/Result_'
components:
schemas:
Gene:
type: object
description: Struct for storing gene information in the result.
required:
- entrez_id
- gene_symbol
properties:
entrez_id:
type: integer
format: int32
description: The NCBI gene ID.
minimum: 0
gene_symbol:
type: string
description: The gene symbol.
hgnc_id:
type:
- string
- 'null'
description: The HGNC ID.
HpoTerm:
type: object
description: Struct for loading an HPO term from JSON.
Expand All @@ -266,9 +296,10 @@ components:
type: string
description: The term ID.
term_name:
type: string
type:
- string
- 'null'
description: The term name (optional).
nullable: true
IcBasedOn:
type: string
description: |-
Expand All @@ -290,36 +321,21 @@ components:
Query:
type: object
title: HpoSimTermGeneQuery
description: |-
Parameters for `handle`.

This allows to compute differences between

- `terms` -- set of terms to use as query
- `gene_ids` -- set of ids for genes to use as "database", can be NCBI\
gene ID or HGNC gene ID.
- `gene_symbols` -- set of symbols for genes to use as
"database"
description: The performed query.
required:
- terms
- genes
properties:
terms:
type: array
items:
type: string
description: Set of terms to use as query.
gene_ids:
$ref: '#/components/schemas/HpoTerm'
description: The query HPO terms.
genes:
type: array
items:
type: string
description: The set of ids for genes to use as "database".
nullable: true
gene_symbols:
type: array
items:
type: string
description: The set of symbols for genes to use as "database".
nullable: true
$ref: '#/components/schemas/Gene'
description: The gene list to score.
ResponseQuery:
type: object
title: HpoSimTermTermQuery
Expand All @@ -343,47 +359,55 @@ components:
description: The second set of HPO terms to compute similarity for.
ic_base:
$ref: '#/components/schemas/IcBasedOn'
description: What should information content be based on.
similarity:
$ref: '#/components/schemas/SimilarityMethod'
description: The similarity method to use.
combiner:
$ref: '#/components/schemas/ScoreCombiner'
description: The score combiner.
Result:
type: object
title: HpoSimTermTermResult
description: Result container.
title: HpoSimTermGeneResult
description: Result container data structure.
required:
- version
- query
- result
properties:
version:
$ref: '#/components/schemas/Version'
description: Version information.
query:
$ref: '#/components/schemas/ResponseQuery'
$ref: '#/components/schemas/Query'
description: The original query records.
result:
type: array
items:
$ref: '#/components/schemas/ResultEntry'
description: The resulting records for the scored genes.
ResultEntry:
type: object
title: HpoSimTermTermResultEntry
description: Result entry for `handle`.
title: HpoSimTermGeneResultEntry
description: Store score for a record with information on individual terms.
required:
- lhs
- rhs
- score
- gene_symbol
- raw_score
properties:
lhs:
type: string
description: The lhs entry.
rhs:
gene_symbol:
type: string
description: The rhs entry.
score:
description: The gene symbol.
raw_score:
type: number
format: float
description: The similarity score.
description: The raw Phenomizer score.
terms:
type:
- array
- 'null'
items:
$ref: '#/components/schemas/TermDetails'
description: Details on individual terms.
ResultGene:
type: object
description: Representation of a gene.
Expand All @@ -400,9 +424,10 @@ components:
type: string
description: The description.
hgnc_id:
type: string
type:
- string
- 'null'
description: The HGNC ID.
nullable: true
ResultHpoTerm:
type: object
description: Representation of an HPO term.
Expand All @@ -427,8 +452,10 @@ components:
properties:
version:
$ref: '#/components/schemas/Version'
description: Version information.
query:
$ref: '#/components/schemas/Query'
description: The original query records.
result:
type: array
items:
Expand Down Expand Up @@ -470,11 +497,13 @@ components:
- score
properties:
term_query:
allOf:
oneOf:
- type: 'null'
- $ref: '#/components/schemas/HpoTerm'
nullable: true
description: The query HPO term.
term_gene:
$ref: '#/components/schemas/HpoTerm'
description: The gene's HPO term.
score:
type: number
format: float
Expand Down
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