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swagger.yaml
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definitions:
Error:
properties:
Message:
type: string
accession:
type: string
file:
type: string
gfe:
type: string
log:
items:
type: string
type: array
rank:
type: integer
sequence:
type: string
term:
type: string
type:
type: string
version:
type: string
required:
- Message
- version
type: object
Sequence:
example:
sequence: >-
TCCCCAGACGCCGAGGATGGCCGTCATGGCGCCCCGAACCCTCCTCCTGCTACTCTCGGGGGCCCTGGCCCTGACCCAGACCTGGGCGGGTGAGTGCGGGGTCGGGAGGGAAACCGCCTCTGCGGGGAGAAGCAAGGGGCCCTCCTGGCGGGGGCGCAGGACCGGGGGAGCCGCGCCGGGACGAGGGTCGGGCAGGTCTCAGCCACTGCTCGCCCCCAGGCTCCCACTCCATGAGGTATTTCTTCACATCCGTGTCCCGGCCCGGCCGCGGGGAGCCCCGCTTCATCGCCGTGGGCTACGTGGACGACACGCAGTTCGTGCGGTTCGACAGCGACGCCGCGAGCCAGAGGATGGAGCCGCGGGCGCCGTGGATAGAGCAGGAGGGGCCGGAGTATTGGGACCAGGAGACACGGAATGTGAAGGCCCAGTCACAGACTGACCGAGTGGACCTGGGGACCCTGCGCGGCTACTACAACCAGAGCGAGGCCGGTGAGTGACCCCGGCCGGGGGCGCAGGTCAGGACCCCTCATCCCCCACGGACGGGCCAGGTCGCCCACAGTCTCCGGGTCCGAGATCCACCCCGAAGCCGCGGGACCCCGAGACCCTTGCCCCGGGAGAGGCCCAGGCGCCTTTACCCGGTTTCATTTTCAGTTTAGGCCAAAAATCCCCCCGGGTTGGTCGGGGCTGGGCGGGGCTCGGGGGACTGGGCTGACCGCGGGGTCGGGGCCAGGTTCTCACACCATCCAGATAATGTATGGCTGCGACGTGGGGTCGGACGGGCGCTTCCTCCGCGGGTACCGGCAGGACGCCTACGACGGCAAGGATTACATCGCCCTGAACGAGGACCTGCGCTCTTGGACCGCGGCGGACATGGCGGCTCAGATCACCAAGCGCAAGTGGGAGGCGGCCCATGAGGCGGAGCAGTTGAGAGCCTACCTGGATGGCACGTGCGTGGAGTGGCTCCGCAGATACCTGGAGAACGGGAAGGAGACGCTGCAGCGCACGGGTACCAGGGGCCACGGGGCGCCTCCCTGATCGCCTGTAGATCTCCCGGGCTGGCCTCCCACAAGGAGGGGAGACAATTGGGACCAACACTAGAATATCACCCTCCCTCTGGTCCTGAGGGAGAGGAATCCTCCTGGGTTCCAGATCCTGTACCAGAGAGTGACTCTGAGGTTCCGCCCTGCTCTCTGACACAATTAAGGGATAAAATCTCTGAAGGAGTGACGGGAAGACGATCCCTCGAATACTGATGAGTGGTTCCCTTTGACACCGGCAGCAGCCTTGGGCCCGTGACTTTTCCTCTCAGGCCTTGTTCTCTGCTTCACACTCAATGTGTGTGGGGGTCTGAGTCCAGCACTTCTGAGTCCCTCAGCCTCCACTCAGGTCAGGACCAGAAGTCGCTGTTCCCTTCTCAGGGAATAGAAGATTATCCCAGGTGCCTGTGTCCAGGCTGGTGTCTGGGTTCTGTGCTCTCTTCCCCATCCCGGGTGTCCTGTCCATTCTCAAGATGGCCACATGCGTGCTGGTGGAGTGTCCCATGACAGATGCAAAATGCCTGAATTTTCTGACTCTTCCCGTCAGACCCCCCCAAGACACATATGACCCACCACCCCATCTCTGACCATGAGGCCACCCTGAGGTGCTGGGCCCTGGGCTTCTACCCTGCGGAGATCACACTGACCTGGCAGCGGGATGGGGAGGACCAGACCCAGGACACGGAGCTCGTGGAGACCAGGCCTGCAGGGGATGGAACCTTCCAGAAGTGGGCGGCTGTGGTGGTGCCTTCTGGAGAGGAGCAGAGATACACCTGCCATGTGCAGCATGAGGGTCTGCCCAAGCCCCTCACCCTGAGATGGGGTAAGGAGGGAGATGGGGGTGTCATGTCTCTTAGGGAAAGCAGGAGCCTCTCTGGAGACCTTTAGCAGGGTCAGGGCCCCTCACCTTCCCCTCTTTTCCCAGAGCTGTCTTCCCAGCCCACCATCCCCATCGTGGGCATCATTGCTGGCCTGGTTCTCCTTGGAGCTGTGATCACTGGAGCTGTGGTCGCTGCCGTGATGTGGAGGAGGAAGAGCTCAGGTGGAGAAGGGGTGAAGGGTGGGGTCTGAGATTTCTTGTCTCACTGAGGGTTCCAAGCCCCAGCTAGAAATGTGCCCTGTCTCATTACTGGGAAGCACCGTCCACAATCATGGGCCTACCCAGTCTGGGCCCCGTGTGCCAGCACTTACTCTTTTGTAAAGCACCTGTTAAAATGAAGGACAGATTTATCACCTTGATTACGGCGGTGATGGGACCTGATCCCAGCAGTCACAAGTCACAGGGGAAGGTCCCTGAGGACAGACCTCAGGAGGGCTATTGGTCCAGGACCCACACCTGCTTTCTTCATGTTTCCTGATCCCGCCCTGGGTCTGCAGTCACACATTTCTGGAAACTTCTCTGGGGTCCAAGACTAGGAGGTTCCTCTAGGACCTTAAGGCCCTGGCTCCTTTCTGGTATCTCACAGGACATTTTCTTCTCACAGATAGAAAAGGAGGGAGTTACACTCAGGCTGCAAGTAAGTATGAAGGAGGCTGATGCCTGAGGTCCTTGGGATATTGTGTTTGGGAGCCCATGGGGGAGCTCACCCACCTCACAATTCCTCCTCTAGCCACATCTTCTGTGGGATCTGACCAGGTTCTGTTTTTGTTCTACCCCAGGCAGTGACAGTGCCCAGGGCTCTGATGTGTCCCTCACAGCTTGTAAAGGTGAGAGCTTGGAGGACCTAATGTGTGTTGGGTGTTGGGCGGAACAGTGGACACAGCTGTGCTATGGGGTTTCTTTGCATTGGATGTATTGAGCATGCGATGGGCTGTTTAAGGTGTGACCCCTCACTGTGATGGATATGAATTTGTTCATGAATATTTTTTTCTATAGTGTGAGACAGCTGCCTTGTGTGGGACTGAG
structure:
- accession: 1
locus: HLA-A
rank: 1
sequence: ACTGACTG
term: exon
- accession: 23
locus: HLA-A
rank: 2
sequence: ACTGACTG
term: exon
version: 1.0.0
properties:
log:
items:
type: string
type: array
sequence:
type: string
structure:
items:
$ref: '#/definitions/Structure'
type: array
version:
type: string
required:
- sequence
- version
type: object
Structure:
example:
accession: 1
locus: HLA-A
rank: 1
sequence: ACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTGACTG
term: exon
properties:
accession:
type: integer
rank:
type: integer
sequence:
type: string
term:
type: string
required:
- term
- rank
- accession
- sequence
type: object
Subject:
example:
id: 012312A
typingData:
- locus: HLA-A
typing:
- gfe: HLA-Aw2-1-7-20-10-32-7-1-1-1-6-1-5-3-5-1-1
imgthla: 'A*01:01:01:01'
structure:
- accession: 1
rank: 1
sequence: ACTGACTG
term: exon
- accession: 23
rank: 2
sequence: ACTGACTG
term: exon
- gfe: HLA-Aw1-1-7-20-10-32-7-1-1-1-6-1-5-3-5-1-1
imgthla: 'A*01:01:01:01'
structure:
- accession: 1
rank: 1
sequence: ACTGACTG
term: exon
- accession: 23
rank: 2
sequence: ACTGACTG
term: exon
- locus: HLA-B
typing:
- gfe: HLA-Bw2-1-7-20-10-32-7-1-1-1-6-1-5-3-5-1-1
imgthla: 'B*04:01:01:01'
structure:
- accession: 1
rank: 1
sequence: ACTGACTG
term: exon
- accession: 23
rank: 2
sequence: ACTGACTG
term: exon
- gfe: HLA-Aw1-1-7-20-10-32-7-1-1-1-6-1-5-3-5-1-1
imgthla: 'B*05:01:01:01'
structure:
- accession: 1
rank: 1
sequence: ACTGACTG
term: exon
- accession: 23
rank: 2
sequence: ACTGACTG
term: exon
properties:
id:
type: string
typingData:
items:
$ref: '#/definitions/TypingData'
type: array
required:
- id
- typingData
type: object
SubjectData:
example:
log:
- >-
2016/11/15 17:37:16 INFO> Annotate.pm:167
GFE::Annotate::setInputFile - Input file:
t/resources/HmlTest.HML
- >-
2016/11/15 17:37:16 INFO> Annotate.pm:185
GFE::Annotate::alignment_file - Alignment file:
t/resources/HmlTest_reformat.csv
subjects:
- id: '111111'
typingData:
- locus: HLA-A
typing:
- gfe: HLA-Aw2-1-7-20-10-32-7-1-1-1-6-1-5-3-5-1-1
imgthla: 'A*01:01:01:01'
structure:
- accession: 1
rank: 1
sequence: ACTGACTG
term: exon
- accession: 23
rank: 2
sequence: ACTGACTG
term: exon
- gfe: HLA-Aw1-1-7-20-10-32-7-1-1-1-6-1-5-3-5-1-1
imgthla: 'A*01:01:01:01'
structure:
- accession: 1
rank: 1
sequence: ACTGACTG
term: exon
- accession: 23
rank: 2
sequence: ACTGACTG
term: exon
- locus: HLA-B
typing:
- gfe: HLA-Bw2-1-7-20-10-32-7-1-1-1-6-1-5-3-5-1-1
imgthla: 'B*04:01:01:01'
structure:
- accession: 1
rank: 1
sequence: ACTGACTG
term: exon
- accession: 23
rank: 2
sequence: ACTGACTG
term: exon
- gfe: HLA-Aw1-1-7-20-10-32-7-1-1-1-6-1-5-3-5-1-1
imgthla: 'B*05:01:01:01'
structure:
- accession: 1
rank: 1
sequence: ACTGACTG
term: exon
- accession: 23
rank: 2
sequence: ACTGACTG
term: exon
- id: '222222222'
typingData:
- locus: HLA-A
typing:
- gfe: HLA-Aw2-1-7-20-10-32-7-1-1-1-6-1-5-3-5-1-1
imgthla: 'A*01:01:01:01'
structure:
- accession: 1
rank: 1
sequence: ACTGACTG
term: exon
- accession: 23
rank: 2
sequence: ACTGACTG
term: exon
- gfe: HLA-Aw1-1-7-20-10-32-7-1-1-1-6-1-5-3-5-1-1
imgthla: 'A*01:01:01:01'
structure:
- accession: 1
rank: 1
sequence: ACTGACTG
term: exon
- accession: 23
rank: 2
sequence: ACTGACTG
term: exon
- locus: HLA-B
typing:
- gfe: HLA-Bw2-1-7-20-10-32-7-1-1-1-6-1-5-3-5-1-1
imgthla: 'B*04:01:01:01'
structure:
- accession: 1
rank: 1
sequence: ACTGACTG
term: exon
- accession: 23
rank: 2
sequence: ACTGACTG
term: exon
- gfe: HLA-Aw1-1-7-20-10-32-7-1-1-1-6-1-5-3-5-1-1
imgthla: 'B*05:01:01:01'
structure:
- accession: 1
rank: 1
sequence: ACTGACTG
term: exon
- accession: 23
rank: 2
sequence: ACTGACTG
term: exon
- id: '3333333333'
typingData:
- locus: HLA-A
typing:
- gfe: HLA-Aw2-1-7-20-10-32-7-1-1-1-6-1-5-3-5-1-1
imgthla: 'A*01:01:01:01'
structure:
- accession: 1
rank: 1
sequence: ACTGACTG
term: exon
- accession: 23
rank: 2
sequence: ACTGACTG
term: exon
- gfe: HLA-Aw1-1-7-20-10-32-7-1-1-1-6-1-5-3-5-1-1
imgthla: 'A*01:01:01:01'
structure:
- accession: 1
rank: 1
sequence: ACTGACTG
term: exon
- accession: 23
rank: 2
sequence: ACTGACTG
term: exon
- locus: HLA-B
typing:
- gfe: HLA-Bw2-1-7-20-10-32-7-1-1-1-6-1-5-3-5-1-1
imgthla: 'B*04:01:01:01'
structure:
- accession: 1
rank: 1
sequence: ACTGACTG
term: exon
- accession: 23
rank: 2
sequence: ACTGACTG
term: exon
- gfe: HLA-Aw1-1-7-20-10-32-7-1-1-1-6-1-5-3-5-1-1
imgthla: 'B*05:01:01:01'
structure:
- accession: 1
rank: 1
sequence: ACTGACTG
term: exon
- accession: 23
rank: 2
sequence: ACTGACTG
term: exon
version: 1.0.7
properties:
log:
items:
type: string
type: array
subjects:
items:
$ref: '#/definitions/Subject'
type: array
version:
type: string
required:
- subjects
- version
type: object
Typing:
example:
aligned: 0.95
gfe: HLA-Aw1-1-7-20-10-32-7-1-1-1-6-1-5-3-5-1-1
imgthla: 'A*01:01:01:01'
locus: HLA-A
structure:
- accession: 1
rank: 1
sequence: ACTGACTG
term: exon
- accession: 23
rank: 2
sequence: ACTGACTG
term: exon
version: 1.0.0
properties:
aligned:
type: number
fullgene:
$ref: '#/definitions/Structure'
gfe:
type: string
imgthla:
type: string
log:
items:
type: string
type: array
version:
type: string
structure:
items:
$ref: '#/definitions/Structure'
type: array
required:
- gfe
type: object
TypingData:
example:
locus: HLA-A
typing:
- gfe: HLA-Aw2-1-7-20-10-32-7-1-1-1-6-1-5-3-5-1-1
imgthla: 'A*01:01:01:01'
structure:
- accession: 1
rank: 1
sequence: ACTGACTG
term: exon
- accession: 23
rank: 2
sequence: ACTGACTG
term: exon
- gfe: HLA-Aw1-1-7-20-10-32-7-1-1-1-6-1-5-3-5-1-1
imgthla: 'A*02:01:01:01'
structure:
- accession: 1
rank: 1
sequence: ACTGACTG
term: exon
- accession: 23
rank: 2
sequence: ACTGACTG
term: exon
properties:
locus:
type: string
typing:
items:
$ref: '#/definitions/Typing'
type: array
required:
- typing
- locus
type: object
info:
contact:
email: mhalagan@nmdp.org
description: >-
The Gene Feature Enumeration (GFE) Submission service provides an API for
converting raw sequence data to GFE. It provides both a RESTful API and a
simple user interface for converting raw sequence data to GFE results.
Sequences can be submitted one at a time or as a fasta file. This service
uses <a
href="https://github.com/nmdp-bioinformatics/service-feature">nmdp-bioinformatics/service-feature</a>
for encoding the raw sequence data and <a
href="https://github.com/nmdp-bioinformatics/HSA">nmdp-bioinformatics/HSA</a>
for aligning the raw sequence data. The code is open source, and available
on <a
href="https://github.com/nmdp-bioinformatics/service-gfe-submission">GitHub</a>.<br><br>Go
to <a
href="http://service-gfe-submission.readthedocs.io">service-gfe-submission.readthedocs.io</a>
for more information
license:
name: GNU GENERAL PUBLIC LICENSE
url: 'https://www.gnu.org/licenses/lgpl.html'
title: Gene Feature Enumeration Service
version: 1.0.7
paths:
/fasta:
post:
description: Get Gene Feature Enumeration (GFE) from fasta file
parameters:
- description: 'Valid HLA, KIR or ABO locus'
in: formData
name: locus
type: string
- description: HML file
in: formData
name: file
type: file
- description: Number of retry requests to feature-service
in: query
name: retry
type: integer
- description: URL for the feature-service
in: query
name: feature_url
type: string
- description: Flag for returning the sequence and accession number of each feature
in: query
name: structures
type: boolean
- description: Flag for running service in verbose
in: query
name: verbose
type: boolean
responses:
'200':
description: Gene Feature Enumeration (GFE) from fasta file
schema:
$ref: '#/definitions/SubjectData'
'404':
description: Failed to generate GFE from fasta
schema:
$ref: '#/definitions/Error'
/flowhml:
post:
description: Get Gene Feature Enumeration (GFE) from HML file using nextflow
parameters:
- description: HML file
in: formData
name: file
type: file
- description: Option for returning HML or JSON
in: query
name: type
type: string
- description: URL for the feature-service
in: query
name: feature_url
type: string
- description: Number of retry requests to feature-service
in: query
name: retry
type: integer
- description: Flag for returning the sequence and accession number of each feature
in: query
name: structures
type: boolean
- description: Flag for running service in verbose
in: query
name: verbose
type: boolean
responses:
'200':
description: Gene Feature Enumeration (GFE) from HML file
schema:
$ref: '#/definitions/SubjectData'
'404':
description: Failed to generate GFE
schema:
$ref: '#/definitions/Error'
/gfe:
post:
description: Get Gene Feature Enumeration (GFE) from sequence and locus
parameters:
- description: 'Valid HLA, KIR or ABO locus'
in: query
name: locus
type: string
- description: Sequence data
in: query
name: sequence
type: string
- description: Number of retry requests to feature-service
in: query
name: retry
type: integer
- description: URL for the feature-service
in: query
name: feature_url
type: string
- description: Flag for returning the sequence and accession number of each feature
in: query
name: structures
type: boolean
- description: Flag for running service in verbose
in: query
name: verbose
type: boolean
responses:
'200':
description: Gene Feature Enumeration (GFE)
schema:
$ref: '#/definitions/Typing'
'404':
description: Failed to generate GFE
schema:
$ref: '#/definitions/Error'
/hml:
post:
description: Get Gene Feature Enumeration (GFE) from HML file
parameters:
- description: HML file
in: formData
name: file
type: file
- description: Option for returning HML or JSON
in: query
name: type
type: string
- description: URL for the feature-service
in: query
name: feature_url
type: string
- description: Number of retry requests to feature-service
in: query
name: retry
type: integer
- description: Flag for returning the sequence and accession number of each feature
in: query
name: structures
type: boolean
- description: Flag for running service in verbose
in: query
name: verbose
type: boolean
responses:
'200':
description: Gene Feature Enumeration (GFE) from HML file
schema:
$ref: '#/definitions/SubjectData'
'404':
description: Failed to generate GFE
schema:
$ref: '#/definitions/Error'
/sequence:
post:
description: Get sequence data from gene feature enumeration (GFE) annotation
parameters:
- description: 'Valid HLA, KIR or ABO locus'
in: query
name: locus
type: string
- description: GFE annotation
in: query
name: gfe
type: string
- description: Number of retry requests to feature-service
in: query
name: retry
type: integer
- description: URL for the feature-service
in: query
name: feature_url
type: string
- description: Flag for returning the sequence and accession number of each feature
in: query
name: structures
type: boolean
- description: Flag for running service in verbose
in: query
name: verbose
type: boolean
responses:
'200':
description: Sequence
schema:
$ref: '#/definitions/Sequence'
'404':
description: Failed to get sequence from GFE
schema:
$ref: '#/definitions/Error'
swagger: '2.0'