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ST
ga4gh-arraymap
Commits
442c0601
Commit
442c0601
authored
Mar 17, 2016
by
Daniel Teixeira
Browse files
adding yaml
parent
c4a9f897
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app/node-app/public/beacon-v03.yaml
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442c0601
swagger
:
'
2.0'
info
:
title
:
Beacon API
description
:
This document represents a proposal for the next version of the API for the GA4GH Beacon Project. The new API is intended to expose new functionalities motivated by potential uses cases contributed by the community.
version
:
'
0.3'
schemes
:
-
https
basePath
:
/v03
produces
:
-
application/json
paths
:
/info
:
get
:
summary
:
Beacon info endpoint
description
:
'
Returns
the
information
about
this
beacon
(name,
description,
API
version,
URL,
etc...)'
responses
:
'
200'
:
description
:
A Beacon info page
schema
:
$ref
:
'
#/definitions/Beacon'
default
:
description
:
Unexpected error
schema
:
$ref
:
'
#/definitions/BeaconError'
tags
:
-
Info
/query
:
get
:
summary
:
Beacon query endpoint
description
:
"
To
actually
ask
the
beacon
for
questions
like
\"
do
you
have
any
genomes
with
an
'A'
at
position
100,735
on
chromosome
3?
\"
And
the
answer
will
be
yes
or
no."
parameters
:
-
name
:
chrom
in
:
query
description
:
'
Chromosome
name.
Accepted
values
are
1-22,
X,
Y
and
MT.'
required
:
true
type
:
string
-
name
:
pos
in
:
query
description
:
Coordinate within a chromosome (0-based)
required
:
true
type
:
number
-
name
:
assembly
in
:
query
description
:
'
The
version
of
the
reference
genome,
NCBI
notation.'
required
:
true
type
:
string
-
name
:
alt
in
:
query
description
:
'
The
bases
that
appear
instead
of
the
reference
bases.
The
semantics
correspond
to
the
field
ALT
in
VCF.
Options
are
base
Strings
made
up
of
A,C,G,T,N,*
(case
insensitive)
or
an
angle-bracketed
ID
or
a
breakend
replacement
string.'
required
:
true
type
:
string
-
name
:
ref
in
:
query
description
:
'
The
reference
bases
for
this
variant,
starting
from
`position`,
in
the
genome
described
by
the
field
`reference`.
The
semantics
correspond
to
the
field
REF
in
VCF.
One
of
A,C,G,T,N
(case
insensitive).
Multiple
bases
are
permitted.'
required
:
true
type
:
string
-
name
:
datasetIds
in
:
query
description
:
'
Limit
to
a
set
of
datasetIds
at
the
target
website.
An
ID
is
specific
to
the
website
that
is
queried
and
can
be
an
accession
ID,
population
or
any
other
identifier'
required
:
false
type
:
array
items
:
type
:
string
tags
:
-
Query
responses
:
'
200'
:
description
:
A beacon allele response
schema
:
type
:
array
items
:
$ref
:
'
#/definitions/BeaconAlleleResponse'
default
:
description
:
Unexpected error
schema
:
$ref
:
'
#/definitions/BeaconError'
definitions
:
BeaconAlleleResponse
:
type
:
object
properties
:
beaconId
:
type
:
string
description
:
Beacon identfier
exists
:
type
:
boolean
description
:
indicates whether the variant has been observed.
alleleRequest
:
type
:
object
items
:
$ref
:
'
#/definitions/BeaconAlleleRequest'
description
:
The request to the Beacon.
datasetAlleleResponses
:
type
:
array
description
:
Datasets for which the variant is found.
items
:
$ref
:
'
#/definitions/DatasetAlleleResponse'
errorInfo
:
type
:
object
items
:
$ref
:
'
#/definitions/BeaconError'
description
:
Error
BeaconAlleleRequest
:
type
:
object
properties
:
chrom
:
type
:
string
description
:
'
Chromosome
name.
Accepted
values
are
1-22,
X,
Y
and
MT.'
pos
:
type
:
number
description
:
Coordinate within a chromosome (0-based).
assembly
:
type
:
string
description
:
'
The
version
of
the
reference
genome,
NCBI
notation.'
alt
:
type
:
string
description
:
'
The
bases
that
appear
instead
of
the
reference
bases.
The
semantics
correspond
to
the
field
ALT
in
VCF.
Options
are
base
Strings
made
up
of
A,C,G,T,N,*
(case
insensitive)
or
an
angle-bracketed
ID
or
a
breakend
replacement
string.'
ref
:
type
:
string
description
:
'
The
reference
bases
for
this
variant,
starting
from
`position`,
in
the
genome
described
by
the
field
`reference`.
The
semantics
correspond
to
the
field
REF
in
VCF.
One
of
A,C,G,T,N
(case
insensitive).
Multiple
bases
are
permitted.'
datasetIds
:
type
:
array
items
:
type
:
string
description
:
'
Limit
to
a
set
of
datasetIds
at
the
target
website.
An
ID
is
specific
to
the
website
that
is
queried
and
can
be
an
accession
ID,
population
or
any
other
identifier.'
BeaconError
:
type
:
object
properties
:
status
:
type
:
number
description
:
The error code.
reason
:
type
:
string
description
:
The reason of the error.
message
:
type
:
string
description
:
An error message.
DatasetAlleleResponse
:
type
:
object
properties
:
exists
:
type
:
boolean
description
:
Can be used to indicate that this variant has been observed before and no other information.
frequency
:
type
:
number
description
:
'
Frequency
of
the
allele
in
the
dataset,
0.0-1.0,
inclusive.'
errorInfo
:
type
:
array
items
:
$ref
:
'
#/definitions/BeaconError'
description
:
Beacon error.
variantCount
:
type
:
number
description
:
Number of variants in the dataset.
callCount
:
type
:
number
description
:
Number of called observations of this allele in the dataset.
sampleCount
:
type
:
number
description
:
Number of observations of this allele in the dataset.
note
:
type
:
string
description
:
Human-readable description of this variant.
externalUrl
:
type
:
string
description
:
URL with more information about a variant.
info
:
type
:
array
items
:
type
:
string
description
:
General information about the query.
BeaconOrganization
:
type
:
object
properties
:
id
:
type
:
string
description
:
Short unique identifier for the organization hosting the beacon.
name
:
type
:
string
description
:
The organization name.
description
:
type
:
string
description
:
The organization description.
address
:
type
:
string
description
:
The address of the organization.
welcomeUrl
:
type
:
string
description
:
URL of homepage with additional info about the organizazion
contactUrl
:
type
:
string
description
:
Beacon contact person in the organization.
logoUrl
:
type
:
string
description
:
URL with a logo shown.
info
:
type
:
array
items
:
type
:
string
description
:
General information about the organization.
Beacon
:
type
:
object
properties
:
id
:
type
:
string
description
:
Short unique identifier for the beacon.
organization
:
$ref
:
'
#/definitions/BeaconOrganization'
description
:
type
:
string
description
:
Longer human-readable description of the beacon.
datasets
:
type
:
array
description
:
List of datasets served by the beacon.
items
:
$ref
:
'
#/definitions/BeaconDataset'
apiVersion
:
type
:
string
description
:
Beacon API version.
welcomeUrl
:
type
:
string
description
:
URL of homepage with additional info about the beacon.
sampleAlleleRequests
:
type
:
array
description
:
Examples of allele requests.
items
:
$ref
:
'
#/definitions/BeaconAlleleRequest'
name
:
type
:
string
description
:
The beacon name.
version
:
type
:
string
description
:
The beacon version.
alternativeUrl
:
type
:
string
description
:
Alternative URL.
created
:
type
:
number
description
:
"
The
beacon's
creation
date."
updated
:
type
:
number
description
:
"
The
beacon's
last
update
date."
info
:
description
:
General information about the beacon.
type
:
array
items
:
type
:
string
BeaconDataset
:
type
:
object
properties
:
id
:
type
:
string
description
:
Short unique identifier for the dataset.
assembly
:
type
:
string
description
:
'
The
version
of
the
reference
genome,
NCBI
notation.'
description
:
type
:
string
description
:
"
The
dataset's
description."
dataUse
:
$ref
:
'
#/definitions/DataUse'
name
:
type
:
string
description
:
"
The
dataset's
name."
created
:
type
:
number
description
:
The dataset creation date.
updated
:
type
:
number
description
:
"
The
dataset's
last
update
date."
version
:
type
:
string
description
:
The version of the dataset.
variantCount
:
type
:
number
description
:
The number of variants in the dataset.
callCount
:
type
:
number
description
:
The number of calls in the dataset.
sampleCount
:
type
:
number
description
:
The number of samples in the dataset.
externalUrl
:
type
:
string
description
:
The URL of a page with additional info about the dataset.
info
:
description
:
General inoformation about the dataset.
type
:
array
items
:
type
:
string
DataUse
:
type
:
object
properties
:
primaryCategory
:
$ref
:
'
#/definitions/DataUseCondition'
requirements
:
description
:
List of data use requirements.
type
:
array
items
:
$ref
:
'
#/definitions/DataUseCondition'
secondaryCategories
:
description
:
List of secondary data use conditions.
type
:
array
items
:
$ref
:
'
#/definitions/DataUseCondition'
DataUseCondition
:
type
:
object
properties
:
description
:
type
:
string
description
:
Data use condition description.
code
:
type
:
string
description
:
Data use condition code.
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