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openapi.yaml
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openapi: 3.0.3
info:
title: Global.health curator service API
description: Server for CRUD operations on Global.health data
termsOfService: 'https://global.health/terms-of-use/'
contact:
name: Global.health
url: https://global.health
email: info@global.health
license:
name: MIT
url: 'https://opensource.org/licenses/MIT'
version: 1.0.0
tags:
- name: Case
description: Case related operations
- name: Suggest
description: Suggestion for input of cases
- name: Geocode
description: Geolocation of a case
- name: User
description: User of the system
- name: Source
description: A source of case data
- name: Upload
description: >
A bundle of case data that were uploaded as part of a batch upload
or an automated ingestion pipeline
- name: Auth
description: Authentication-related operations
paths:
/auth/register:
post:
tags:
- Auth
- User
summary: >
Creates a local user for testing.The user can have any specified roles
in the request and the returned cookies can be used for subsequent
requests acting as this new user.
Note that this endpoint is only exposed in a local environment.
servers:
- url: http://localhost:3001/api
operationId: registerAuth
requestBody:
description: User to register
required: true
content:
application/json:
schema:
$ref: '#/components/schemas/User'
responses:
'200':
$ref: '#/components/responses/200Auth'
'400':
$ref: '#/components/responses/400'
'500':
$ref: '#/components/responses/500'
/sources:
get:
tags: [Source]
summary: Lists sources
operationId: listSources
parameters:
- name: page
in: query
description: The pages of sources to skip before starting to collect the result set
required: false
schema:
type: integer
format: int32
minimum: 1
default: 1
- name: limit
in: query
description: The number of sources to return
required: false
schema:
type: integer
format: int32
minimum: 1
maximum: 100
default: 10
- name: url
in: query
description: Origin URL substring on which to filter the result set
required: false
allowEmptyValue: true
allowReserved: true
schema:
type: string
- name: access_token
description: Bearer token used by automated ingestion lambdas.
in: query
required: false
schema:
type: string
responses:
'200':
$ref: '#/components/responses/200SourceArray'
'400':
$ref: '#/components/responses/400'
'403':
$ref: '#/components/responses/403'
'422':
$ref: '#/components/responses/422'
'500':
$ref: '#/components/responses/500'
post:
tags: [Source]
summary: Creates a new source
operationId: createSource
requestBody:
description: Source to add
required: true
content:
application/json:
schema:
$ref: '#/components/schemas/NewSource'
responses:
'201':
$ref: '#/components/responses/201Source'
'400':
$ref: '#/components/responses/400'
'403':
$ref: '#/components/responses/403'
'422':
$ref: '#/components/responses/422'
'500':
$ref: '#/components/responses/500'
/acknowledgment-sources:
get:
tags: [Source]
summary: Lists sources for acknowledgments table
operationId: listSourcesForTable
responses:
'200':
$ref: '#/components/responses/200AcknowledgmentSource'
'422':
$ref: '#/components/responses/422'
'500':
$ref: '#/components/responses/500'
/sources/{id}:
parameters:
- name: id
in: path
description: The source ID
required: true
schema:
type: string
pattern: '^[a-f\d]{24}$'
get:
tags: [Source]
summary: Gets a specific source
operationId: getSource
responses:
'200':
$ref: '#/components/responses/200Source'
'400':
$ref: '#/components/responses/400'
'403':
$ref: '#/components/responses/403'
'404':
$ref: '#/components/responses/404'
'422':
$ref: '#/components/responses/422'
'500':
$ref: '#/components/responses/500'
put:
tags: [Source]
summary: Updates a specific source
operationId: updateSource
requestBody:
description: Source to update
required: true
content:
application/json:
schema:
$ref: '#/components/schemas/Source'
responses:
'200':
$ref: '#/components/responses/200Source'
'400':
$ref: '#/components/responses/400'
'403':
$ref: '#/components/responses/403'
'404':
$ref: '#/components/responses/404'
'422':
$ref: '#/components/responses/422'
'500':
$ref: '#/components/responses/500'
delete:
tags: [Source]
summary: Deletes a specific source
operationId: deleteSource
responses:
'204':
description: Source deleted
'400':
$ref: '#/components/responses/400'
'403':
$ref: '#/components/responses/403'
'404':
$ref: '#/components/responses/404'
'500':
$ref: '#/components/responses/500'
/sources/{id}/retrieve:
parameters:
- name: id
in: path
description: The source ID for which to retrieve content
required: true
schema:
type: string
pattern: '^[a-f\d]{24}$'
- name: parse_start_date
in: query
description: >
The date on which to begin parsing/ingesting data (inclusive).
Provided in YYYY-MM-DD format.
required: false
schema:
type: string
pattern: '^[\d]{4}-[\d]{2}-[\d]{2}$'
- name: parse_end_date
in: query
description: >
The date on which to end parsing/ingesting data (inclusive).
Provided in YYYY-MM-DD format.
required: false
schema:
type: string
pattern: '^[\d]{4}-[\d]{2}-[\d]{2}$'
post:
tags: [Source]
summary: Trigger a retrieval of the content for the specified source
operationId: retrieve
responses:
'200':
$ref: '#/components/responses/200Retrieval'
'400':
$ref: '#/components/responses/400'
'403':
$ref: '#/components/responses/403'
'404':
$ref: '#/components/responses/404'
'500':
$ref: '#/components/responses/500'
/sources/uploads:
get:
tags: [Source, Upload]
summary: Lists all uploads for all sources
operationId: listUploads
parameters:
- name: page
in: query
description: The pages of uploads to skip before starting to collect the result set
required: false
schema:
type: integer
format: int32
minimum: 1
default: 1
- name: limit
in: query
description: The number of uploads to return
required: false
schema:
type: integer
format: int32
minimum: 1
maximum: 100
default: 10
- name: changes_only
in: query
description: >
Filters successful uploads to only include those that created or modified
cases. The response will still include non-successful uploads.
required: false
schema:
type: boolean
default: false
responses:
'200':
$ref: '#/components/responses/200UploadsArray'
'400':
$ref: '#/components/responses/400'
'403':
$ref: '#/components/responses/403'
'500':
$ref: '#/components/responses/500'
/sources/{sourceId}/uploads:
parameters:
- name: sourceId
in: path
description: The parent source ID in which to create the upload
required: true
schema:
type: string
pattern: '^[a-f\d]{24}$'
post:
tags: [Source, Upload]
summary: Creates a new upload in the specified source
operationId: createUpload
requestBody:
description: Upload to add
required: true
content:
application/json:
schema:
$ref: '#/components/schemas/Upload'
responses:
'201':
$ref: '#/components/responses/201Upload'
'400':
$ref: '#/components/responses/400'
'403':
$ref: '#/components/responses/403'
'404':
$ref: '#/components/responses/404'
'422':
$ref: '#/components/responses/422'
'500':
$ref: '#/components/responses/500'
/sources/{sourceId}/uploads/{id}:
parameters:
- name: sourceId
in: path
description: The parent source ID in which to find the upload
required: true
schema:
type: string
pattern: '^[a-f\d]{24}$'
- name: id
in: path
description: The ID of the upload to update
required: true
schema:
type: string
pattern: '^[a-f\d]{24}$'
put:
tags: [Source, Upload]
summary: Updates an existing upload in the specified source
operationId: updateUpload
requestBody:
description: New upload content
required: true
content:
application/json:
schema:
$ref: '#/components/schemas/Upload'
responses:
'200':
$ref: '#/components/responses/200Upload'
'400':
$ref: '#/components/responses/400'
'403':
$ref: '#/components/responses/403'
'404':
$ref: '#/components/responses/404'
'422':
$ref: '#/components/responses/422'
'500':
$ref: '#/components/responses/500'
/sources/parsers:
get:
summary: Lists parsers available for automated ingestion
tags: [Suggest]
operationId: listParsers
responses:
'200':
$ref: '#/components/responses/200ParsersArray'
'500':
$ref: '#/components/responses/500'
/cases:
get:
tags: [Case]
summary: Lists cases
operationId: listCases
parameters:
- name: page
in: query
description: The pages of sources to skip before starting to collect the result set
required: false
schema:
type: integer
format: int32
minimum: 1
default: 1
- name: limit
in: query
description: The number of cases to return
required: false
schema:
type: integer
format: int32
minimum: 1
maximum: 100
default: 10
- name: count_limit
in: query
description: The maximum number of documents that will be counted in mongoDB to make queries faster
required: false
schema:
type: integer
format: int32
minimum: 100
default: 10000
maximum: 50000
- name: sort_by
in: query
description: Keyword to sort by
required: false
schema:
type: string
- name: order
in: query
description: Sorting order
required: false
schema:
type: string
- name: q
in: query
description: The search query
required: false
allowEmptyValue: true
allowReserved: true
schema:
type: string
responses:
'200':
$ref: '#/components/responses/200CaseArray'
'400':
$ref: '#/components/responses/400'
'403':
$ref: '#/components/responses/403'
'422':
$ref: '#/components/responses/422'
'500':
$ref: '#/components/responses/500'
post:
tags: [Case]
summary: Creates one (or multiple identical) new cases
operationId: createCase
requestBody:
description: Case to add
required: true
content:
application/json:
schema:
$ref: '#/components/schemas/NewCase'
parameters:
- name: validate_only
in: query
description: Whether to validate the case without creating it
required: false
schema:
type: boolean
default: false
allowEmptyValue: true
- name: num_cases
in: query
description: The number of cases to create
required: false
schema:
type: integer
format: int32
minimum: 1
default: 1
responses:
'201':
$ref: '#/components/responses/201Create'
'400':
$ref: '#/components/responses/400'
'403':
$ref: '#/components/responses/403'
'422':
$ref: '#/components/responses/422'
'500':
$ref: '#/components/responses/500'
put:
tags: [Case]
summary: Upserts a case
description: >
Creates or updates a case, depending on whether the provided values for
the `caseReference.sourceId` and `caseReference.sourceEntryId` fields
correspond to an existing case record.
operationId: upsertCase
requestBody:
description: Case to upsert
required: true
content:
application/json:
schema:
allOf:
- $ref: '#/components/schemas/NewCase'
required:
- caseReference
responses:
'200':
$ref: '#/components/responses/200Case'
'201':
$ref: '#/components/responses/201Case'
'400':
$ref: '#/components/responses/400'
'403':
$ref: '#/components/responses/403'
'422':
$ref: '#/components/responses/422'
'500':
$ref: '#/components/responses/500'
delete:
summary: >
Deletes multiple cases. It is required to supply exactly one of either
caseIds or query in the request body. If caseIds are supplied, cases
corresponding to those caseIds will be deleted. If query is supplied,
all cases that match the query will be deleted.
tags: [Case]
operationId: deleteCases
requestBody:
description: Cases to delete
required: true
content:
application/json:
schema:
type: object
properties:
caseIds:
description: Cases corresponding to these ids will be deleted
type: array
items:
type: string
query:
description: >
Cases matching this query will be deleted. Must contain
non-whitespace characters.
type: string
pattern: \S+
oneOf:
- required: [caseIds]
- required: [query]
responses:
'204':
description: Cases deleted
'400':
$ref: '#/components/responses/400'
'403':
$ref: '#/components/responses/403'
'404':
$ref: '#/components/responses/404'
'422':
$ref: '#/components/responses/422'
'500':
$ref: '#/components/responses/500'
/cases/download:
post:
summary: >
Streams a CSV, TSV or JSON attachment of cases matching the search query.
If caseIds are supplied the CSV only contains cases with those ids.
You cannot supply both query and caseIds.
tags: [Case]
operationId: downloadCases
requestBody:
content:
application/x-www-form-urlencoded:
schema:
type: object
properties:
caseIds:
description: Cases corresponding to these ids will be returned
type: array
items:
type: string
pattern: '^[a-f\d]{24}$'
query:
description: >
Cases matching this query will be returned. This is ignored
if empty.
type: string
limit:
description: >
Max number of rows that can be downloaded when query is provided
type: string
format:
description: Format of data to be downloaded
type: string
responses:
'200':
$ref: '#/components/responses/200CasesDownload'
'500':
$ref: '#/components/responses/500'
/cases/downloadAsync:
post:
summary: >
Streams an attachment of cases matching the search query.
tags: [Case]
operationId: downloadAsync
requestBody:
content:
application/json:
schema:
type: object
properties:
query:
description: >
Cases matching this query will be returned.
type: string
responses:
'200':
$ref: '#/components/responses/200FilteredDataSetDownload'
'204':
$ref: '#/components/responses/204'
'500':
$ref: '#/components/responses/500'
/cases/getDownloadLink:
post:
summary: >
Generates signed URL to download full data set from AWS S3
tags: [Case]
operationId: generateSignedUrl
requestBody:
content:
application/json:
schema:
properties:
format:
description: Format in which data should be downloaded
type: string
responses:
'200':
$ref: '#/components/responses/200FullDataSetDownload'
'500':
$ref: '#components/responses/500'
/cases/symptoms:
get:
summary: Lists most frequently used sypmtoms
tags: [Suggest]
operationId: listSymptoms
parameters:
- name: limit
in: query
description: The number of items to return
required: false
schema:
type: integer
format: int32
minimum: 1
maximum: 100
default: 5
responses:
'200':
$ref: '#/components/responses/200SymptomArray'
'400':
$ref: '#/components/responses/400'
'403':
$ref: '#/components/responses/403'
'500':
$ref: '#/components/responses/500'
/cases/placesOfTransmission:
get:
summary: Lists most frequently used places of transmission
tags: [Suggest]
operationId: listPlacesOfTransmission
parameters:
- name: limit
in: query
description: The number of items to return
required: false
schema:
type: integer
format: int32
minimum: 1
maximum: 100
default: 5
responses:
'200':
$ref: '#/components/responses/200PlacesOfTransmissionArray'
'400':
$ref: '#/components/responses/400'
'403':
$ref: '#/components/responses/403'
'500':
$ref: '#/components/responses/500'
/cases/occupations:
get:
summary: Lists most frequently used occupations
tags: [Suggest]
operationId: listOccupations
parameters:
- name: limit
in: query
description: The number of items to return
required: false
schema:
type: integer
format: int32
minimum: 1
maximum: 100
default: 5
responses:
'200':
$ref: '#/components/responses/200OccupationArray'
'400':
$ref: '#/components/responses/400'
'403':
$ref: '#/components/responses/403'
'500':
$ref: '#/components/responses/500'
/cases/batchStatusChange:
post:
summary: Changes status for a list of cases
tags: [Case]
operationId: batchStatusChange
requestBody:
description: >
Case IDs are passed through an array of strings, note may be provided as well.
A query may be provided instead of list of IDs, this will change status for all
cases matching the query.
required: true
content:
application/json:
schema:
properties:
caseIds:
description: >
Cases having IDs provided here will have their
status changed to one specified in status field.
type: array
items:
type: string
status:
$ref: '#/components/schemas/CaseStatus'
query:
description: >
Cases matching this query will have their status
changed. Must contain non-whitespace characters.
type: string
pattern: \S+
note:
description: >
The reason behind exclusion (or other important info).
This field is ignored if a status is not "Excluded".
type: string
oneOf:
- required: [caseIds]
- required: [query]
required:
- status
responses:
'200':
$ref: '#/components/responses/200'
'400':
$ref: '#/components/responses/400'
'422':
$ref: '#/components/responses/422'
'500':
$ref: '#/components/responses/500'
/cases/batchUpsert:
post:
tags: [Case]
summary: Upserts multiple cases
operationId: batchUpsertCase
requestBody:
description: Cases to upsert
required: true
content:
application/json:
schema:
$ref: '#/components/schemas/CaseArray'
responses:
'200':
$ref: '#/components/responses/200BatchCaseUpsert'
'207':
$ref: '#/components/responses/207BatchCaseUpsert'
'500':
$ref: '#/components/responses/500'
/cases/batchUpdate:
post:
summary: Batch updates cases
tags: [Case]
operationId: batchUpdateCases
requestBody:
description: Cases to update
required: true
content:
application/json:
schema:
$ref: '#/components/schemas/CaseArray'
responses:
'200':
$ref: '#/components/responses/200BatchCaseUpdateResponse'
'400':
$ref: '#/components/responses/400'
'422':
$ref: '#/components/responses/422'
'500':
$ref: '#/components/responses/500'
/cases/batchUpdateQuery:
post:
summary: Batch updates cases that match the query property
tags: [Case]
operationId: batchUpdateQueryCases
requestBody:
description: Cases to update
required: true
content:
application/json:
schema:
properties:
query:
description: >
Cases matching this query will be updated. Must contain
non-whitespace characters.
type: string
pattern: \S+
case:
$ref: '#/components/schemas/Case'
required:
- query
- case
responses:
'200':
$ref: '#/components/responses/200BatchCaseUpdateResponse'
'400':
$ref: '#/components/responses/400'
'422':
$ref: '#/components/responses/422'
'500':
$ref: '#/components/responses/500'
/cases/{id}:
parameters:
- name: id
in: path
description: The case ID
required: true
schema:
type: string
pattern: '^[a-f\d]{24}$'
get:
tags: [Case]
summary: Gets a specific case
operationId: getCase
responses:
'200':
$ref: '#/components/responses/200Case'
'400':
$ref: '#/components/responses/400'
'403':
$ref: '#/components/responses/403'
'404':
$ref: '#/components/responses/404'
'422':
$ref: '#/components/responses/422'
'500':
$ref: '#/components/responses/500'
put:
tags: [Case]
summary: Updates a specific case
operationId: updateCase
requestBody:
description: Case to update
required: true
content:
application/json:
schema:
$ref: '#/components/schemas/Case'
responses:
'200':
$ref: '#/components/responses/200Case'
'400':
$ref: '#/components/responses/400'
'403':
$ref: '#/components/responses/403'
'404':
$ref: '#/components/responses/404'
'422':
$ref: '#/components/responses/422'
'500':
$ref: '#/components/responses/500'
delete:
tags: [Case]
summary: Deletes a specific case
operationId: deleteCase
responses:
'204':
description: Case deleted
'400':
$ref: '#/components/responses/400'
'403':
$ref: '#/components/responses/403'
'404':
$ref: '#/components/responses/404'
'500':
$ref: '#/components/responses/500'
/geocode/seed:
post:
tags: [Geocode]
summary: Adds geocodes to the geocoding database
operationId: seedGeocodes
requestBody:
description: A single geocode record
required: true
content:
application/json:
schema:
type: object
responses:
'200':
$ref: '#/components/responses/200'
/geocode/clear:
post:
tags: [Geocode]
summary: Clears geocodes from the geocoding database
operationId: clearGeocodes
responses:
'200':
$ref: '#/components/responses/200'
/geocode/suggest:
get:
tags: [Suggest, Geocode]
summary: Suggests geocodes for a given query string
operationId: suggestGeocodes
parameters:
- name: q
in: query
description: The location string for which to find geocodes
required: true
allowReserved: true
schema:
type: string
- name: limitToResolution
in: query
allowReserved: true
schema:
type: string
description: >
Comma-separated list of resolutions to restrict geocoding to.
Allowed values are: Point, Admin3, Admin2, Admin1, Country.
responses:
'200':
$ref: '#/components/responses/200LocationArray'
'403':
$ref: '#/components/responses/403'
'422':
$ref: '#/components/responses/422'
'500':
$ref: '#/components/responses/500'
/geocode/convertUTM:
get:
tags: [Geocode]
summary: Convert UTM coordinates to latitude/longitude.
operationId: convert
parameters:
- name: n
in: query
description: The northing coordinate (UTMY)
required: true
schema:
type: number
- name: e
in: query
description: The easting coordinate (UTMX)
required: true
schema:
type: number
- name: z
in: query
required: true
description: The UTM zone.
schema:
type: number
responses:
'200':
$ref: '#/components/responses/200Position'
'400':
$ref: '#/components/responses/400'
'500':
$ref: '#/components/responses/500'
/geocode/countryNames:
get:
tags: [Geocode]
summary: Get a list of all the ISO-3166-1 country codes in use, and the names we accept for those countries.
operationId: countryNames
responses:
'200':
$ref: '#/components/responses/200CountryNames'
'500':
$ref: '#/components/responses/500'
/users:
get:
tags: [User]
summary: Lists users
operationId: listUsers
parameters:
- name: page
in: query
description: The pages of users to skip before starting to collect the result set
required: false
schema: