Organism Specific ID Service vv1.0.0

Resources

Returns an array of the organisms currently registered with the OSID service.

The results may be optionally filtered to a single result by use of the organismName query parameter.

Parameters

Parameter	Type	Description
Query
organismName	string	Name of the organism to look up. This field supports wildcards using the asterisk (`*`) character.
createdAfter ZeroBasedLong	integer	Unix timestamp of the earliest records this query should match. No records created before this timestamp will be returned. Max. value: 9223372036854776000 Format: int64 Inherits: integer
createdBefore ZeroBasedLong	integer	Unix timestamp of the latest records this query should match. No records created after this timestamp will be returned. Max. value: 9223372036854776000 Format: int64 Inherits: integer
createdBy	string	Filter results on the ID or name of the user that created the records.

Secured By

basic basic

HTTP Basic Authentication

curl -X GET \
  undefined/organisms?organismName=<value>&ZeroBasedLong=<value>&ZeroBasedLong=<value>&createdBy=<value>

Parameter	Type	Description
[] OrganismResponse	object	Inherits: object
[].organismId* organismId	integer	Internal primary key value assigned to this organism record. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
[].organismName*	string	Min. length: 3
[].template* template	string	Currently assigned gene ID template string. Pattern: ^.%[0-9,+\- $.]d.*$ Min. length: 5 Inherits: string
[].geneIntStart* geneIntStart	integer	Starting point for the gene ID integer counter. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
[].transcriptIntStart* transcriptIntStart	integer	Starting point for the transcript ID integer counter. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
[].geneIntCurrent* geneIntCurrent	integer	Current value for the gene ID integer counter. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
[].transcriptIntCurrent* transcriptIntCurrent	integer	Current value for the transcript ID integer counter. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
[].createdOn*	datetime	Timestamp of when this record was created.
[].createdBy* createdBy	integer	User ID of the user/app that created this record. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer

Response Body

[
  {
    "organismId": 24,
    "organismName": "Plasmodium falciparum 3D7",
    "template": "PF3D7_%07d",
    "geneIntStart": 1500000,
    "geneIntCurrent": 1501203,
    "transcriptIntStart": 1,
    "transcriptIntCurrent": 57,
    "createdOn": "2020-08-25T11:43:16Z",
    "createdBy": 26
  }
]

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "unauthorized",
  "message": "users must be logged in to access this resource"
}

Forbidden ForbiddenError

application/json

Server understood the request but is refusing it.

Could be caused by incorrect instructions or an authenticated client requesting a resource or action that requires permissions that the client does not have assigned.

Discriminator: status

Discriminator value: forbidden

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "forbidden",
  "message": "the current user is not permitted to perform this action"
}

Unprocessable Entity UnprocessableEntityError

application/json

The request payload or parameters are correctly structured but fail resource specific validation.

Discriminator: status

Discriminator value: invalid-input

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string
errors*	object	Additional properties: Yes
errors.general*	array	Non-field specific errors.
errors.general[]	string
errors.byKey*	object	Field specific errors Additional properties: Yes
errors.byKey.//*	array
errors.byKey.//[]	string

Response Body

{
  "status": "invalid-input",
  "message": "JSON validation failed",
  "errors": {
    "general": [],
    "byKey": {
      "id": [
        "Given ID value does not point to an existing record."
      ]
    }
  }
}

Discriminator: status

Discriminator value: server-error

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string
requestId*	string

Response Body

{
  "status": "server-error",
  "message": "Datastore connection lost",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

Registers a new organism with the OSID service, returning the ID of the newly registered organism record on success.

Secured By

basic basic

HTTP Basic Authentication

curl -X POST \
  -H "Content-type: application/json"
  -d @body.json \
  undefined/organisms

Inherits: object

Parameter	Type	Description
organismName*	string	Min. length: 3
template* template	string	Gene ID template string. Must include at least 1 integer format parameter for injecting the id counter value into the template. The template string will be expanded using Java's String.format method which will expect a Java format parameter. See the Java string formatting cheatsheet for possible parameters and modifiers. The example parameter for this field is `%07d` which breaks down to: `%` = parameter start marker `07` = left pad the number with zeros for a total length of 7 digits `d` = format as an int NOTE: When used, this template string will be passed exactly one int64 value and nothing else. Templates should only include `%d` based formats. If the template needs more than one instance of the counter int64 value, positional parameters may be used. Pattern: ^.%[0-9,+\- $.]d.*$ Min. length: 5 Inherits: string
geneIntStart* geneIntStart	integer	Starting point for the gene ID integer counter. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
transcriptIntStart transcriptIntStart	integer	Starting point for the transcript ID integer counter. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Default value: 1 Inherits: integer

Request Body

{
  "organismName": "Plasmodium falciparum 3D7",
  "template": "PF3D7_%07d",
  "geneIntStart": 1500000,
  "transcriptIntStart": 1
}

OneBasedLong OneBasedLong

application/json

Primary key value for the newly created organism record.

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: integer

Bad Request BadRequestError

application/json

Request could not be parsed or was otherwise unusable.

Discriminator: status

Discriminator value: bad-request

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "bad-request",
  "message": "malformed JSON"
}

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "unauthorized",
  "message": "users must be logged in to access this resource"
}

Forbidden ForbiddenError

application/json

Server understood the request but is refusing it.

Could be caused by incorrect instructions or an authenticated client requesting a resource or action that requires permissions that the client does not have assigned.

Discriminator: status

Discriminator value: forbidden

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "forbidden",
  "message": "the current user is not permitted to perform this action"
}

Unprocessable Entity UnprocessableEntityError

application/json

The request payload or parameters are correctly structured but fail resource specific validation.

Discriminator: status

Discriminator value: invalid-input

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string
errors*	object	Additional properties: Yes
errors.general*	array	Non-field specific errors.
errors.general[]	string
errors.byKey*	object	Field specific errors Additional properties: Yes
errors.byKey.//*	array
errors.byKey.//[]	string

Response Body

{
  "status": "invalid-input",
  "message": "JSON validation failed",
  "errors": {
    "general": [],
    "byKey": {
      "id": [
        "Given ID value does not point to an existing record."
      ]
    }
  }
}

Discriminator: status

Discriminator value: server-error

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string
requestId*	string

Response Body

{
  "status": "server-error",
  "message": "Datastore connection lost",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

Looks up and returns the details of a single organism record by record id.

Parameters

Parameter	Type	Description
Path
organism-id*	string	May be either the primary key value for the specific organism or the organism name.

Secured By

basic basic

HTTP Basic Authentication

curl -X GET \
  undefined/organisms/{organism-id}

Inherits: object

Parameter	Type	Description
organismId* organismId	integer	Internal primary key value assigned to this organism record. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
organismName*	string	Min. length: 3
template* template	string	Currently assigned gene ID template string. Pattern: ^.%[0-9,+\- $.]d.*$ Min. length: 5 Inherits: string
geneIntStart* geneIntStart	integer	Starting point for the gene ID integer counter. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
transcriptIntStart* transcriptIntStart	integer	Starting point for the transcript ID integer counter. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
geneIntCurrent* geneIntCurrent	integer	Current value for the gene ID integer counter. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
transcriptIntCurrent* transcriptIntCurrent	integer	Current value for the transcript ID integer counter. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
createdOn*	datetime	Timestamp of when this record was created.
createdBy* createdBy	integer	User ID of the user/app that created this record. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer

Response Body

{
  "organismId": 24,
  "organismName": "Plasmodium falciparum 3D7",
  "template": "PF3D7_%07d",
  "geneIntStart": 1500000,
  "geneIntCurrent": 1501203,
  "transcriptIntStart": 1,
  "transcriptIntCurrent": 57,
  "createdOn": "2020-08-25T11:43:16Z",
  "createdBy": 26
}

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "unauthorized",
  "message": "users must be logged in to access this resource"
}

Not Found NotFoundError

application/json

The requested resource was not found on this server.

Discriminator: status

Discriminator value: not-found

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "not-found",
  "message": "the requested resource could not be found"
}

Discriminator: status

Discriminator value: server-error

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string
requestId*	string

Response Body

{
  "status": "server-error",
  "message": "Datastore connection lost",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

Updates a specific organism record by replacing specific fields with the new values in the request body.

Put requests will be rejected if they violate the following rules:

The new startingInt value must not be lower than the organism record's currentInt value.
The template value must not be null or empty.
The template value must contain a single printf integer placeholder. (See the Java string formatting cheatsheet)
The organismName value must not be null or empty.

Parameters

Parameter	Type	Description
Path
organism-id*	string	May be either the primary key value for the specific organism or the organism name.

Secured By

basic basic

HTTP Basic Authentication

curl -X PUT \
  -H "Content-type: application/json"
  -d @body.json \
  undefined/organisms/{organism-id}

Inherits: object

Parameter Type Description

Parameter	Type	Description
template* template	string	Gene ID template string. Must include at least 1 integer format parameter for injecting the id counter value into the template. The template string will be expanded using Java's String.format method which will expect a Java format parameter. See the Java string formatting cheatsheet for possible parameters and modifiers. The example parameter for this field is `%07d` which breaks down to: `%` = parameter start marker `07` = left pad the number with zeros for a total length of 7 digits `d` = format as an int NOTE: When used, this template string will be passed exactly one int64 value and nothing else. Templates should only include `%d` based formats. If the template needs more than one instance of the counter int64 value, positional parameters may be used. Pattern: ^.%[0-9,+\- $.]d.*$ Min. length: 5 Inherits: string
geneIntStart geneIntStart	integer	Starting point for the gene ID integer counter. NOTE This field may only be changed if no gene ids have yet been issued for this organism. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
transcriptIntStart transcriptIntStart	integer	Starting point for the transcript ID integer counter. NOTE This field may only be changed if no transcript ids have yet been issued for this organism. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer

template* template

string

Gene ID template string. Must include at least 1 integer format parameter for injecting the id counter value into the template.

The template string will be expanded using Java's String.format method which will expect a Java format parameter.

See the Java string formatting cheatsheet for possible parameters and modifiers.

The example parameter for this field is %07d which breaks down to:

% = parameter start marker
07 = left pad the number with zeros for a total length of 7 digits
d = format as an int

NOTE: When used, this template string will be passed exactly one int64 value and nothing else. Templates should only include %d based formats. If the template needs more than one instance of the counter int64 value, positional parameters may be used.

Pattern: ^.*%[0-9,+\- $.]*d.*$

Min. length: 5

Inherits: string

geneIntStart geneIntStart

integer

Starting point for the gene ID integer counter.

NOTE This field may only be changed if no gene ids have yet been issued for this organism.

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: integer

transcriptIntStart transcriptIntStart

integer

Starting point for the transcript ID integer counter.

NOTE This field may only be changed if no transcript ids have yet been issued for this organism.

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: integer

Request Body

{
  "template": "PF3D7_%07d",
  "geneIntStart": 1500000,
  "transcriptIntStart": 1
}

Bad Request BadRequestError

application/json

Request could not be parsed or was otherwise unusable.

Discriminator: status

Discriminator value: bad-request

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "bad-request",
  "message": "malformed JSON"
}

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "unauthorized",
  "message": "users must be logged in to access this resource"
}

Forbidden ForbiddenError

application/json

Server understood the request but is refusing it.

Could be caused by incorrect instructions or an authenticated client requesting a resource or action that requires permissions that the client does not have assigned.

Discriminator: status

Discriminator value: forbidden

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "forbidden",
  "message": "the current user is not permitted to perform this action"
}

Not Found NotFoundError

application/json

The requested resource was not found on this server.

Discriminator: status

Discriminator value: not-found

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "not-found",
  "message": "the requested resource could not be found"
}

Unprocessable Entity UnprocessableEntityError

application/json

The request payload or parameters are correctly structured but fail resource specific validation.

Discriminator: status

Discriminator value: invalid-input

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string
errors*	object	Additional properties: Yes
errors.general*	array	Non-field specific errors.
errors.general[]	string
errors.byKey*	object	Field specific errors Additional properties: Yes
errors.byKey.//*	array
errors.byKey.//[]	string

Response Body

{
  "status": "invalid-input",
  "message": "JSON validation failed",
  "errors": {
    "general": [],
    "byKey": {
      "id": [
        "Given ID value does not point to an existing record."
      ]
    }
  }
}

Discriminator: status

Discriminator value: server-error

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string
requestId*	string

Response Body

{
  "status": "server-error",
  "message": "Datastore connection lost",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

Parameters

Parameter	Type	Description
Query
createdAfter ZeroBasedLong	integer	Int64 value with a valid value range of `[0..9223372036854775807]`. Max. value: 9223372036854776000 Format: int64 Inherits: integer
createdBefore ZeroBasedLong	integer	Int64 value with a valid value range of `[0..9223372036854775807]`. Max. value: 9223372036854776000 Format: int64 Inherits: integer
createdBy	string

Secured By

basic basic

HTTP Basic Authentication

curl -X GET \
  undefined/idSets?ZeroBasedLong=<value>&ZeroBasedLong=<value>&createdBy=<value>

Parameter	Type	Description
[] IdSetResponse	object	Inherits: object
[].idSetId* idSetId	integer	Internal storage primary key for an ID set. Used to make requests that operate on or retrieve one specific ID set. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
[].organismId* organismId	integer	Int64 value with a valid value range of `[1..9223372036854775807]`. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
[].template* template	string	Gene ID template string. Must include at least 1 integer format parameter for injecting the id counter value into the template. The template string will be expanded using Java's String.format method which will expect a Java format parameter. See the Java string formatting cheatsheet for possible parameters and modifiers. The example parameter for this field is `%07d` which breaks down to: `%` = parameter start marker `07` = left pad the number with zeros for a total length of 7 digits `d` = format as an int NOTE: When used, this template string will be passed exactly one int64 value and nothing else. Templates should only include `%d` based formats. If the template needs more than one instance of the counter int64 value, positional parameters may be used. Pattern: ^.%[0-9,+\- $.]d.*$ Min. length: 5 Inherits: string
[].geneIntStart* geneIntStart	integer	Int64 value with a valid value range of `[1..9223372036854775807]`. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
[].generatedGeneCount* generatedGeneCount	integer	Int32 value with a valid value range of `[0..2147483647]`. Max. value: 2147483647 Format: int32 Inherits: integer
[].generatedIds*	array
[].generatedIds[]	object	Inherits: GeneratedTranscriptEntry
[].generatedIds[].geneId*	string	Min. length: 3
[].generatedIds[].transcripts*	array
[].generatedIds[].transcripts[]	string
[].generatedIds[].proteins*	array
[].generatedIds[].proteins[]	string
[].createdOn*	datetime
[].createdBy* createdBy	integer	Int64 value with a valid value range of `[1..9223372036854775807]`. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer

Response Body

[
  {
    "idSetId": 48,
    "organismId": 1,
    "template": "PF3D7_%07d",
    "geneIntStart": 150000,
    "generatedGeneCount": 2,
    "generatedIds": [
      {
        "geneId": "PF3D7_0145842",
        "transcripts": [
          "PF3D7_0145842.R57",
          "PF3D7_0145842.R58",
          "PF3D7_0145842.R59",
          "PF3D7_0145842.R78"
        ],
        "proteins": [
          "PF3D7_0145842.P57",
          "PF3D7_0145842.P58",
          "PF3D7_0145842.P59",
          "PF3D7_0145842.P78"
        ]
      },
      {
        "geneId": "PF3D7_150001",
        "transcripts": [],
        "proteins": []
      },
      {
        "geneId": "PF3D7_150002",
        "transcripts": [
          "PF3D7_150002.R79"
        ],
        "proteins": [
          "PF3D7_150002.P79"
        ]
      }
    ],
    "createdOn": "2020-08-25T11:43:16Z",
    "createdBy": 215
  }
]

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "unauthorized",
  "message": "users must be logged in to access this resource"
}

Forbidden ForbiddenError

application/json

Server understood the request but is refusing it.

Could be caused by incorrect instructions or an authenticated client requesting a resource or action that requires permissions that the client does not have assigned.

Discriminator: status

Discriminator value: forbidden

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "forbidden",
  "message": "the current user is not permitted to perform this action"
}

Discriminator: status

Discriminator value: server-error

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string
requestId*	string

Response Body

{
  "status": "server-error",
  "message": "Datastore connection lost",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

Secured By

basic basic

HTTP Basic Authentication

curl -X POST \
  -H "Content-type: application/json"
  -d @body.json \
  undefined/idSets

Inherits: object

Parameter	Type	Description
organismId* organismId	integer	Internal storage primary key for an organism registered with the OSID service. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
generateGenes* generateGenes	integer	Number of gene IDs generated by the OSID service for the current organism. Max. value: 2147483647 Format: int32 Inherits: integer

Parameter

Type

Description

organismId* organismId

integer

Internal storage primary key for an organism registered with the OSID service.

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: integer

generateGenes* generateGenes

integer

Number of gene IDs generated by the OSID service for the current organism.

Max. value: 2147483647

Format: int32

Inherits: integer

Inherits: object

Parameter	Type	Description
idSetId* idSetId	integer	Internal storage primary key for an ID set. Used to make requests that operate on or retrieve one specific ID set. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
organismId* organismId	integer	Int64 value with a valid value range of `[1..9223372036854775807]`. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
template* template	string	Gene ID template string. Must include at least 1 integer format parameter for injecting the id counter value into the template. The template string will be expanded using Java's String.format method which will expect a Java format parameter. See the Java string formatting cheatsheet for possible parameters and modifiers. The example parameter for this field is `%07d` which breaks down to: `%` = parameter start marker `07` = left pad the number with zeros for a total length of 7 digits `d` = format as an int NOTE: When used, this template string will be passed exactly one int64 value and nothing else. Templates should only include `%d` based formats. If the template needs more than one instance of the counter int64 value, positional parameters may be used. Pattern: ^.%[0-9,+\- $.]d.*$ Min. length: 5 Inherits: string
geneIntStart* geneIntStart	integer	Int64 value with a valid value range of `[1..9223372036854775807]`. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
generatedGeneCount* generatedGeneCount	integer	Int32 value with a valid value range of `[0..2147483647]`. Max. value: 2147483647 Format: int32 Inherits: integer
generatedIds*	array
generatedIds[]	object	Inherits: GeneratedTranscriptEntry
generatedIds[].geneId*	string	Min. length: 3
generatedIds[].transcripts*	array
generatedIds[].transcripts[]	string
generatedIds[].proteins*	array
generatedIds[].proteins[]	string
createdOn*	datetime
createdBy* createdBy	integer	Int64 value with a valid value range of `[1..9223372036854775807]`. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer

Response Body

{
  "idSetId": 48,
  "organismId": 1,
  "template": "PF3D7_%07d",
  "geneIntStart": 150000,
  "generatedGeneCount": 2,
  "generatedIds": [
    {
      "geneId": "PF3D7_150001",
      "transcripts": [],
      "proteins": []
    },
    {
      "geneId": "PF3D7_150002",
      "transcripts": [],
      "proteins": []
    }
  ],
  "createdOn": "2020-08-25T11:43:16Z",
  "createdBy": 123
}

Bad Request BadRequestError

application/json

Request could not be parsed or was otherwise unusable.

Discriminator: status

Discriminator value: bad-request

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "bad-request",
  "message": "malformed JSON"
}

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "unauthorized",
  "message": "users must be logged in to access this resource"
}

Forbidden ForbiddenError

application/json

Server understood the request but is refusing it.

Could be caused by incorrect instructions or an authenticated client requesting a resource or action that requires permissions that the client does not have assigned.

Discriminator: status

Discriminator value: forbidden

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "forbidden",
  "message": "the current user is not permitted to perform this action"
}

Unprocessable Entity UnprocessableEntityError

application/json

The request payload or parameters are correctly structured but fail resource specific validation.

Discriminator: status

Discriminator value: invalid-input

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string
errors*	object	Additional properties: Yes
errors.general*	array	Non-field specific errors.
errors.general[]	string
errors.byKey*	object	Field specific errors Additional properties: Yes
errors.byKey.//*	array
errors.byKey.//[]	string

Response Body

{
  "status": "invalid-input",
  "message": "JSON validation failed",
  "errors": {
    "general": [],
    "byKey": {
      "id": [
        "Given ID value does not point to an existing record."
      ]
    }
  }
}

Discriminator: status

Discriminator value: server-error

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string
requestId*	string

Response Body

{
  "status": "server-error",
  "message": "Datastore connection lost",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

Parameters

Parameter Type Description

Path

Parameter	Type	Description
id-set-id* OneBasedLong	integer	Int64 value with a valid value range of `[1..9223372036854775807]`. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer

id-set-id* OneBasedLong

integer

Int64 value with a valid value range of [1..9223372036854775807].

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: integer

Secured By

basic basic

HTTP Basic Authentication

curl -X GET \
  undefined/idSets/{id-set-id}

Inherits: object

Parameter	Type	Description
idSetId* idSetId	integer	Internal storage primary key for an ID set. Used to make requests that operate on or retrieve one specific ID set. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
organismId* organismId	integer	Int64 value with a valid value range of `[1..9223372036854775807]`. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
template* template	string	Gene ID template string. Must include at least 1 integer format parameter for injecting the id counter value into the template. The template string will be expanded using Java's String.format method which will expect a Java format parameter. See the Java string formatting cheatsheet for possible parameters and modifiers. The example parameter for this field is `%07d` which breaks down to: `%` = parameter start marker `07` = left pad the number with zeros for a total length of 7 digits `d` = format as an int NOTE: When used, this template string will be passed exactly one int64 value and nothing else. Templates should only include `%d` based formats. If the template needs more than one instance of the counter int64 value, positional parameters may be used. Pattern: ^.%[0-9,+\- $.]d.*$ Min. length: 5 Inherits: string
geneIntStart* geneIntStart	integer	Int64 value with a valid value range of `[1..9223372036854775807]`. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
generatedGeneCount* generatedGeneCount	integer	Int32 value with a valid value range of `[0..2147483647]`. Max. value: 2147483647 Format: int32 Inherits: integer
generatedIds*	array
generatedIds[]	object	Inherits: GeneratedTranscriptEntry
generatedIds[].geneId*	string	Min. length: 3
generatedIds[].transcripts*	array
generatedIds[].transcripts[]	string
generatedIds[].proteins*	array
generatedIds[].proteins[]	string
createdOn*	datetime
createdBy* createdBy	integer	Int64 value with a valid value range of `[1..9223372036854775807]`. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer

Response Body

{
  "idSetId": 48,
  "organismId": 1,
  "template": "PF3D7_%07d",
  "geneIntStart": 150000,
  "generatedGeneCount": 2,
  "generatedIds": [
    {
      "geneId": "PF3D7_0145842",
      "transcripts": [
        "PF3D7_0145842.R57",
        "PF3D7_0145842.R58",
        "PF3D7_0145842.R59",
        "PF3D7_0145842.R78"
      ],
      "proteins": [
        "PF3D7_0145842.P57",
        "PF3D7_0145842.P58",
        "PF3D7_0145842.P59",
        "PF3D7_0145842.P78"
      ]
    },
    {
      "geneId": "PF3D7_150001",
      "transcripts": [],
      "proteins": []
    },
    {
      "geneId": "PF3D7_150002",
      "transcripts": [
        "PF3D7_150002.R79"
      ],
      "proteins": [
        "PF3D7_150002.P79"
      ]
    }
  ],
  "createdOn": "2020-08-25T11:43:16Z",
  "createdBy": 546
}

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "unauthorized",
  "message": "users must be logged in to access this resource"
}

Forbidden ForbiddenError

application/json

Server understood the request but is refusing it.

Could be caused by incorrect instructions or an authenticated client requesting a resource or action that requires permissions that the client does not have assigned.

Discriminator: status

Discriminator value: forbidden

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "forbidden",
  "message": "the current user is not permitted to perform this action"
}

Not Found NotFoundError

application/json

The requested resource was not found on this server.

Discriminator: status

Discriminator value: not-found

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "not-found",
  "message": "the requested resource could not be found"
}

Discriminator: status

Discriminator value: server-error

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string
requestId*	string

Response Body

{
  "status": "server-error",
  "message": "Datastore connection lost",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

Parameters

Parameter Type Description

Path

Parameter	Type	Description
id-set-id* OneBasedLong	integer	Int64 value with a valid value range of `[1..9223372036854775807]`. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer

id-set-id* OneBasedLong

integer

Int64 value with a valid value range of [1..9223372036854775807].

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: integer

Secured By

basic basic

HTTP Basic Authentication

curl -X PATCH \
  -H "Content-type: application/json"
  -d @body.json \
  undefined/idSets/{id-set-id}

Parameter Type Description

Parameter	Type	Description
[] IdSetPatchEntry	object	Inherits: object
[].geneId*	string	Min. length: 3
[].transcripts* transcripts	integer	Int32 value with a valid value range of `[0..2147483647]`. Max. value: 2147483647 Format: int32 Inherits: integer

[] IdSetPatchEntry

object

Inherits: object

[].geneId*

string

Min. length: 3

[].transcripts* transcripts

integer

Int32 value with a valid value range of [0..2147483647].

Max. value: 2147483647

Format: int32

Inherits: integer

Request Body

[
  {
    "geneId": "PF3D7_0145842",
    "transcripts": 4
  },
  {
    "geneId": "PF3D7_0120354",
    "transcripts": 18
  }
]

Inherits: object

Parameter	Type	Description
idSetId* idSetId	integer	Internal storage primary key for an ID set. Used to make requests that operate on or retrieve one specific ID set. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
organismId* organismId	integer	Int64 value with a valid value range of `[1..9223372036854775807]`. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
template* template	string	Gene ID template string. Must include at least 1 integer format parameter for injecting the id counter value into the template. The template string will be expanded using Java's String.format method which will expect a Java format parameter. See the Java string formatting cheatsheet for possible parameters and modifiers. The example parameter for this field is `%07d` which breaks down to: `%` = parameter start marker `07` = left pad the number with zeros for a total length of 7 digits `d` = format as an int NOTE: When used, this template string will be passed exactly one int64 value and nothing else. Templates should only include `%d` based formats. If the template needs more than one instance of the counter int64 value, positional parameters may be used. Pattern: ^.%[0-9,+\- $.]d.*$ Min. length: 5 Inherits: string
geneIntStart* geneIntStart	integer	Int64 value with a valid value range of `[1..9223372036854775807]`. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
generatedGeneCount* generatedGeneCount	integer	Int32 value with a valid value range of `[0..2147483647]`. Max. value: 2147483647 Format: int32 Inherits: integer
generatedIds*	array
generatedIds[]	object	Inherits: GeneratedTranscriptEntry
generatedIds[].geneId*	string	Min. length: 3
generatedIds[].transcripts*	array
generatedIds[].transcripts[]	string
generatedIds[].proteins*	array
generatedIds[].proteins[]	string
createdOn*	datetime
createdBy* createdBy	integer	Int64 value with a valid value range of `[1..9223372036854775807]`. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer

Bad Request BadRequestError

application/json

Request could not be parsed or was otherwise unusable.

Discriminator: status

Discriminator value: bad-request

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "bad-request",
  "message": "malformed JSON"
}

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "unauthorized",
  "message": "users must be logged in to access this resource"
}

Forbidden ForbiddenError

application/json

Server understood the request but is refusing it.

Could be caused by incorrect instructions or an authenticated client requesting a resource or action that requires permissions that the client does not have assigned.

Discriminator: status

Discriminator value: forbidden

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "forbidden",
  "message": "the current user is not permitted to perform this action"
}

Not Found NotFoundError

application/json

The requested resource was not found on this server.

Discriminator: status

Discriminator value: not-found

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "not-found",
  "message": "the requested resource could not be found"
}

Discriminator: status

Discriminator value: server-error

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string
requestId*	string

Response Body

{
  "status": "server-error",
  "message": "Datastore connection lost",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

This endpoint may only be used by a user or application with access to the admin credentials.

Secured By

basic basic

HTTP Basic Authentication

curl -X POST \
  -H "Content-type: application/json"
  -d @body.json \
  undefined/auth

Inherits: object

Parameter	Type	Description
username*	string	Min. length: 3

Request Body

{
  "username": "someApplicationName"
}

Inherits: object

Parameter	Type	Description
userId* userId	integer	Int64 value with a valid value range of `[1..9223372036854775807]`. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
username*	string
apiKey*	string
issued*	datetime

Response Body

{
  "userId": 123456,
  "username": "some user name",
  "apiKey": "d831d10e47de4154912ea7a8f1c633c3",
  "issued": "2020-05-25T13:18:26Z"
}

Bad Request BadRequestError

application/json

Request could not be parsed or was otherwise unusable.

Discriminator: status

Discriminator value: bad-request

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "bad-request",
  "message": "malformed JSON"
}

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "unauthorized",
  "message": "users must be logged in to access this resource"
}

Forbidden ForbiddenError

application/json

Server understood the request but is refusing it.

Could be caused by incorrect instructions or an authenticated client requesting a resource or action that requires permissions that the client does not have assigned.

Discriminator: status

Discriminator value: forbidden

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "forbidden",
  "message": "the current user is not permitted to perform this action"
}

Unprocessable Entity UnprocessableEntityError

application/json

The request payload or parameters are correctly structured but fail resource specific validation.

Discriminator: status

Discriminator value: invalid-input

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string
errors*	object	Additional properties: Yes
errors.general*	array	Non-field specific errors.
errors.general[]	string
errors.byKey*	object	Field specific errors Additional properties: Yes
errors.byKey.//*	array
errors.byKey.//[]	string

Response Body

{
  "status": "invalid-input",
  "message": "JSON validation failed",
  "errors": {
    "general": [],
    "byKey": {
      "id": [
        "Given ID value does not point to an existing record."
      ]
    }
  }
}

Discriminator: status

Discriminator value: server-error

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string
requestId*	string

Response Body

{
  "status": "server-error",
  "message": "Datastore connection lost",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

Look up a user by name or ID.

This endpoint may only be used by a user or application with access to the admin credentials.

Parameters

Parameter	Type	Description
Path
user-identifier*	string	Either the primary key id or the exact username of the user to lookup.

Secured By

basic basic

HTTP Basic Authentication

curl -X GET \
  undefined/auth/{user-identifier}

Inherits: object

Parameter	Type	Description
userId* userId	integer	Int64 value with a valid value range of `[1..9223372036854775807]`. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
username*	string
apiKey*	string
issued*	datetime

Response Body

{
  "userId": 123456,
  "username": "some user name",
  "apiKey": "d831d10e47de4154912ea7a8f1c633c3",
  "issued": "2020-05-25T13:18:26Z"
}

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Response Body

{
  "status": "unauthorized",
  "message": "users must be logged in to access this resource"
}

Discriminator: status

Discriminator value: server-error

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string
requestId*	string

Response Body

{
  "status": "server-error",
  "message": "Datastore connection lost",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

Renders the API documentation for this service.

Secured By

basic basic

HTTP Basic Authentication

curl -X GET \
  undefined/api

Prints information about the overall service health.

Secured By

basic basic

HTTP Basic Authentication

curl -X GET \
  undefined/health

HealthResponse HealthResponse

application/json

Health details about the service

Inherits: object

Parameter	Type	Description
status*	string	Status describes the overall service state. A status of "healthy" indicates that everything is running smoothly and all service dependencies are reachable and online. A status of "unhealthy" indicates that something is wrong with either this service or one or more of it's dependency services. Enum: healthy unhealthy
dependencies*	array	A list of external services that this service depends on and some details about them.
dependencies[]	object	Inherits: DependencyStatus
dependencies[].name*	string	Name of the external depdendency.
dependencies[].reachable*	boolean	Whether or not the external service is reachable.
dependencies[].online*	string	Whether or not the external service is online and available for requests. Enum: yes unknown no
info*	object	Additional properties: Yes
info.threads*	integer	Min. value: 1
info.uptime*	string
info.uptimeMillis*	integer	Min. value: 1 Format: int64

Discriminator: status

Discriminator value: server-error

Inherits: error.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string
requestId*	string

Response Body

{
  "status": "server-error",
  "message": "Datastore connection lost",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

Prometheus metrics for the service.

Secured By

basic basic

HTTP Basic Authentication

curl -X GET \
  undefined/metrics

Security Schemes

HTTP Basic Authentication

curl -X <method> \
  /<path>

Types

Gene ID template string. Must include at least 1 integer format parameter for injecting the id counter value into the template.

The template string will be expanded using Java's String.format method which will expect a Java format parameter.

See the Java string formatting cheatsheet for possible parameters and modifiers.

The example parameter for this field is %07d which breaks down to:

% = parameter start marker
07 = left pad the number with zeros for a total length of 7 digits
d = format as an int

Pattern: ^.*%[0-9,+\- $.]*d.*$

Min. length: 5

Inherits: string

Examples

PF3D7_%07d

Int32 value with a valid value range of [0..2147483647].

Max. value: 2147483647

Format: int32

Inherits: integer

Int64 value with a valid value range of [0..9223372036854775807].

Max. value: 9223372036854776000

Format: int64

Inherits: integer

Int64 value with a valid value range of [1..9223372036854775807].

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: integer

Inherits: object

Model

Parameter

Type

Description

organismId* organismId

integer

Internal storage primary key for an organism registered with the OSID service.

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: integer

generateGenes* generateGenes

integer

Number of gene IDs generated by the OSID service for the current organism.

Max. value: 2147483647

Format: int32

Inherits: integer

Inherits: object

Model

Parameter	Type	Description
idSetId* idSetId	integer	Internal storage primary key for an ID set. Used to make requests that operate on or retrieve one specific ID set. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
organismId* organismId	integer	Int64 value with a valid value range of `[1..9223372036854775807]`. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
template* template	string	Gene ID template string. Must include at least 1 integer format parameter for injecting the id counter value into the template. The template string will be expanded using Java's String.format method which will expect a Java format parameter. See the Java string formatting cheatsheet for possible parameters and modifiers. The example parameter for this field is `%07d` which breaks down to: `%` = parameter start marker `07` = left pad the number with zeros for a total length of 7 digits `d` = format as an int NOTE: When used, this template string will be passed exactly one int64 value and nothing else. Templates should only include `%d` based formats. If the template needs more than one instance of the counter int64 value, positional parameters may be used. Pattern: ^.%[0-9,+\- $.]d.*$ Min. length: 5 Inherits: string
geneIntStart* geneIntStart	integer	Int64 value with a valid value range of `[1..9223372036854775807]`. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
generatedGeneCount* generatedGeneCount	integer	Int32 value with a valid value range of `[0..2147483647]`. Max. value: 2147483647 Format: int32 Inherits: integer
generatedIds*	array
generatedIds[]	object	Inherits: GeneratedTranscriptEntry
generatedIds[].geneId*	string	Min. length: 3
generatedIds[].transcripts*	array
generatedIds[].transcripts[]	string
generatedIds[].proteins*	array
generatedIds[].proteins[]	string
createdOn*	datetime
createdBy* createdBy	integer	Int64 value with a valid value range of `[1..9223372036854775807]`. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer

Inherits: object

Model

Parameter	Type	Description
geneId*	string	Min. length: 3
transcripts*	array
transcripts[]	string
proteins*	array
proteins[]	string

Examples

{
  "geneId": "PF3D7_0145842",
  "transcripts": [
    "PF3D7_0145842.R57",
    "PF3D7_0145842.R58",
    "PF3D7_0145842.R59",
    "PF3D7_0145842.R78"
  ],
  "proteins": [
    "PF3D7_0145842.P57",
    "PF3D7_0145842.P58",
    "PF3D7_0145842.P59",
    "PF3D7_0145842.P78"
  ]
}

Inherits: object

Model

Parameter Type Description

geneId*

string

Min. length: 3

transcripts* transcripts

integer

Int32 value with a valid value range of [0..2147483647].

Max. value: 2147483647

Format: int32

Inherits: integer

Examples

{
  "geneId": "PF3D7_0145842",
  "transcripts": 4
}

Inherits: object

Model

Parameter	Type	Description
organismName*	string	Min. length: 3
template* template	string	Gene ID template string. Must include at least 1 integer format parameter for injecting the id counter value into the template. The template string will be expanded using Java's String.format method which will expect a Java format parameter. See the Java string formatting cheatsheet for possible parameters and modifiers. The example parameter for this field is `%07d` which breaks down to: `%` = parameter start marker `07` = left pad the number with zeros for a total length of 7 digits `d` = format as an int NOTE: When used, this template string will be passed exactly one int64 value and nothing else. Templates should only include `%d` based formats. If the template needs more than one instance of the counter int64 value, positional parameters may be used. Pattern: ^.%[0-9,+\- $.]d.*$ Min. length: 5 Inherits: string
geneIntStart* geneIntStart	integer	Starting point for the gene ID integer counter. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
transcriptIntStart transcriptIntStart	integer	Starting point for the transcript ID integer counter. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Default value: 1 Inherits: integer

Examples

{
  "organismName": "Plasmodium falciparum 3D7",
  "template": "PF3D7_%07d",
  "geneIntStart": 1500000,
  "transcriptIntStart": 1
}

Inherits: object

Model

Parameter Type Description

template* template

string

Gene ID template string. Must include at least 1 integer format parameter for injecting the id counter value into the template.

The template string will be expanded using Java's String.format method which will expect a Java format parameter.

See the Java string formatting cheatsheet for possible parameters and modifiers.

The example parameter for this field is %07d which breaks down to:

% = parameter start marker
07 = left pad the number with zeros for a total length of 7 digits
d = format as an int

Pattern: ^.*%[0-9,+\- $.]*d.*$

Min. length: 5

Inherits: string

geneIntStart geneIntStart

integer

Starting point for the gene ID integer counter.

NOTE This field may only be changed if no gene ids have yet been issued for this organism.

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: integer

transcriptIntStart transcriptIntStart

integer

Starting point for the transcript ID integer counter.

NOTE This field may only be changed if no transcript ids have yet been issued for this organism.

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: integer

Examples

{
  "template": "PF3D7_%07d",
  "geneIntStart": 1500000,
  "transcriptIntStart": 1
}

Inherits: object

Model

Parameter	Type	Description
organismId* organismId	integer	Internal primary key value assigned to this organism record. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
organismName*	string	Min. length: 3
template* template	string	Currently assigned gene ID template string. Pattern: ^.%[0-9,+\- $.]d.*$ Min. length: 5 Inherits: string
geneIntStart* geneIntStart	integer	Starting point for the gene ID integer counter. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
transcriptIntStart* transcriptIntStart	integer	Starting point for the transcript ID integer counter. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
geneIntCurrent* geneIntCurrent	integer	Current value for the gene ID integer counter. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
transcriptIntCurrent* transcriptIntCurrent	integer	Current value for the transcript ID integer counter. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
createdOn*	datetime	Timestamp of when this record was created.
createdBy* createdBy	integer	User ID of the user/app that created this record. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer

Examples

{
  "organismId": 24,
  "organismName": "Plasmodium falciparum 3D7",
  "template": "PF3D7_%07d",
  "geneIntStart": 1500000,
  "geneIntCurrent": 1501203,
  "transcriptIntStart": 1,
  "transcriptIntCurrent": 57,
  "createdOn": "2020-08-25T11:43:16Z",
  "createdBy": 26
}

Inherits: object

Model

Parameter	Type	Description
userId* userId	integer	Int64 value with a valid value range of `[1..9223372036854775807]`. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
username*	string
apiKey*	string
issued*	datetime

Examples

{
  "userId": 123456,
  "username": "some user name",
  "apiKey": "d831d10e47de4154912ea7a8f1c633c3",
  "issued": "2020-05-25T13:18:26Z"
}

Inherits: object

Model

Parameter	Type	Description
username*	string	Min. length: 3

Examples

{
  "username": "some user name"
}

Discriminator: status

Inherits: object

Model

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Enum:

bad-request
unauthorized
forbidden
not-found
bad-method
invalid-input
server-error

Inherits: string

Request could not be parsed or was otherwise unusable.

Discriminator: status

Discriminator value: bad-request

Inherits: error.Error

Model

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Examples

{
  "status": "bad-request",
  "message": "malformed JSON"
}

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: error.Error

Model

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Examples

{
  "status": "unauthorized",
  "message": "users must be logged in to access this resource"
}

Server understood the request but is refusing it.

Could be caused by incorrect instructions or an authenticated client requesting a resource or action that requires permissions that the client does not have assigned.

Discriminator: status

Discriminator value: forbidden

Inherits: error.Error

Model

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Examples

{
  "status": "forbidden",
  "message": "the current user is not permitted to perform this action"
}

The requested resource was not found on this server.

Discriminator: status

Discriminator value: not-found

Inherits: error.Error

Model

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Examples

{
  "status": "not-found",
  "message": "the requested resource could not be found"
}

The HTTP method used to request a resource is not allowed or configured by the server.

Discriminator: status

Discriminator value: bad-method

Inherits: error.Error

Model

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string

Examples

{
  "status": "bad-method",
  "message": "PUT requests are not permitted on this endpoint"
}

The request payload or parameters are correctly structured but fail resource specific validation.

Discriminator: status

Discriminator value: invalid-input

Inherits: error.Error

Model

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string
errors*	object	Additional properties: Yes
errors.general*	array	Non-field specific errors.
errors.general[]	string
errors.byKey*	object	Field specific errors Additional properties: Yes
errors.byKey.//*	array
errors.byKey.//[]	string

Examples

{
  "status": "invalid-input",
  "message": "JSON validation failed",
  "errors": {
    "general": [],
    "byKey": {
      "id": [
        "Given ID value does not point to an existing record."
      ]
    }
  }
}

Discriminator: status

Discriminator value: server-error

Inherits: error.Error

Model

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method invalid-input server-error Inherits: error.ErrorType
message*	string
requestId*	string

Examples

{
  "status": "server-error",
  "message": "Datastore connection lost",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

Health details about the service

Inherits: object

Model

Parameter	Type	Description
status*	string	Status describes the overall service state. A status of "healthy" indicates that everything is running smoothly and all service dependencies are reachable and online. A status of "unhealthy" indicates that something is wrong with either this service or one or more of it's dependency services. Enum: healthy unhealthy
dependencies*	array	A list of external services that this service depends on and some details about them.
dependencies[]	object	Inherits: DependencyStatus
dependencies[].name*	string	Name of the external depdendency.
dependencies[].reachable*	boolean	Whether or not the external service is reachable.
dependencies[].online*	string	Whether or not the external service is online and available for requests. Enum: yes unknown no
info*	object	Additional properties: Yes
info.threads*	integer	Min. value: 1
info.uptime*	string
info.uptimeMillis*	integer	Min. value: 1 Format: int64

Inherits: object

Model

Parameter	Type	Description
name*	string	Name of the external depdendency.
reachable*	boolean	Whether or not the external service is reachable.
online*	string	Whether or not the external service is online and available for requests. Enum: yes unknown no

Organism Specific ID Service vv1.0.0

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500 Internal Server Error

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500 Internal Server Error