VEuPathDB Dataset Installer v2.1.0

Resources

Returns a list of datasets available to the requesting user, optionally filtered by query parameters.

Results are sorted by creation date in reverse order. This means the most recently created datasets will be first and the oldest dataset will be last in the list.

Parameters

Parameter	Type	Description
Query
project_id Project ID	string	ID of the VEuPathDB project that results should be filtered to. This means only datasets that are relevant to the project ID given will be returned. Additionally, this controls the sites on which the dataset installation status will be checked. Meaning, if this parameter is specified and set to, for example, `PlasmoDB`, the status block in the response objects will only include installation status details for `PlasmoDB` and not any other sites that the dataset may have been installed into. Inherits: string
ownership Dataset Ownership Filter	string	Ownership status filter. Enum of: `any` `owned` `shared` If set to `any` the results are not filtered. If set to `owned`, the results will be filtered to only results that are owned by the requesting user. If set to `shared`, the results will be filtered to only results that are shared with the requesting user. Default value: "any"

curl -X GET \
  undefined/vdi-datasets?ProjectID=<value>&ownership=<value>

Parameter Type Description

[] Dataset List Item

object

Short entry with basic details about a dataset.

Inherits: object

[].datasetId* Dataset ID

string

Unique VDI Dataset identifier string.

Pattern: ^[a-zA-Z0-9_-]{14}$

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

[].owner* Owner Details

object

Details about the owner of a VDI dataset.

Inherits: lib.DatasetOwner

[].owner.userId* Owner User ID

integer

VEuPathDB user ID of the owner of the dataset.

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

[].owner.firstName Owner First Name string

[].owner.lastName Owner Last Name string

[].owner.email Owner Email string

[].owner.organization Owner Organization string

[].datasetType* Dataset Type

object

Information about a specific dataset type.

Inherits: lib.DatasetTypeInfo

[].datasetType.name* Type Name string

[].datasetType.displayName Type Display Name

string

Display name for the type. This field is ignored in requests and will always be present in responses.

[].datasetType.version* Type Version string

[].visibility* Dataset Visibility

string

Enum:

private
protected
public

Inherits: lib.DatasetVisibility

[].name* Dataset Name

string

User provided name for the dataset.

[].shortName string

[].shortAttribution string

[].category string

[].summary Dataset Summary

string

User provided summary of the dataset.

[].description Dataset Description

string

User provided description of the dataset.

[].sourceUrl Source URL

string

URL of the dataset data source, if the dataset was uploaded via URL.

[].origin* Dataset Origin

string

String representing the origin of the dataset. Examples include direct-upload, nephele, or galaxy.

[].projectIds* Project IDs

array

Project IDs for projects the dataset record was submitted to.

[].projectIds[] Project ID

string

Name or ID of a target VEuPathDB project.

Valid project IDs are:

AmoebaDB
ClinEpiDB
CryptoDB
FungiDB
GiardiaDB
HostDB
MicrobiomeDB
MicrosporidiaDB
PiroplasmaDB
PlasmoDB
ToxoDB
TrichDB
TriTrypDB
VectorBase
VEuPathDB

Inherits: lib.ProjectID

[].status* Status Info

object

Information about the import and install status of a dataset.

Inherits: lib.DatasetStatusInfo

[].status.import*

string

Import status of the dataset.

Value	Description
`queued`	The dataset has not yet been processed and is waiting in the queue.
`in-progress`	The dataset is currently being import processed.
`complete`	The dataset has been processed and imported for installation.
`invalid`	The dataset failed import validation.
`failed`	The dataset import failed due to an internal server error.

Enum:

queued
in-progress
complete
invalid
failed

Inherits: lib.DatasetImportStatus

[].status.install array

[].status.install[] Dataset Install Status Entry

object

Entry in a list of install statuses for a dataset.

Inherits: lib.DatasetInstallStatusEntry

[].status.install[].projectId*

string

Name or ID of a target VEuPathDB project.

Valid project IDs are:

AmoebaDB
ClinEpiDB
CryptoDB
FungiDB
GiardiaDB
HostDB
MicrobiomeDB
MicrosporidiaDB
PiroplasmaDB
PlasmoDB
ToxoDB
TrichDB
TriTrypDB
VectorBase
VEuPathDB

Inherits: lib.ProjectID

[].status.install[].metaStatus*

string

Enum:

running
complete
failed-validation
failed-installation
ready-for-reinstall
missing-dependency

Inherits: lib.DatasetInstallStatus

[].status.install[].metaMessage string

[].status.install[].dataStatus

string

Enum:

running
complete
failed-validation
failed-installation
ready-for-reinstall
missing-dependency

Inherits: lib.DatasetInstallStatus

[].status.install[].dataMessage string

[].shares* Shared With array

[].shares[]

object

Inherits: object

[].shares[].userId*

integer

Unique user identifier

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

[].shares[].firstName* string

[].shares[].lastName* string

[].shares[].organization* string

[].shares[].accepted* boolean

[].fileCount* File Count

integer

Number of files uploaded for this dataset.

[].fileSizeTotal* File Size Total

integer

Sum of the sizes of all the files uploaded for this dataset.

Format: int64

[].created* Creation Timestamp

datetime

Timestamp of the creation of this dataset.

Response Body

[
  {
    "datasetId": "zaZqAAGLGJhBgg",
    "owner": {
      "userId": 123456,
      "firstName": "Joe",
      "lastName": "User",
      "organization": "University of Joe"
    },
    "datasetType": {
      "name": "ISA",
      "version": "1.0"
    },
    "name": "My Dataset",
    "summary": "A short description of my dataset.",
    "description": "A longer description of my dataset.",
    "origin": "direct-upload",
    "visibility": "public",
    "projectIds": [
      "PlasmoDB",
      "ToxoDB"
    ],
    "status": {
      "import": "complete",
      "install": [
        {
          "projectId": "PlasmoDB",
          "metaStatus": "complete",
          "dataStatus": "failed-installation",
          "dataMessage": "Failed due to some reason."
        },
        {
          "projectId": "ToxoDB",
          "metaStatus": "complete",
          "dataStatus": "complete"
        }
      ]
    },
    "shares": [
      {
        "userId": 1234,
        "firstName": "Billy",
        "lastName": "Mays",
        "organization": "OxiClean",
        "accepted": true
      }
    ],
    "fileCount": 2,
    "fileSizeTotal": 123456789,
    "created": "2023-10-31T23:59:59.999Z"
  }
]

Bad Request BadRequestError

application/json

Request could not be parsed or was otherwise unusable.

Discriminator: status

Discriminator value: bad-request

Inherits: lib.Error

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

Response Body

{
  "status": "bad-request",
  "message": "Invalid project_id value."
}

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: lib.Error

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

Response Body

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

Discriminator: status

Discriminator value: server-error

Inherits: lib.Error

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

Response Body

{
  "status": "server-error",
  "message": "Dataset store is unreachable",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

multipart/form-data HTTP POST request to upload a new dataset.

Note, the body description below is of the multipart form data fields and not of a JSON object.

The meta field, however, is expected to be a JSON blob.

The file field may be one of:

a raw data file to import
a .zip file containing one or more files to import
a .tar.gz or .tgz file containing one or more files to import.

The url field may point to a file that is one of the allowed upload types.

The url and file fields cannot both be used at the same time, one must be used or the other.

curl -X POST \
  -H "Content-type: multipart/form-data"
  -d @file \
  undefined/vdi-datasets

Dataset Post Request DatasetPostRequest

multipart/form-data

HTTP POST request body requesting the creation of a dataset from the components included in the request.

For a request to be considered valid, it must contain exactly 1 of the optional parameters file or url. If a request body contains both a file and a url field value, the service will return a 400 error.

Inherits: object

Parameter	Type	Description
meta* Dataset Meta	object	Metadata about the dataset being submitted. Inherits: lib.DatasetPostMeta
meta.datasetType* Dataset Type	object	Type of the dataset that is being uploaded. Inherits: lib.DatasetPostType
meta.datasetType.name*	string
meta.datasetType.version*	string
meta.name* Dataset Name	string	User provided name for the dataset.
meta.shortName	string	Max. length: 300
meta.shortAttribution	string	Max. length: 300
meta.category	string	Max. length: 100
meta.visibility Dataset Visibility	string	Default value: "private" Enum: private protected public Inherits: lib.DatasetVisibility
meta.summary Dataset Summary	string	User provided summary for the dataset. Max. length: 4000
meta.description Dataset Description	string	User provided description for the dataset.
meta.origin* Dataset Origin	string	String representing the origin of the dataset. Examples include `direct-upload`, `nephele`, or `galaxy`.
meta.projects* Project IDs	array	IDs of the projects this dataset is being submitted to. Unique items: Yes
meta.projects[] Project ID	string	Name or ID of a target VEuPathDB project. Valid project IDs are: AmoebaDB ClinEpiDB CryptoDB FungiDB GiardiaDB HostDB MicrobiomeDB MicrosporidiaDB PiroplasmaDB PlasmoDB ToxoDB TrichDB TriTrypDB VectorBase VEuPathDB Inherits: lib.ProjectID
meta.dependencies* Dataset Dependencies	array	Unique items: Yes
meta.dependencies[]	object	Inherits: lib.DatasetDependency
meta.dependencies[].resourceIdentifier*	string
meta.dependencies[].resourceDisplayName*	string
meta.dependencies[].resourceVersion*	string
meta.publications Dataset Publications	array	Unique items: Yes
meta.publications[]	object	Inherits: lib.DatasetPublication
meta.publications[].pubMedId*	string	Min. length: 3 Max. length: 30
meta.publications[].citation	string	Min. length: 3 Max. length: 2000
meta.hyperlinks Dataset Hyperlinks	array	Unique items: Yes
meta.hyperlinks[]	object	Inherits: lib.DatasetHyperlink
meta.hyperlinks[].url*	string	Min. length: 3 Max. length: 200
meta.hyperlinks[].text*	string	Min. length: 3 Max. length: 300
meta.hyperlinks[].description	string	Max. length: 4000
meta.hyperlinks[].isPublication	boolean
meta.organisms Dataset Organisms	array	Unique items: Yes
meta.organisms[]	string	Max. length: 200
meta.contacts Dataset Contacts	array	Unique items: Yes
meta.contacts[]	object	Inherits: lib.DatasetContact
meta.contacts[].name*	string	Min. length: 3 Max. length: 300
meta.contacts[].email	string	Min. length: 5 Max. length: 4000
meta.contacts[].affiliation	string	Max. length: 4000
meta.contacts[].city	string	Max. length: 200
meta.contacts[].state	string	Max. length: 200
meta.contacts[].country	string	Max. length: 200
meta.contacts[].address	string	Max. length: 1000
meta.contacts[].isPrimary	boolean
meta.createdOn Creation Date	datetime-only
file Dataset File	file	Dataset file to upload. This field is incompatible with the `url` field.
url Dataset URL	string	URL to a dataset file to upload. This field is incompatible with the `file` field.

Dataset Upload Response DatasetPostResponse

application/json

Response object returned on successful upload of a dataset.

Note that this response does not mean the uploaded dataset has been made available on the target site(s). The upload must first be processed and installed into the target sites before the dataset will become available for use.

Inherits: object

Parameter

Type

Description

datasetId*

string

Unique VDI Dataset identifier string.

Pattern: ^[a-zA-Z0-9_-]{14}$

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

Response Body

{
  "datasetId": "zaZqAAGLGJhBgg"
}

Bad Request BadRequestError

application/json

Request could not be parsed or was otherwise unusable.

Discriminator: status

Discriminator value: bad-request

Inherits: lib.Error

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

Response Body

{
  "status": "bad-request",
  "message": "Invalid project_id value."
}

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: lib.Error

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

Response Body

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

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: lib.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method conflict gone invalid-input failed-dependency server-error Inherits: lib.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: failed-dependency

Inherits: lib.Error

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

Response Body

{
  "status": "failed-dependency",
  "dependency": "google.com",
  "message": "unexpected status code 403 from google.com"
}

Discriminator: status

Discriminator value: server-error

Inherits: lib.Error

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

Response Body

{
  "status": "server-error",
  "message": "Dataset store is unreachable",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

Triggers a full reconciliation run if one is not already in progress.

curl -X POST \
  undefined/admin/reconciler

Upload a dataset on behalf of another user.

Headers

Parameter	Type	Description
User-ID* VEuPathDB User ID	integer	ID of the target user on whose behalf a dataset is being uploaded Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer

Parameter

Type

Description

User-ID* VEuPathDB User ID

integer

ID of the target user on whose behalf a dataset is being uploaded

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: integer

curl -X POST \
  -H "User-ID: <value>" \
  -H "Content-type: multipart/form-data"
  -d @file \
  undefined/admin/proxy-upload

Dataset Post Request DatasetPostRequest

multipart/form-data

multipart/form-data HTTP POST request to upload a new dataset.

Note, the body description below is of the multipart form data fields and not of a JSON object.

The meta field, however, is expected to be a JSON blob.

Inherits: object

Parameter	Type	Description
meta* Dataset Meta	object	Metadata about the dataset being submitted. Inherits: lib.DatasetPostMeta
meta.datasetType* Dataset Type	object	Type of the dataset that is being uploaded. Inherits: lib.DatasetPostType
meta.datasetType.name*	string
meta.datasetType.version*	string
meta.name* Dataset Name	string	User provided name for the dataset.
meta.shortName	string	Max. length: 300
meta.shortAttribution	string	Max. length: 300
meta.category	string	Max. length: 100
meta.visibility Dataset Visibility	string	Default value: "private" Enum: private protected public Inherits: lib.DatasetVisibility
meta.summary Dataset Summary	string	User provided summary for the dataset. Max. length: 4000
meta.description Dataset Description	string	User provided description for the dataset.
meta.origin* Dataset Origin	string	String representing the origin of the dataset. Examples include `direct-upload`, `nephele`, or `galaxy`.
meta.projects* Project IDs	array	IDs of the projects this dataset is being submitted to. Unique items: Yes
meta.projects[] Project ID	string	Name or ID of a target VEuPathDB project. Valid project IDs are: AmoebaDB ClinEpiDB CryptoDB FungiDB GiardiaDB HostDB MicrobiomeDB MicrosporidiaDB PiroplasmaDB PlasmoDB ToxoDB TrichDB TriTrypDB VectorBase VEuPathDB Inherits: lib.ProjectID
meta.dependencies* Dataset Dependencies	array	Unique items: Yes
meta.dependencies[]	object	Inherits: lib.DatasetDependency
meta.dependencies[].resourceIdentifier*	string
meta.dependencies[].resourceDisplayName*	string
meta.dependencies[].resourceVersion*	string
meta.publications Dataset Publications	array	Unique items: Yes
meta.publications[]	object	Inherits: lib.DatasetPublication
meta.publications[].pubMedId*	string	Min. length: 3 Max. length: 30
meta.publications[].citation	string	Min. length: 3 Max. length: 2000
meta.hyperlinks Dataset Hyperlinks	array	Unique items: Yes
meta.hyperlinks[]	object	Inherits: lib.DatasetHyperlink
meta.hyperlinks[].url*	string	Min. length: 3 Max. length: 200
meta.hyperlinks[].text*	string	Min. length: 3 Max. length: 300
meta.hyperlinks[].description	string	Max. length: 4000
meta.hyperlinks[].isPublication	boolean
meta.organisms Dataset Organisms	array	Unique items: Yes
meta.organisms[]	string	Max. length: 200
meta.contacts Dataset Contacts	array	Unique items: Yes
meta.contacts[]	object	Inherits: lib.DatasetContact
meta.contacts[].name*	string	Min. length: 3 Max. length: 300
meta.contacts[].email	string	Min. length: 5 Max. length: 4000
meta.contacts[].affiliation	string	Max. length: 4000
meta.contacts[].city	string	Max. length: 200
meta.contacts[].state	string	Max. length: 200
meta.contacts[].country	string	Max. length: 200
meta.contacts[].address	string	Max. length: 1000
meta.contacts[].isPrimary	boolean
meta.createdOn Creation Date	datetime-only
file Dataset File	file	Dataset file to upload. This field is incompatible with the `url` field.
url Dataset URL	string	URL to a dataset file to upload. This field is incompatible with the `file` field.

Dataset Upload Response DatasetPostResponse

application/json

Response object returned on successful upload of a dataset.

Inherits: object

Parameter

Type

Description

datasetId*

string

Unique VDI Dataset identifier string.

Pattern: ^[a-zA-Z0-9_-]{14}$

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

Response Body

{
  "datasetId": "zaZqAAGLGJhBgg"
}

Bad Request BadRequestError

application/json

Request could not be parsed or was otherwise unusable.

Discriminator: status

Discriminator value: bad-request

Inherits: lib.Error

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

Response Body

{
  "status": "bad-request",
  "message": "Invalid project_id value."
}

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: lib.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method conflict gone invalid-input failed-dependency server-error Inherits: lib.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: lib.Error

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

Response Body

{
  "status": "forbidden",
  "message": "Target user does not exist."
}

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: lib.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method conflict gone invalid-input failed-dependency server-error Inherits: lib.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: lib.Error

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

Response Body

{
  "status": "server-error",
  "message": "Dataset store is unreachable",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

Lists datasets that failed to import.

Note: A failed import is different from an invalid import. Failed imports are caused by process bugs or errors, invalid imports are caused by bad user input.

Parameters

Parameter	Type	Description
Query
user VEuPathDB User ID	integer	Unique user identifier Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
before	string	Filter results to only those records created before the given date-time value. Examples: 2023 2023-10 2023-10-02 2023-10-02T17:10 2023-10-02T17:10:00 2023-10-02T17:10:00.000 2023-10-02T17:10:00.000Z If no timezone is provided, the service will assume its local zone.
after	string	Filter results to only those records created after the given date-time value. Examples: 2023 2023-10 2023-10-02 2023-10-02T17:10 2023-10-02T17:10:00 2023-10-02T17:10:00.000 2023-10-02T17:10:00.000Z If no timezone is provided, the service will assume its local zone.
limit	integer	Max. value: 250 Default value: 100
offset	integer
sort	string	One of: date Default value: "date"
order	string	One of: asc desc Default value: "desc"

curl -X GET \
  undefined/admin/failed-imports?User-ID=<value>&before=<value>&after=<value>&limit=<value>&offset=<value>&sort=<value>&order=<value>

Inherits: object

Parameter	Type	Description
meta*	object	Inherits: lib.BrokenImportListingMeta
meta.count* Result Count	integer	Number of records in the result.
meta.before	string
meta.after	string
meta.user	integer	Unique user identifier Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: lib.User-ID
meta.limit	integer
meta.offset	integer
results*	array
results[] Broken Import Details	object	Inherits: lib.BrokenImportDetails
results[].datasetId*	string	Unique VDI Dataset identifier string. Pattern: ^[a-zA-Z0-9_-]{14}$ Min. length: 14 Max. length: 14 Inherits: lib.VDI-ID
results[].owner*	integer	Unique user identifier Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: lib.User-ID
results[].datasetType*	object	Information about a specific dataset type. Inherits: lib.DatasetTypeInfo
results[].datasetType.name* Type Name	string
results[].datasetType.displayName Type Display Name	string	Display name for the type. This field is ignored in requests and will always be present in responses.
results[].datasetType.version* Type Version	string
results[].projectIds*	array
results[].projectIds[] Project ID	string	Name or ID of a target VEuPathDB project. Valid project IDs are: AmoebaDB ClinEpiDB CryptoDB FungiDB GiardiaDB HostDB MicrobiomeDB MicrosporidiaDB PiroplasmaDB PlasmoDB ToxoDB TrichDB TriTrypDB VectorBase VEuPathDB Inherits: lib.ProjectID
results[].messages*	array
results[].messages[]	string

Lists datasets that failed installation due to non-user error.

Parameters

Parameter	Type	Description
Query
expanded Expanded Dataset List	boolean	Whether the returned broken dataset install list should be expanded to include additional details about each dataset or should be just a simple list of dataset IDs. Default value: true

curl -X GET \
  undefined/admin/list-broken?expanded=<value>

Inherits: object

Parameter Type Description

details array

details[] Broken Dataset Details

object

Inherits: lib.BrokenDatasetDetails

details[].datasetId*

string

Unique VDI Dataset identifier string.

Pattern: ^[a-zA-Z0-9_-]{14}$

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

details[].owner*

integer

Unique user identifier

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

details[].datasetType*

object

Information about a specific dataset type.

Inherits: lib.DatasetTypeInfo

details[].datasetType.name* Type Name string

details[].datasetType.displayName Type Display Name

string

Display name for the type. This field is ignored in requests and will always be present in responses.

details[].datasetType.version* Type Version string

details[].projectIds* array

details[].projectIds[] Project ID

string

Name or ID of a target VEuPathDB project.

Valid project IDs are:

AmoebaDB
ClinEpiDB
CryptoDB
FungiDB
GiardiaDB
HostDB
MicrobiomeDB
MicrosporidiaDB
PiroplasmaDB
PlasmoDB
ToxoDB
TrichDB
TriTrypDB
VectorBase
VEuPathDB

Inherits: lib.ProjectID

details[].status*

object

Information about the import and install status of a dataset.

Inherits: lib.DatasetStatusInfo

details[].status.import*

string

Import status of the dataset.

Value	Description
`queued`	The dataset has not yet been processed and is waiting in the queue.
`in-progress`	The dataset is currently being import processed.
`complete`	The dataset has been processed and imported for installation.
`invalid`	The dataset failed import validation.
`failed`	The dataset import failed due to an internal server error.

Enum:

queued
in-progress
complete
invalid
failed

Inherits: lib.DatasetImportStatus

details[].status.install array

details[].status.install[] Dataset Install Status Entry

object

Entry in a list of install statuses for a dataset.

Inherits: lib.DatasetInstallStatusEntry

details[].status.install[].projectId*

string

Name or ID of a target VEuPathDB project.

Valid project IDs are:

AmoebaDB
ClinEpiDB
CryptoDB
FungiDB
GiardiaDB
HostDB
MicrobiomeDB
MicrosporidiaDB
PiroplasmaDB
PlasmoDB
ToxoDB
TrichDB
TriTrypDB
VectorBase
VEuPathDB

Inherits: lib.ProjectID

details[].status.install[].metaStatus*

string

Enum:

running
complete
failed-validation
failed-installation
ready-for-reinstall
missing-dependency

Inherits: lib.DatasetInstallStatus

details[].status.install[].metaMessage string

details[].status.install[].dataStatus

string

Enum:

running
complete
failed-validation
failed-installation
ready-for-reinstall
missing-dependency

Inherits: lib.DatasetInstallStatus

details[].status.install[].dataMessage string

ids array

ids[] VDI ID

string

Unique VDI Dataset identifier string.

Pattern: ^[a-zA-Z0-9_-]{14}$

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: lib.Error

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

Response Body

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

Discriminator: status

Discriminator value: server-error

Inherits: lib.Error

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

Response Body

{
  "status": "server-error",
  "message": "Dataset store is unreachable",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

Marks all or target datasets that are in a status of installation failure into a ready-for-reinstall status then runs the dataset reinstallation process which attempts to uninstall and reinstall all datasets in that status.

The request body should specify exactly one of all or targets to select whether install cleanup should target all failed datasets across all sites, or if install cleanup should target only specific datasets on specific sites.

If the request specifies neither all or targets the endpoint will do nothing.

Optionally the query param skip-run may be provided to skip the execution of the dataset reinstallation process. This may be used in situations where multiple batches of datasets are being marked as ready-for-reinstall.

Parameters

Parameter	Type	Description
Query
skip-run	boolean

curl -X POST \
  -H "Content-type: application/json"
  -d @body.json \
  undefined/admin/fix-broken-installs?skip-run=<value>

Install Cleanup Request InstallCleanupRequest

application/json

Object controlling the install cleanup process and what datasets it should target.

Requesters should specify one of the fields all or targets to control what datasets will be cleaned up. If neither is specified the endpoint will do nothing.

Inherits: object

Parameter	Type	Description
all	boolean
targets	array	Unique items: Yes
targets[] Install Cleanup Target	object	Inherits: lib.InstallCleanupTarget
targets[].datasetId*	string	Unique VDI Dataset identifier string. Pattern: ^[a-zA-Z0-9_-]{14}$ Min. length: 14 Max. length: 14 Inherits: lib.VDI-ID
targets[].projectId*	string	Name or ID of a target VEuPathDB project. Valid project IDs are: AmoebaDB ClinEpiDB CryptoDB FungiDB GiardiaDB HostDB MicrobiomeDB MicrosporidiaDB PiroplasmaDB PlasmoDB ToxoDB TrichDB TriTrypDB VectorBase VEuPathDB Inherits: lib.ProjectID

Request Body

All Example

{
  "all": true
}

Target Example

{
  "targets": [
    {
      "datasetId": "zaZqAAGLGJhBgg",
      "projectId": "PlasmoDB"
    }
  ]
}

Bad Request BadRequestError

application/json

Request could not be parsed or was otherwise unusable.

Discriminator: status

Discriminator value: bad-request

Inherits: lib.Error

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

Response Body

{
  "status": "bad-request",
  "message": "Invalid project_id value."
}

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: lib.Error

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

Response Body

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

Discriminator: status

Discriminator value: server-error

Inherits: lib.Error

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

Response Body

{
  "status": "server-error",
  "message": "Dataset store is unreachable",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

Permanently delete jobs that were soft deleted more than 24 hours prior to the execution of this task.

curl -X POST \
  undefined/admin/delete-cleanup

Bad Request BadRequestError

application/json

Request could not be parsed or was otherwise unusable.

Discriminator: status

Discriminator value: bad-request

Inherits: lib.Error

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

Response Body

{
  "status": "bad-request",
  "message": "Invalid project_id value."
}

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: lib.Error

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

Response Body

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

Discriminator: status

Discriminator value: server-error

Inherits: lib.Error

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

Response Body

{
  "status": "server-error",
  "message": "Dataset store is unreachable",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

Parameters

Parameter	Type	Description
Query
datasetId*	string

curl -X GET \
  undefined/admin/dataset-details?datasetId=<value>

Inherits: object

Parameter	Type	Description
datasetType*	object	Information about a specific dataset type. Inherits: lib.DatasetTypeInfo
datasetType.name* Type Name	string
datasetType.displayName Type Display Name	string	Display name for the type. This field is ignored in requests and will always be present in responses.
datasetType.version* Type Version	string
owner*	integer	Unique user identifier Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: lib.User-ID
isDeleted*	boolean
origin*	string
created*	datetime
inserted*	datetime
name*	string
shortName	string
shortAttribution	string
category	string
summary	string
description	string
visibility*	string	Enum: private protected public Inherits: lib.DatasetVisibility
sourceUrl	string
projectIds*	array
projectIds[] Project ID	string	Name or ID of a target VEuPathDB project. Valid project IDs are: AmoebaDB ClinEpiDB CryptoDB FungiDB GiardiaDB HostDB MicrobiomeDB MicrosporidiaDB PiroplasmaDB PlasmoDB ToxoDB TrichDB TriTrypDB VectorBase VEuPathDB Inherits: lib.ProjectID
status*	string
syncControl	object	Inherits: object
syncControl.sharesUpdateTime*	datetime
syncControl.dataUpdateTime*	datetime
syncControl.metaUpdateTime*	datetime
uploadFiles	array
uploadFiles[]	string
installFiles	array
installFiles[]	string
importMessages*	array
importMessages[]	string

Lists all the objects currently in the S3 object store backing VDI.

This endpoint returns the data in TSV format with the following columns for each object in the store:

Key/path
Size (in bytes)
Last modified date

curl -X GET \
  undefined/admin/list-s3-objects

Response Body

/foo/bar/fizz	342345	2023-08-13T15:34:04.0342Z
/foo/bar/buzz	32125	2023-08-13T15:34:06.1254Z

Lists all datasets known to VDI via the internal cache database.

Parameters

Parameter	Type	Description
Query
offset	integer
limit	integer	Min. value: 1 Default value: 100
project_id	string	Optionally filter the results to only datasets that target the given project ID.
include_deleted	boolean

curl -X GET \
  undefined/admin/list-all-datasets?offset=<value>&limit=<value>&project_id=<value>&include_deleted=<value>

Inherits: object

Parameter Type Description

meta*

object

Inherits: lib.AllDatasetsListMeta

meta.count* integer

meta.offset* integer

meta.limit* integer

meta.total* integer

results* array

results[]

object

Inherits: lib.AllDatasetsListEntry

results[].datasetId*

string

Unique VDI Dataset identifier string.

Pattern: ^[a-zA-Z0-9_-]{14}$

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

results[].owner*

integer

Unique user identifier

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

results[].datasetType*

object

Information about a specific dataset type.

Inherits: lib.DatasetTypeInfo

results[].datasetType.name* Type Name string

results[].datasetType.displayName Type Display Name

string

Display name for the type. This field is ignored in requests and will always be present in responses.

results[].datasetType.version* Type Version string

results[].visibility*

string

Enum:

private
protected
public

Inherits: lib.DatasetVisibility

results[].name* string

results[].shortName string

results[].shortAttribution string

results[].category string

results[].summary string

results[].description string

results[].sourceUrl string

results[].origin* string

results[].projectIds* array

results[].projectIds[] Project ID

string

Name or ID of a target VEuPathDB project.

Valid project IDs are:

AmoebaDB
ClinEpiDB
CryptoDB
FungiDB
GiardiaDB
HostDB
MicrobiomeDB
MicrosporidiaDB
PiroplasmaDB
PlasmoDB
ToxoDB
TrichDB
TriTrypDB
VectorBase
VEuPathDB

Inherits: lib.ProjectID

results[].status*

object

Information about the import and install status of a dataset.

Inherits: lib.DatasetStatusInfo

results[].status.import*

string

Import status of the dataset.

Value	Description
`queued`	The dataset has not yet been processed and is waiting in the queue.
`in-progress`	The dataset is currently being import processed.
`complete`	The dataset has been processed and imported for installation.
`invalid`	The dataset failed import validation.
`failed`	The dataset import failed due to an internal server error.

Enum:

queued
in-progress
complete
invalid
failed

Inherits: lib.DatasetImportStatus

results[].status.install array

results[].status.install[] Dataset Install Status Entry

object

Entry in a list of install statuses for a dataset.

Inherits: lib.DatasetInstallStatusEntry

results[].status.install[].projectId*

string

Name or ID of a target VEuPathDB project.

Valid project IDs are:

AmoebaDB
ClinEpiDB
CryptoDB
FungiDB
GiardiaDB
HostDB
MicrobiomeDB
MicrosporidiaDB
PiroplasmaDB
PlasmoDB
ToxoDB
TrichDB
TriTrypDB
VectorBase
VEuPathDB

Inherits: lib.ProjectID

results[].status.install[].metaStatus*

string

Enum:

running
complete
failed-validation
failed-installation
ready-for-reinstall
missing-dependency

Inherits: lib.DatasetInstallStatus

results[].status.install[].metaMessage string

results[].status.install[].dataStatus

string

Enum:

running
complete
failed-validation
failed-installation
ready-for-reinstall
missing-dependency

Inherits: lib.DatasetInstallStatus

results[].status.install[].dataMessage string

results[].created* datetime

results[].isDeleted* boolean

Removes a dataset from the object store and internal postgres database.

This is intended to be used exclusively for clearing bad state created by errors or bugs.

This action does not perform dataset uninstalls, and may leave VDI in a bad state if run against a dataset that isn't broken.

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

Parameter	Type	Description
userId* VEuPathDB User ID	integer	Unique user identifier Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
datasetId* VDI ID	string	Unique VDI Dataset identifier string. Pattern: ^[a-zA-Z0-9_-]{14}$ Min. length: 14 Max. length: 14 Inherits: string

Parameter

Type

Description

userId* VEuPathDB User ID

integer

Unique user identifier

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: integer

datasetId* VDI ID

string

Unique VDI Dataset identifier string.

Pattern: ^[a-zA-Z0-9_-]{14}$

Min. length: 14

Max. length: 14

Inherits: string

Bad Request BadRequestError

application/json

Request could not be parsed or was otherwise unusable.

Discriminator: status

Discriminator value: bad-request

Inherits: lib.Error

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

Response Body

{
  "status": "bad-request",
  "message": "Invalid project_id value."
}

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: lib.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method conflict gone invalid-input failed-dependency server-error Inherits: lib.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: lib.Error

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

Response Body

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

Discriminator: status

Discriminator value: server-error

Inherits: lib.Error

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

Response Body

{
  "status": "server-error",
  "message": "Dataset store is unreachable",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

Returns a list of datasets that have been made "public" by the owner setting the dataset visibilities to a setting other than private.

curl -X GET \
  undefined/vdi-datasets/community

Parameter Type Description

[] Dataset List Item

object

Short entry with basic details about a dataset.

Inherits: object

[].datasetId* Dataset ID

string

Unique VDI Dataset identifier string.

Pattern: ^[a-zA-Z0-9_-]{14}$

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

[].owner* Owner Details

object

Details about the owner of a VDI dataset.

Inherits: lib.DatasetOwner

[].owner.userId* Owner User ID

integer

VEuPathDB user ID of the owner of the dataset.

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

[].owner.firstName Owner First Name string

[].owner.lastName Owner Last Name string

[].owner.email Owner Email string

[].owner.organization Owner Organization string

[].datasetType* Dataset Type

object

Information about a specific dataset type.

Inherits: lib.DatasetTypeInfo

[].datasetType.name* Type Name string

[].datasetType.displayName Type Display Name

string

Display name for the type. This field is ignored in requests and will always be present in responses.

[].datasetType.version* Type Version string

[].visibility* Dataset Visibility

string

Enum:

private
protected
public

Inherits: lib.DatasetVisibility

[].name* Dataset Name

string

User provided name for the dataset.

[].shortName string

[].shortAttribution string

[].category string

[].summary Dataset Summary

string

User provided summary of the dataset.

[].description Dataset Description

string

User provided description of the dataset.

[].sourceUrl Source URL

string

URL of the dataset data source, if the dataset was uploaded via URL.

[].origin* Dataset Origin

string

String representing the origin of the dataset. Examples include direct-upload, nephele, or galaxy.

[].projectIds* Project IDs

array

Project IDs for projects the dataset record was submitted to.

[].projectIds[] Project ID

string

Name or ID of a target VEuPathDB project.

Valid project IDs are:

AmoebaDB
ClinEpiDB
CryptoDB
FungiDB
GiardiaDB
HostDB
MicrobiomeDB
MicrosporidiaDB
PiroplasmaDB
PlasmoDB
ToxoDB
TrichDB
TriTrypDB
VectorBase
VEuPathDB

Inherits: lib.ProjectID

[].status* Status Info

object

Information about the import and install status of a dataset.

Inherits: lib.DatasetStatusInfo

[].status.import*

string

Import status of the dataset.

Value	Description
`queued`	The dataset has not yet been processed and is waiting in the queue.
`in-progress`	The dataset is currently being import processed.
`complete`	The dataset has been processed and imported for installation.
`invalid`	The dataset failed import validation.
`failed`	The dataset import failed due to an internal server error.

Enum:

queued
in-progress
complete
invalid
failed

Inherits: lib.DatasetImportStatus

[].status.install array

[].status.install[] Dataset Install Status Entry

object

Entry in a list of install statuses for a dataset.

Inherits: lib.DatasetInstallStatusEntry

[].status.install[].projectId*

string

Name or ID of a target VEuPathDB project.

Valid project IDs are:

AmoebaDB
ClinEpiDB
CryptoDB
FungiDB
GiardiaDB
HostDB
MicrobiomeDB
MicrosporidiaDB
PiroplasmaDB
PlasmoDB
ToxoDB
TrichDB
TriTrypDB
VectorBase
VEuPathDB

Inherits: lib.ProjectID

[].status.install[].metaStatus*

string

Enum:

running
complete
failed-validation
failed-installation
ready-for-reinstall
missing-dependency

Inherits: lib.DatasetInstallStatus

[].status.install[].metaMessage string

[].status.install[].dataStatus

string

Enum:

running
complete
failed-validation
failed-installation
ready-for-reinstall
missing-dependency

Inherits: lib.DatasetInstallStatus

[].status.install[].dataMessage string

[].shares* Shared With array

[].shares[]

object

Inherits: object

[].shares[].userId*

integer

Unique user identifier

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

[].shares[].firstName* string

[].shares[].lastName* string

[].shares[].organization* string

[].shares[].accepted* boolean

[].fileCount* File Count

integer

Number of files uploaded for this dataset.

[].fileSizeTotal* File Size Total

integer

Sum of the sizes of all the files uploaded for this dataset.

Format: int64

[].created* Creation Timestamp

datetime

Timestamp of the creation of this dataset.

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: lib.Error

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

Response Body

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

Discriminator: status

Discriminator value: server-error

Inherits: lib.Error

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

Response Body

{
  "status": "server-error",
  "message": "Dataset store is unreachable",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

Fetch details about a dataset and its status(es).

If the target dataset has just been posted, this endpoint may return a 404 for several seconds until the post has been asynchronously processed.

Parameters

Parameter

Type

Description

Path

vd-id* VDI ID

string

Unique VDI Dataset identifier string.

Pattern: ^[a-zA-Z0-9_-]{14}$

Min. length: 14

Max. length: 14

Inherits: string

curl -X GET \
  undefined/vdi-datasets/{vd-id}

Dataset Details DatasetDetails

application/json

Details about a specific singular dataset.

Inherits: object

Parameter Type Description

datasetId* Dataset ID

string

Unique VDI Dataset identifier string.

Pattern: ^[a-zA-Z0-9_-]{14}$

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

owner* Owner Details

object

Details about the owner of a VDI dataset.

Inherits: lib.DatasetOwner

owner.userId* Owner User ID

integer

VEuPathDB user ID of the owner of the dataset.

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

owner.firstName Owner First Name string

owner.lastName Owner Last Name string

owner.email Owner Email string

owner.organization Owner Organization string

datasetType* Dataset Type Info

object

Information about a specific dataset type.

Inherits: lib.DatasetTypeInfo

datasetType.name* Type Name string

datasetType.displayName Type Display Name

string

Display name for the type. This field is ignored in requests and will always be present in responses.

datasetType.version* Type Version string

name* Dataset Name string

shortName string

shortAttribution string

category string

summary Dataset Summary string

description Dataset Description string

sourceUrl Source URL

string

URL of the dataset data source, if the dataset was uploaded via URL.

origin* Dataset Origin

string

String representing the origin of the dataset. Examples include direct-upload, nephele, or galaxy.

projectIds* Project IDs

array

Project IDs for projects the user dataset record was submitted to.

Unique items: Yes

projectIds[] Project ID

string

Name or ID of a target VEuPathDB project.

Valid project IDs are:

AmoebaDB
ClinEpiDB
CryptoDB
FungiDB
GiardiaDB
HostDB
MicrobiomeDB
MicrosporidiaDB
PiroplasmaDB
PlasmoDB
ToxoDB
TrichDB
TriTrypDB
VectorBase
VEuPathDB

Inherits: lib.ProjectID

visibility* Dataset Visibility

string

Enum:

private
protected
public

Inherits: lib.DatasetVisibility

importMessages Import Messages

array

Log lines from the import process.

These messages will be warnings and/or validation errors.

Default value: []

importMessages[] string

status* Dataset Status Info

object

Information about the import and install status of a dataset.

Inherits: lib.DatasetStatusInfo

status.import*

string

Import status of the dataset.

Value	Description
`queued`	The dataset has not yet been processed and is waiting in the queue.
`in-progress`	The dataset is currently being import processed.
`complete`	The dataset has been processed and imported for installation.
`invalid`	The dataset failed import validation.
`failed`	The dataset import failed due to an internal server error.

Enum:

queued
in-progress
complete
invalid
failed

Inherits: lib.DatasetImportStatus

status.install array

status.install[] Dataset Install Status Entry

object

Entry in a list of install statuses for a dataset.

Inherits: lib.DatasetInstallStatusEntry

status.install[].projectId*

string

Name or ID of a target VEuPathDB project.

Valid project IDs are:

AmoebaDB
ClinEpiDB
CryptoDB
FungiDB
GiardiaDB
HostDB
MicrobiomeDB
MicrosporidiaDB
PiroplasmaDB
PlasmoDB
ToxoDB
TrichDB
TriTrypDB
VectorBase
VEuPathDB

Inherits: lib.ProjectID

status.install[].metaStatus*

string

Enum:

running
complete
failed-validation
failed-installation
ready-for-reinstall
missing-dependency

Inherits: lib.DatasetInstallStatus

status.install[].metaMessage string

status.install[].dataStatus

string

Enum:

running
complete
failed-validation
failed-installation
ready-for-reinstall
missing-dependency

Inherits: lib.DatasetInstallStatus

status.install[].dataMessage string

shares Shares

array

Array of share offers that have been created by the owner of this dataset to share it with other users.

shares[] Share Offer

object

Inherits: lib.ShareOffer

shares[].recipient*

object

I AM A UNION!

Inherits: lib.ShareOfferRecipient

shares[].recipient.userId* User ID

integer

Format: int64

shares[].recipient.firstName First Name string

shares[].recipient.lastName Last Name string

shares[].recipient.organization Organization string

shares[].recipient.email Email string

shares[].status*

string

Enum:

grant
revoke

Inherits: lib.ShareOfferAction

created* Creation Timestamp

datetime

Timestamp for when this dataset was created.

dependencies* Dataset Dependencies

array

Unique items: Yes

dependencies[]

object

Inherits: lib.DatasetDependency

dependencies[].resourceIdentifier* string

dependencies[].resourceDisplayName* string

dependencies[].resourceVersion* string

publications Dataset Publications

array

Unique items: Yes

publications[]

object

Inherits: lib.DatasetPublication

publications[].pubMedId*

string

Min. length: 3

Max. length: 30

publications[].citation

string

Min. length: 3

Max. length: 2000

hyperlinks Dataset Hyperlinks

array

Unique items: Yes

hyperlinks[]

object

Inherits: lib.DatasetHyperlink

hyperlinks[].url*

string

Min. length: 3

Max. length: 200

hyperlinks[].text*

string

Min. length: 3

Max. length: 300

hyperlinks[].description

string

Max. length: 4000

hyperlinks[].isPublication boolean

organisms Dataset Organism Abbreviations

array

Unique items: Yes

organisms[]

string

Max. length: 20

contacts Dataset Contacts

array

Unique items: Yes

contacts[]

object

Inherits: lib.DatasetContact

contacts[].name*

string

Min. length: 3

Max. length: 300

contacts[].email

string

Min. length: 5

Max. length: 4000

contacts[].affiliation

string

Max. length: 4000

contacts[].city

string

Max. length: 200

contacts[].state

string

Max. length: 200

contacts[].country

string

Max. length: 200

contacts[].address

string

Max. length: 1000

contacts[].isPrimary boolean

Response Body

{
  "datasetId": "zaZqAAGLGJhBgg",
  "owner": {
    "userId": 123456,
    "firstName": "Joe",
    "lastName": "User",
    "organization": "University of Joe"
  },
  "datasetType": {
    "name": "ISA",
    "version": "1.0"
  },
  "name": "My Dataset",
  "summary": "A short description of my dataset.",
  "description": "A longer description of my dataset.",
  "origin": "direct-upload",
  "visibility": "public",
  "projectIds": [
    "PlasmoDB",
    "ToxoDB"
  ],
  "importMessages": [
    "Import warning 1",
    "Import warning 2"
  ],
  "status": {
    "import": "complete",
    "install": [
      {
        "projectId": "PlasmoDB",
        "metaStatus": "complete",
        "dataStatus": "failed-installation",
        "dataMessage": "Failed due to some reason."
      },
      {
        "projectId": "ToxoDB",
        "metaStatus": "complete",
        "dataStatus": "complete"
      }
    ]
  },
  "created": "2023-10-31T11:59:59.999Z",
  "dependencies": [
    {
      "resourceIdentifier": "someDependency",
      "resourceDisplayName": "Some Dependency",
      "resourceVersion": "1.0"
    }
  ]
}

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: lib.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method conflict gone invalid-input failed-dependency server-error Inherits: lib.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: lib.Error

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

Response Body

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

Discriminator: status

Discriminator value: server-error

Inherits: lib.Error

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

Response Body

{
  "status": "server-error",
  "message": "Dataset store is unreachable",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

Updates the metadata for a target dataset.

If a field in the request body is null, the matching metedata field will retain it's previous value. To "clear" a field, it must be set to an empty string.

The name field, if provided, must not be blank.

Parameters

Parameter

Type

Description

Path

vd-id* VDI ID

string

Unique VDI Dataset identifier string.

Pattern: ^[a-zA-Z0-9_-]{14}$

Min. length: 14

Max. length: 14

Inherits: string

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

Dataset Patch Request DatasetPatchRequest

application/json

Request to update the metadata for a dataset.

Inherits: object

Parameter	Type	Description
visibility Dataset Visibility	string	Enum: private protected public Inherits: lib.DatasetVisibility
name Dataset Name	string	User provided name for a dataset.
shortName	string
shortAttribution	string
category	string
summary Dataset Summary	string	User provided summary for a dataset.
description Dataset Description	string	User provided description for a dataset.
publications Dataset Publications	array	Unique items: Yes
publications[]	object	Inherits: lib.DatasetPublication
publications[].pubMedId*	string	Min. length: 3 Max. length: 30
publications[].citation	string	Min. length: 3 Max. length: 2000
hyperlinks Dataset Hyperlinks	array	Unique items: Yes
hyperlinks[]	object	Inherits: lib.DatasetHyperlink
hyperlinks[].url*	string	Min. length: 3 Max. length: 200
hyperlinks[].text*	string	Min. length: 3 Max. length: 300
hyperlinks[].description	string	Max. length: 4000
hyperlinks[].isPublication	boolean
organisms Dataset Organism Abbreviations	array	Unique items: Yes
organisms[]	string	Max. length: 20
contacts Dataset Contacts	array	Unique items: Yes
contacts[]	object	Inherits: lib.DatasetContact
contacts[].name*	string	Min. length: 3 Max. length: 300
contacts[].email	string	Min. length: 5 Max. length: 4000
contacts[].affiliation	string	Max. length: 4000
contacts[].city	string	Max. length: 200
contacts[].state	string	Max. length: 200
contacts[].country	string	Max. length: 200
contacts[].address	string	Max. length: 1000
contacts[].isPrimary	boolean

Request Body

{
  "name": "My Dataset",
  "summary": "A short summary of my dataset.",
  "description": "A longer description of my dataset."
}

Bad Request BadRequestError

application/json

Request could not be parsed or was otherwise unusable.

Discriminator: status

Discriminator value: bad-request

Inherits: lib.Error

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

Response Body

{
  "status": "bad-request",
  "message": "Invalid project_id value."
}

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: lib.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method conflict gone invalid-input failed-dependency server-error Inherits: lib.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: lib.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method conflict gone invalid-input failed-dependency server-error Inherits: lib.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: lib.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method conflict gone invalid-input failed-dependency server-error Inherits: lib.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: lib.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method conflict gone invalid-input failed-dependency server-error Inherits: lib.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: lib.Error

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

Response Body

{
  "status": "server-error",
  "message": "Dataset store is unreachable",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

Marks the target dataset as deleted.

Datasets that have been marked as deleted are still recoverable for a short period of time before they are permanently deleted from the system.

Parameters

Parameter

Type

Description

Path

vd-id* VDI ID

string

Unique VDI Dataset identifier string.

Pattern: ^[a-zA-Z0-9_-]{14}$

Min. length: 14

Max. length: 14

Inherits: string

curl -X DELETE \
  undefined/vdi-datasets/{vd-id}

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: lib.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method conflict gone invalid-input failed-dependency server-error Inherits: lib.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: lib.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method conflict gone invalid-input failed-dependency server-error Inherits: lib.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: lib.Error

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

Response Body

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

Discriminator: status

Discriminator value: server-error

Inherits: lib.Error

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

Response Body

{
  "status": "server-error",
  "message": "Dataset store is unreachable",
  "requestId": "b296c3d9-4032-41b1-906e-c97ccfc447e3"
}

Lists the dataset zip files for the original user upload as well as the install files (when available).

If this endpoint is hit before the dataset has been imported, the upload zip size will be -1 which may be used as an indicator to clients that the zip size cannot yet be shown.

Parameters

Parameter

Type

Description

Path

vd-id* VDI ID

string

Unique VDI Dataset identifier string.

Pattern: ^[a-zA-Z0-9_-]{14}$

Min. length: 14

Max. length: 14

Inherits: string

curl -X GET \
  undefined/vdi-datasets/{vd-id}/files

Inherits: object

Parameter	Type	Description
upload*	object	Inherits: lib.DatasetZipDetails
upload.zipSize*	integer	Format: int64
upload.contents*	array
upload.contents[] Dataset File Details	object	Inherits: lib.DatasetFileDetails
upload.contents[].fileName* File Name	string
upload.contents[].fileSize* File Size	integer	Size of the file in bytes. Format: int64
install	object	Inherits: lib.DatasetZipDetails
install.zipSize*	integer	Format: int64
install.contents*	array
install.contents[] Dataset File Details	object	Inherits: lib.DatasetFileDetails
install.contents[].fileName* File Name	string
install.contents[].fileSize* File Size	integer	Size of the file in bytes. Format: int64

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: lib.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method conflict gone invalid-input failed-dependency server-error Inherits: lib.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: lib.Error

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

Response Body

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

Discriminator: status

Discriminator value: server-error

Inherits: lib.Error

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

Response Body

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

Returns a zip file containing the contents of the original upload to the dataset importer.

Parameters

Parameter

Type

Description

Path

vd-id* VDI ID

string

Unique VDI Dataset identifier string.

Pattern: ^[a-zA-Z0-9_-]{14}$

Min. length: 14

Max. length: 14

Inherits: string

curl -X GET \
  undefined/vdi-datasets/{vd-id}/files/upload

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: lib.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method conflict gone invalid-input failed-dependency server-error Inherits: lib.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: lib.Error

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

Response Body

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

Discriminator: status

Discriminator value: server-error

Inherits: lib.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method conflict gone invalid-input failed-dependency server-error Inherits: lib.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

vd-id* VDI ID

string

Unique VDI Dataset identifier string.

Pattern: ^[a-zA-Z0-9_-]{14}$

Min. length: 14

Max. length: 14

Inherits: string

curl -X GET \
  undefined/vdi-datasets/{vd-id}/files/data

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: lib.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method conflict gone invalid-input failed-dependency server-error Inherits: lib.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: lib.Error

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

Response Body

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

Discriminator: status

Discriminator value: server-error

Inherits: lib.Error

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

Response Body

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

PUT a record that is either an offer to share a dataset with another target user, or the revocation of an existing open share offer with a target user.

Parameters

Parameter

Type

Description

Path

vd-id* VDI ID

string

Unique VDI Dataset identifier string.

Pattern: ^[a-zA-Z0-9_-]{14}$

Min. length: 14

Max. length: 14

Inherits: string

recipient-user-id* VEuPathDB User ID

integer

Unique user identifier

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: integer

curl -X PUT \
  -H "Content-type: application/json"
  -d @body.json \
  undefined/vdi-datasets/{vd-id}/shares/{recipient-user-id}/offer

Dataset Share Offer DatasetShareOffer

application/json

An offer to share (or un-share) a dataset with a single target user.

Inherits: object

Parameter	Type	Description
action* Offer Action	string	What action to take with the dataset share offer. Either `grant` or `revoke`. A value of `grant` means the share should be offered to the user if they do not already have the dataset, or continue to be allowed if they already have access to the dataset. A value of `revoke` means the share should not be offered to the target user if they do not already have the dataset, or the sharing should be stopped if the user did already have access to the dataset. Enum: grant revoke Inherits: lib.ShareOfferAction

Request Body

Grant Example

{
  "action": "grant"
}

Revoke Example

{
  "action": "revoke"
}

Bad Request BadRequestError

application/json

Request could not be parsed or was otherwise unusable.

Discriminator: status

Discriminator value: bad-request

Inherits: lib.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method conflict gone invalid-input failed-dependency server-error Inherits: lib.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: lib.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method conflict gone invalid-input failed-dependency server-error Inherits: lib.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: lib.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method conflict gone invalid-input failed-dependency server-error Inherits: lib.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: lib.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method conflict gone invalid-input failed-dependency server-error Inherits: lib.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: lib.Error

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

Response Body

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

PUT a receipt of a dataset share offer, marking the share offer as either accepted or rejected.

Parameters

Parameter

Type

Description

Path

vd-id* VDI ID

string

Unique VDI Dataset identifier string.

Pattern: ^[a-zA-Z0-9_-]{14}$

Min. length: 14

Max. length: 14

Inherits: string

recipient-user-id* VEuPathDB User ID

integer

Unique user identifier

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: integer

curl -X PUT \
  -H "Content-type: application/json"
  -d @body.json \
  undefined/vdi-datasets/{vd-id}/shares/{recipient-user-id}/receipt

Dataset Share Receipt DatasetShareReceipt

application/json

A receipt or response to a share offer of a dataset to a single user.

Inherits: object

Parameter	Type	Description
action* Acknowledgement Action	string	What action to take with acknowledging a dataset share offer. Either `accept` or `reject`. A value of `accept` means that the dataset that a share was offered for should become available to the accepting user. A value of `reject` means that the dataset that a share was offered for should become unavailable to the rejecting user. Enum: accept reject Inherits: lib.ShareReceiptAction

Request Body

Accept Example

{
  "action": "accept"
}

Reject Example

{
  "action": "reject"
}

Bad Request BadRequestError

application/json

Request could not be parsed or was otherwise unusable.

Discriminator: status

Discriminator value: bad-request

Inherits: lib.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method conflict gone invalid-input failed-dependency server-error Inherits: lib.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: lib.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method conflict gone invalid-input failed-dependency server-error Inherits: lib.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: lib.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method conflict gone invalid-input failed-dependency server-error Inherits: lib.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: lib.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method conflict gone invalid-input failed-dependency server-error Inherits: lib.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: lib.Error

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

Response Body

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

Endpoint to list dataset shares that have been offered to the requesting user.

Parameters

Parameter Type Description

Query

status Share Status

string

Controls the results by filtering them to only shares that are in the specified target status.

Valid status values are:

open
accepted
rejected
all

These status values mean:

Status	Description
`open`	Only return share offers that have not yet been accepted or rejected.
`accepted`	Only return share offers that have been accepted by the requesting user.
`rejected`	Only return share offers that have been rejected by the requesting user.
`all`	Return all share offers regardless of whether they have been acknowledged, accepted, or rejected.

Default value: "open"

curl -X GET \
  undefined/vdi-datasets/share-offers?status=<value>

Parameter	Type	Description
[] Share Offer	object	Inherits: object
[].datasetId*	string	Unique VDI Dataset identifier string. Pattern: ^[a-zA-Z0-9_-]{14}$ Min. length: 14 Max. length: 14 Inherits: lib.VDI-ID
[].owner*	object	Details about the owner of a VDI dataset. Inherits: lib.DatasetOwner
[].owner.userId* Owner User ID	integer	VEuPathDB user ID of the owner of the dataset. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: lib.User-ID
[].owner.firstName Owner First Name	string
[].owner.lastName Owner Last Name	string
[].owner.email Owner Email	string
[].owner.organization Owner Organization	string
[].shareStatus*	string	Enum: open accepted rejected Inherits: lib.ShareOfferStatus
[].datasetType*	object	Information about a specific dataset type. Inherits: lib.DatasetTypeInfo
[].datasetType.name* Type Name	string
[].datasetType.displayName Type Display Name	string	Display name for the type. This field is ignored in requests and will always be present in responses.
[].datasetType.version* Type Version	string
[].projectIds*	array
[].projectIds[] Project ID	string	Name or ID of a target VEuPathDB project. Valid project IDs are: AmoebaDB ClinEpiDB CryptoDB FungiDB GiardiaDB HostDB MicrobiomeDB MicrosporidiaDB PiroplasmaDB PlasmoDB ToxoDB TrichDB TriTrypDB VectorBase VEuPathDB Inherits: lib.ProjectID

Response Body

[
  {
    "datasetId": "zaZqAAGLGJhBgg",
    "owner": {
      "userId": 202203,
      "firstName": "Joe",
      "lastName": "User",
      "organization": "University of Joe"
    },
    "shareStatus": "accepted",
    "datasetType": {
      "name": "ISA",
      "version": "1.0"
    },
    "projectIds": [
      "PlasmoDB",
      "VectorBase",
      "ToxoDB"
    ]
  }
]

Bad Request BadRequestError

application/json

Request could not be parsed or was otherwise unusable.

Discriminator: status

Discriminator value: bad-request

Inherits: lib.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method conflict gone invalid-input failed-dependency server-error Inherits: lib.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: lib.Error

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

Response Body

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

Discriminator: status

Discriminator value: server-error

Inherits: lib.Error

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

Response Body

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

List the plugins currently registered with the VDI instance.

Parameters

Parameter	Type	Description
Query
project Project Filter	string	Optional parameter that may be used to filter the results of this endpoint to only those that are allowed to be used with the target project. Valid values (non-case-sensitive): AmoebaDB ClinEpiDB CryptoDB FungiDB GiardiaDB HostDB MicrobiomeDB MicrosporidiaDB PiroplasmaDB PlasmoDB ToxoDB TrichDB TriTrypDB VectorBase VEuPathDB

curl -X GET \
  undefined/vdi-plugins?project=<value>

Parameter	Type	Description
[] Plugin Listing Entry	object	Inherits: object
[].displayName* Plugin Display Name	string
[].typeName* Dataset Type Name	string
[].typeVersion* Dataset Type Version	string
[].projects Relevant Projects	array	Projects that this plugin is restricted to. An empty or absent list indicates that the plugin has no project restrictions and may be used on any site.
[].projects[]	string

Response Body

[
  {
    "displayName": "Gene List",
    "typeName": "genelist",
    "typeVersion": "1.0",
    "projects": [
      "AmoebaDB",
      "ClinEpiDB",
      "CryptoDB",
      "FungiDB",
      "GiardiaDB",
      "HostDB",
      "MicrosporidiaDB",
      "PiroplasmaDB",
      "PlasmoDB",
      "ToxoDB",
      "TrichDB",
      "TriTrypDB",
      "VectorBase"
    ]
  }
]

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: lib.Error

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

Response Body

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

Discriminator: status

Discriminator value: server-error

Inherits: lib.Error

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

Response Body

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

Get user metadata.

curl -X GET \
  undefined/vdi-users/self/meta

Inherits: object

Parameter	Type	Description
quota*	object	Inherits: lib.UserQuotaDetails
quota.limit*	integer	Max number of bytes a user is allowed to upload. Format: int64
quota.usage*	integer	Current number of bytes counted against the user's quota. Format: int64

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: lib.Error

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

Response Body

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

Discriminator: status

Discriminator value: server-error

Inherits: lib.Error

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method conflict gone invalid-input failed-dependency server-error Inherits: lib.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.

curl -X GET \
  undefined/api

Prints information about the overall service health.

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.

curl -X GET \
  undefined/metrics

Security Schemes

Types

Inherits: object

Model

Parameter Type Description

details array

details[] Broken Dataset Details

object

Inherits: lib.BrokenDatasetDetails

details[].datasetId*

string

Unique VDI Dataset identifier string.

Pattern: ^[a-zA-Z0-9_-]{14}$

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

details[].owner*

integer

Unique user identifier

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

details[].datasetType*

object

Information about a specific dataset type.

Inherits: lib.DatasetTypeInfo

details[].datasetType.name* Type Name string

details[].datasetType.displayName Type Display Name

string

Display name for the type. This field is ignored in requests and will always be present in responses.

details[].datasetType.version* Type Version string

details[].projectIds* array

details[].projectIds[] Project ID

string

Name or ID of a target VEuPathDB project.

Valid project IDs are:

AmoebaDB
ClinEpiDB
CryptoDB
FungiDB
GiardiaDB
HostDB
MicrobiomeDB
MicrosporidiaDB
PiroplasmaDB
PlasmoDB
ToxoDB
TrichDB
TriTrypDB
VectorBase
VEuPathDB

Inherits: lib.ProjectID

details[].status*

object

Information about the import and install status of a dataset.

Inherits: lib.DatasetStatusInfo

details[].status.import*

string

Import status of the dataset.

Value	Description
`queued`	The dataset has not yet been processed and is waiting in the queue.
`in-progress`	The dataset is currently being import processed.
`complete`	The dataset has been processed and imported for installation.
`invalid`	The dataset failed import validation.
`failed`	The dataset import failed due to an internal server error.

Enum:

queued
in-progress
complete
invalid
failed

Inherits: lib.DatasetImportStatus

details[].status.install array

details[].status.install[] Dataset Install Status Entry

object

Entry in a list of install statuses for a dataset.

Inherits: lib.DatasetInstallStatusEntry

details[].status.install[].projectId*

string

Name or ID of a target VEuPathDB project.

Valid project IDs are:

AmoebaDB
ClinEpiDB
CryptoDB
FungiDB
GiardiaDB
HostDB
MicrobiomeDB
MicrosporidiaDB
PiroplasmaDB
PlasmoDB
ToxoDB
TrichDB
TriTrypDB
VectorBase
VEuPathDB

Inherits: lib.ProjectID

details[].status.install[].metaStatus*

string

Enum:

running
complete
failed-validation
failed-installation
ready-for-reinstall
missing-dependency

Inherits: lib.DatasetInstallStatus

details[].status.install[].metaMessage string

details[].status.install[].dataStatus

string

Enum:

running
complete
failed-validation
failed-installation
ready-for-reinstall
missing-dependency

Inherits: lib.DatasetInstallStatus

details[].status.install[].dataMessage string

ids array

ids[] VDI ID

string

Unique VDI Dataset identifier string.

Pattern: ^[a-zA-Z0-9_-]{14}$

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

Inherits: object

Model

Parameter Type Description

datasetId*

string

Unique VDI Dataset identifier string.

Pattern: ^[a-zA-Z0-9_-]{14}$

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

owner*

integer

Unique user identifier

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

datasetType*

object

Information about a specific dataset type.

Inherits: lib.DatasetTypeInfo

datasetType.name* Type Name string

datasetType.displayName Type Display Name

string

Display name for the type. This field is ignored in requests and will always be present in responses.

datasetType.version* Type Version string

projectIds* array

projectIds[] Project ID

string

Name or ID of a target VEuPathDB project.

Valid project IDs are:

AmoebaDB
ClinEpiDB
CryptoDB
FungiDB
GiardiaDB
HostDB
MicrobiomeDB
MicrosporidiaDB
PiroplasmaDB
PlasmoDB
ToxoDB
TrichDB
TriTrypDB
VectorBase
VEuPathDB

Inherits: lib.ProjectID

status*

object

Information about the import and install status of a dataset.

Inherits: lib.DatasetStatusInfo

status.import*

string

Import status of the dataset.

Value	Description
`queued`	The dataset has not yet been processed and is waiting in the queue.
`in-progress`	The dataset is currently being import processed.
`complete`	The dataset has been processed and imported for installation.
`invalid`	The dataset failed import validation.
`failed`	The dataset import failed due to an internal server error.

Enum:

queued
in-progress
complete
invalid
failed

Inherits: lib.DatasetImportStatus

status.install array

status.install[] Dataset Install Status Entry

object

Entry in a list of install statuses for a dataset.

Inherits: lib.DatasetInstallStatusEntry

status.install[].projectId*

string

Name or ID of a target VEuPathDB project.

Valid project IDs are:

AmoebaDB
ClinEpiDB
CryptoDB
FungiDB
GiardiaDB
HostDB
MicrobiomeDB
MicrosporidiaDB
PiroplasmaDB
PlasmoDB
ToxoDB
TrichDB
TriTrypDB
VectorBase
VEuPathDB

Inherits: lib.ProjectID

status.install[].metaStatus*

string

Enum:

running
complete
failed-validation
failed-installation
ready-for-reinstall
missing-dependency

Inherits: lib.DatasetInstallStatus

status.install[].metaMessage string

status.install[].dataStatus

string

Enum:

running
complete
failed-validation
failed-installation
ready-for-reinstall
missing-dependency

Inherits: lib.DatasetInstallStatus

status.install[].dataMessage string

Inherits: object

Model

Parameter	Type	Description
meta*	object	Inherits: lib.BrokenImportListingMeta
meta.count* Result Count	integer	Number of records in the result.
meta.before	string
meta.after	string
meta.user	integer	Unique user identifier Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: lib.User-ID
meta.limit	integer
meta.offset	integer
results*	array
results[] Broken Import Details	object	Inherits: lib.BrokenImportDetails
results[].datasetId*	string	Unique VDI Dataset identifier string. Pattern: ^[a-zA-Z0-9_-]{14}$ Min. length: 14 Max. length: 14 Inherits: lib.VDI-ID
results[].owner*	integer	Unique user identifier Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: lib.User-ID
results[].datasetType*	object	Information about a specific dataset type. Inherits: lib.DatasetTypeInfo
results[].datasetType.name* Type Name	string
results[].datasetType.displayName Type Display Name	string	Display name for the type. This field is ignored in requests and will always be present in responses.
results[].datasetType.version* Type Version	string
results[].projectIds*	array
results[].projectIds[] Project ID	string	Name or ID of a target VEuPathDB project. Valid project IDs are: AmoebaDB ClinEpiDB CryptoDB FungiDB GiardiaDB HostDB MicrobiomeDB MicrosporidiaDB PiroplasmaDB PlasmoDB ToxoDB TrichDB TriTrypDB VectorBase VEuPathDB Inherits: lib.ProjectID
results[].messages*	array
results[].messages[]	string

Inherits: object

Model

Parameter	Type	Description
count* Result Count	integer	Number of records in the result.
before	string
after	string
user	integer	Unique user identifier Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: lib.User-ID
limit	integer
offset	integer

Inherits: object

Model

Parameter	Type	Description
datasetId*	string	Unique VDI Dataset identifier string. Pattern: ^[a-zA-Z0-9_-]{14}$ Min. length: 14 Max. length: 14 Inherits: lib.VDI-ID
owner*	integer	Unique user identifier Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: lib.User-ID
datasetType*	object	Information about a specific dataset type. Inherits: lib.DatasetTypeInfo
datasetType.name* Type Name	string
datasetType.displayName Type Display Name	string	Display name for the type. This field is ignored in requests and will always be present in responses.
datasetType.version* Type Version	string
projectIds*	array
projectIds[] Project ID	string	Name or ID of a target VEuPathDB project. Valid project IDs are: AmoebaDB ClinEpiDB CryptoDB FungiDB GiardiaDB HostDB MicrobiomeDB MicrosporidiaDB PiroplasmaDB PlasmoDB ToxoDB TrichDB TriTrypDB VectorBase VEuPathDB Inherits: lib.ProjectID
messages*	array
messages[]	string

Inherits: object

Model

Parameter Type Description

meta*

object

Inherits: lib.AllDatasetsListMeta

meta.count* integer

meta.offset* integer

meta.limit* integer

meta.total* integer

results* array

results[]

object

Inherits: lib.AllDatasetsListEntry

results[].datasetId*

string

Unique VDI Dataset identifier string.

Pattern: ^[a-zA-Z0-9_-]{14}$

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

results[].owner*

integer

Unique user identifier

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

results[].datasetType*

object

Information about a specific dataset type.

Inherits: lib.DatasetTypeInfo

results[].datasetType.name* Type Name string

results[].datasetType.displayName Type Display Name

string

Display name for the type. This field is ignored in requests and will always be present in responses.

results[].datasetType.version* Type Version string

results[].visibility*

string

Enum:

private
protected
public

Inherits: lib.DatasetVisibility

results[].name* string

results[].shortName string

results[].shortAttribution string

results[].category string

results[].summary string

results[].description string

results[].sourceUrl string

results[].origin* string

results[].projectIds* array

results[].projectIds[] Project ID

string

Name or ID of a target VEuPathDB project.

Valid project IDs are:

AmoebaDB
ClinEpiDB
CryptoDB
FungiDB
GiardiaDB
HostDB
MicrobiomeDB
MicrosporidiaDB
PiroplasmaDB
PlasmoDB
ToxoDB
TrichDB
TriTrypDB
VectorBase
VEuPathDB

Inherits: lib.ProjectID

results[].status*

object

Information about the import and install status of a dataset.

Inherits: lib.DatasetStatusInfo

results[].status.import*

string

Import status of the dataset.

Value	Description
`queued`	The dataset has not yet been processed and is waiting in the queue.
`in-progress`	The dataset is currently being import processed.
`complete`	The dataset has been processed and imported for installation.
`invalid`	The dataset failed import validation.
`failed`	The dataset import failed due to an internal server error.

Enum:

queued
in-progress
complete
invalid
failed

Inherits: lib.DatasetImportStatus

results[].status.install array

results[].status.install[] Dataset Install Status Entry

object

Entry in a list of install statuses for a dataset.

Inherits: lib.DatasetInstallStatusEntry

results[].status.install[].projectId*

string

Name or ID of a target VEuPathDB project.

Valid project IDs are:

AmoebaDB
ClinEpiDB
CryptoDB
FungiDB
GiardiaDB
HostDB
MicrobiomeDB
MicrosporidiaDB
PiroplasmaDB
PlasmoDB
ToxoDB
TrichDB
TriTrypDB
VectorBase
VEuPathDB

Inherits: lib.ProjectID

results[].status.install[].metaStatus*

string

Enum:

running
complete
failed-validation
failed-installation
ready-for-reinstall
missing-dependency

Inherits: lib.DatasetInstallStatus

results[].status.install[].metaMessage string

results[].status.install[].dataStatus

string

Enum:

running
complete
failed-validation
failed-installation
ready-for-reinstall
missing-dependency

Inherits: lib.DatasetInstallStatus

results[].status.install[].dataMessage string

results[].created* datetime

results[].isDeleted* boolean

Inherits: object

Model

Parameter	Type	Description
count*	integer
offset*	integer
limit*	integer
total*	integer

Inherits: object

Model

Parameter Type Description

datasetId*

string

Unique VDI Dataset identifier string.

Pattern: ^[a-zA-Z0-9_-]{14}$

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

owner*

integer

Unique user identifier

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

datasetType*

object

Information about a specific dataset type.

Inherits: lib.DatasetTypeInfo

datasetType.name* Type Name string

datasetType.displayName Type Display Name

string

Display name for the type. This field is ignored in requests and will always be present in responses.

datasetType.version* Type Version string

visibility*

string

Enum:

private
protected
public

Inherits: lib.DatasetVisibility

name* string

shortName string

shortAttribution string

category string

summary string

description string

sourceUrl string

origin* string

projectIds* array

projectIds[] Project ID

string

Name or ID of a target VEuPathDB project.

Valid project IDs are:

AmoebaDB
ClinEpiDB
CryptoDB
FungiDB
GiardiaDB
HostDB
MicrobiomeDB
MicrosporidiaDB
PiroplasmaDB
PlasmoDB
ToxoDB
TrichDB
TriTrypDB
VectorBase
VEuPathDB

Inherits: lib.ProjectID

status*

object

Information about the import and install status of a dataset.

Inherits: lib.DatasetStatusInfo

status.import*

string

Import status of the dataset.

Value	Description
`queued`	The dataset has not yet been processed and is waiting in the queue.
`in-progress`	The dataset is currently being import processed.
`complete`	The dataset has been processed and imported for installation.
`invalid`	The dataset failed import validation.
`failed`	The dataset import failed due to an internal server error.

Enum:

queued
in-progress
complete
invalid
failed

Inherits: lib.DatasetImportStatus

status.install array

status.install[] Dataset Install Status Entry

object

Entry in a list of install statuses for a dataset.

Inherits: lib.DatasetInstallStatusEntry

status.install[].projectId*

string

Name or ID of a target VEuPathDB project.

Valid project IDs are:

AmoebaDB
ClinEpiDB
CryptoDB
FungiDB
GiardiaDB
HostDB
MicrobiomeDB
MicrosporidiaDB
PiroplasmaDB
PlasmoDB
ToxoDB
TrichDB
TriTrypDB
VectorBase
VEuPathDB

Inherits: lib.ProjectID

status.install[].metaStatus*

string

Enum:

running
complete
failed-validation
failed-installation
ready-for-reinstall
missing-dependency

Inherits: lib.DatasetInstallStatus

status.install[].metaMessage string

status.install[].dataStatus

string

Enum:

running
complete
failed-validation
failed-installation
ready-for-reinstall
missing-dependency

Inherits: lib.DatasetInstallStatus

status.install[].dataMessage string

created* datetime

isDeleted* boolean

Inherits: object

Model

Parameter	Type	Description
sharesUpdateTime*	datetime
dataUpdateTime*	datetime
metaUpdateTime*	datetime

Inherits: object

Model

Parameter	Type	Description
datasetType*	object	Information about a specific dataset type. Inherits: lib.DatasetTypeInfo
datasetType.name* Type Name	string
datasetType.displayName Type Display Name	string	Display name for the type. This field is ignored in requests and will always be present in responses.
datasetType.version* Type Version	string
owner*	integer	Unique user identifier Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: lib.User-ID
isDeleted*	boolean
origin*	string
created*	datetime
inserted*	datetime
name*	string
shortName	string
shortAttribution	string
category	string
summary	string
description	string
visibility*	string	Enum: private protected public Inherits: lib.DatasetVisibility
sourceUrl	string
projectIds*	array
projectIds[] Project ID	string	Name or ID of a target VEuPathDB project. Valid project IDs are: AmoebaDB ClinEpiDB CryptoDB FungiDB GiardiaDB HostDB MicrobiomeDB MicrosporidiaDB PiroplasmaDB PlasmoDB ToxoDB TrichDB TriTrypDB VectorBase VEuPathDB Inherits: lib.ProjectID
status*	string
syncControl	object	Inherits: object
syncControl.sharesUpdateTime*	datetime
syncControl.dataUpdateTime*	datetime
syncControl.metaUpdateTime*	datetime
uploadFiles	array
uploadFiles[]	string
installFiles	array
installFiles[]	string
importMessages*	array
importMessages[]	string

Object controlling the install cleanup process and what datasets it should target.

Requesters should specify one of the fields all or targets to control what datasets will be cleaned up. If neither is specified the endpoint will do nothing.

Inherits: object

Model

Parameter	Type	Description
all	boolean
targets	array	Unique items: Yes
targets[] Install Cleanup Target	object	Inherits: lib.InstallCleanupTarget
targets[].datasetId*	string	Unique VDI Dataset identifier string. Pattern: ^[a-zA-Z0-9_-]{14}$ Min. length: 14 Max. length: 14 Inherits: lib.VDI-ID
targets[].projectId*	string	Name or ID of a target VEuPathDB project. Valid project IDs are: AmoebaDB ClinEpiDB CryptoDB FungiDB GiardiaDB HostDB MicrobiomeDB MicrosporidiaDB PiroplasmaDB PlasmoDB ToxoDB TrichDB TriTrypDB VectorBase VEuPathDB Inherits: lib.ProjectID

Inherits: object

Model

Parameter

Type

Description

datasetId*

string

Unique VDI Dataset identifier string.

Pattern: ^[a-zA-Z0-9_-]{14}$

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

projectId*

string

Name or ID of a target VEuPathDB project.

Valid project IDs are:

AmoebaDB
ClinEpiDB
CryptoDB
FungiDB
GiardiaDB
HostDB
MicrobiomeDB
MicrosporidiaDB
PiroplasmaDB
PlasmoDB
ToxoDB
TrichDB
TriTrypDB
VectorBase
VEuPathDB

Inherits: lib.ProjectID

Inherits: object

Model

Parameter	Type	Description
userId*	integer	Unique user identifier Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: lib.User-ID
firstName*	string
lastName*	string
organization*	string
accepted*	boolean

Short entry with basic details about a dataset.

Inherits: object

Model

Parameter Type Description

datasetId* Dataset ID

string

Unique VDI Dataset identifier string.

Pattern: ^[a-zA-Z0-9_-]{14}$

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

owner* Owner Details

object

Details about the owner of a VDI dataset.

Inherits: lib.DatasetOwner

owner.userId* Owner User ID

integer

VEuPathDB user ID of the owner of the dataset.

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

owner.firstName Owner First Name string

owner.lastName Owner Last Name string

owner.email Owner Email string

owner.organization Owner Organization string

datasetType* Dataset Type

object

Information about a specific dataset type.

Inherits: lib.DatasetTypeInfo

datasetType.name* Type Name string

datasetType.displayName Type Display Name

string

Display name for the type. This field is ignored in requests and will always be present in responses.

datasetType.version* Type Version string

visibility* Dataset Visibility

string

Enum:

private
protected
public

Inherits: lib.DatasetVisibility

name* Dataset Name

string

User provided name for the dataset.

shortName string

shortAttribution string

category string

summary Dataset Summary

string

User provided summary of the dataset.

description Dataset Description

string

User provided description of the dataset.

sourceUrl Source URL

string

URL of the dataset data source, if the dataset was uploaded via URL.

origin* Dataset Origin

string

String representing the origin of the dataset. Examples include direct-upload, nephele, or galaxy.

projectIds* Project IDs

array

Project IDs for projects the dataset record was submitted to.

projectIds[] Project ID

string

Name or ID of a target VEuPathDB project.

Valid project IDs are:

AmoebaDB
ClinEpiDB
CryptoDB
FungiDB
GiardiaDB
HostDB
MicrobiomeDB
MicrosporidiaDB
PiroplasmaDB
PlasmoDB
ToxoDB
TrichDB
TriTrypDB
VectorBase
VEuPathDB

Inherits: lib.ProjectID

status* Status Info

object

Information about the import and install status of a dataset.

Inherits: lib.DatasetStatusInfo

status.import*

string

Import status of the dataset.

Value	Description
`queued`	The dataset has not yet been processed and is waiting in the queue.
`in-progress`	The dataset is currently being import processed.
`complete`	The dataset has been processed and imported for installation.
`invalid`	The dataset failed import validation.
`failed`	The dataset import failed due to an internal server error.

Enum:

queued
in-progress
complete
invalid
failed

Inherits: lib.DatasetImportStatus

status.install array

status.install[] Dataset Install Status Entry

object

Entry in a list of install statuses for a dataset.

Inherits: lib.DatasetInstallStatusEntry

status.install[].projectId*

string

Name or ID of a target VEuPathDB project.

Valid project IDs are:

AmoebaDB
ClinEpiDB
CryptoDB
FungiDB
GiardiaDB
HostDB
MicrobiomeDB
MicrosporidiaDB
PiroplasmaDB
PlasmoDB
ToxoDB
TrichDB
TriTrypDB
VectorBase
VEuPathDB

Inherits: lib.ProjectID

status.install[].metaStatus*

string

Enum:

running
complete
failed-validation
failed-installation
ready-for-reinstall
missing-dependency

Inherits: lib.DatasetInstallStatus

status.install[].metaMessage string

status.install[].dataStatus

string

Enum:

running
complete
failed-validation
failed-installation
ready-for-reinstall
missing-dependency

Inherits: lib.DatasetInstallStatus

status.install[].dataMessage string

shares* Shared With array

shares[]

object

Inherits: object

shares[].userId*

integer

Unique user identifier

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

shares[].firstName* string

shares[].lastName* string

shares[].organization* string

shares[].accepted* boolean

fileCount* File Count

integer

Number of files uploaded for this dataset.

fileSizeTotal* File Size Total

integer

Sum of the sizes of all the files uploaded for this dataset.

Format: int64

created* Creation Timestamp

datetime

Timestamp of the creation of this dataset.

HTTP POST request body requesting the creation of a dataset from the components included in the request.

Inherits: object

Model

Parameter	Type	Description
meta* Dataset Meta	object	Metadata about the dataset being submitted. Inherits: lib.DatasetPostMeta
meta.datasetType* Dataset Type	object	Type of the dataset that is being uploaded. Inherits: lib.DatasetPostType
meta.datasetType.name*	string
meta.datasetType.version*	string
meta.name* Dataset Name	string	User provided name for the dataset.
meta.shortName	string	Max. length: 300
meta.shortAttribution	string	Max. length: 300
meta.category	string	Max. length: 100
meta.visibility Dataset Visibility	string	Default value: "private" Enum: private protected public Inherits: lib.DatasetVisibility
meta.summary Dataset Summary	string	User provided summary for the dataset. Max. length: 4000
meta.description Dataset Description	string	User provided description for the dataset.
meta.origin* Dataset Origin	string	String representing the origin of the dataset. Examples include `direct-upload`, `nephele`, or `galaxy`.
meta.projects* Project IDs	array	IDs of the projects this dataset is being submitted to. Unique items: Yes
meta.projects[] Project ID	string	Name or ID of a target VEuPathDB project. Valid project IDs are: AmoebaDB ClinEpiDB CryptoDB FungiDB GiardiaDB HostDB MicrobiomeDB MicrosporidiaDB PiroplasmaDB PlasmoDB ToxoDB TrichDB TriTrypDB VectorBase VEuPathDB Inherits: lib.ProjectID
meta.dependencies* Dataset Dependencies	array	Unique items: Yes
meta.dependencies[]	object	Inherits: lib.DatasetDependency
meta.dependencies[].resourceIdentifier*	string
meta.dependencies[].resourceDisplayName*	string
meta.dependencies[].resourceVersion*	string
meta.publications Dataset Publications	array	Unique items: Yes
meta.publications[]	object	Inherits: lib.DatasetPublication
meta.publications[].pubMedId*	string	Min. length: 3 Max. length: 30
meta.publications[].citation	string	Min. length: 3 Max. length: 2000
meta.hyperlinks Dataset Hyperlinks	array	Unique items: Yes
meta.hyperlinks[]	object	Inherits: lib.DatasetHyperlink
meta.hyperlinks[].url*	string	Min. length: 3 Max. length: 200
meta.hyperlinks[].text*	string	Min. length: 3 Max. length: 300
meta.hyperlinks[].description	string	Max. length: 4000
meta.hyperlinks[].isPublication	boolean
meta.organisms Dataset Organisms	array	Unique items: Yes
meta.organisms[]	string	Max. length: 200
meta.contacts Dataset Contacts	array	Unique items: Yes
meta.contacts[]	object	Inherits: lib.DatasetContact
meta.contacts[].name*	string	Min. length: 3 Max. length: 300
meta.contacts[].email	string	Min. length: 5 Max. length: 4000
meta.contacts[].affiliation	string	Max. length: 4000
meta.contacts[].city	string	Max. length: 200
meta.contacts[].state	string	Max. length: 200
meta.contacts[].country	string	Max. length: 200
meta.contacts[].address	string	Max. length: 1000
meta.contacts[].isPrimary	boolean
meta.createdOn Creation Date	datetime-only
file Dataset File	file	Dataset file to upload. This field is incompatible with the `url` field.
url Dataset URL	string	URL to a dataset file to upload. This field is incompatible with the `file` field.

Inherits: object

Model

Parameter	Type	Description
datasetType* Dataset Type	object	Type of the dataset that is being uploaded. Inherits: lib.DatasetPostType
datasetType.name*	string
datasetType.version*	string
name* Dataset Name	string	User provided name for the dataset.
shortName	string	Max. length: 300
shortAttribution	string	Max. length: 300
category	string	Max. length: 100
visibility Dataset Visibility	string	Default value: "private" Enum: private protected public Inherits: lib.DatasetVisibility
summary Dataset Summary	string	User provided summary for the dataset. Max. length: 4000
description Dataset Description	string	User provided description for the dataset.
origin* Dataset Origin	string	String representing the origin of the dataset. Examples include `direct-upload`, `nephele`, or `galaxy`.
projects* Project IDs	array	IDs of the projects this dataset is being submitted to. Unique items: Yes
projects[] Project ID	string	Name or ID of a target VEuPathDB project. Valid project IDs are: AmoebaDB ClinEpiDB CryptoDB FungiDB GiardiaDB HostDB MicrobiomeDB MicrosporidiaDB PiroplasmaDB PlasmoDB ToxoDB TrichDB TriTrypDB VectorBase VEuPathDB Inherits: lib.ProjectID
dependencies* Dataset Dependencies	array	Unique items: Yes
dependencies[]	object	Inherits: lib.DatasetDependency
dependencies[].resourceIdentifier*	string
dependencies[].resourceDisplayName*	string
dependencies[].resourceVersion*	string
publications Dataset Publications	array	Unique items: Yes
publications[]	object	Inherits: lib.DatasetPublication
publications[].pubMedId*	string	Min. length: 3 Max. length: 30
publications[].citation	string	Min. length: 3 Max. length: 2000
hyperlinks Dataset Hyperlinks	array	Unique items: Yes
hyperlinks[]	object	Inherits: lib.DatasetHyperlink
hyperlinks[].url*	string	Min. length: 3 Max. length: 200
hyperlinks[].text*	string	Min. length: 3 Max. length: 300
hyperlinks[].description	string	Max. length: 4000
hyperlinks[].isPublication	boolean
organisms Dataset Organisms	array	Unique items: Yes
organisms[]	string	Max. length: 200
contacts Dataset Contacts	array	Unique items: Yes
contacts[]	object	Inherits: lib.DatasetContact
contacts[].name*	string	Min. length: 3 Max. length: 300
contacts[].email	string	Min. length: 5 Max. length: 4000
contacts[].affiliation	string	Max. length: 4000
contacts[].city	string	Max. length: 200
contacts[].state	string	Max. length: 200
contacts[].country	string	Max. length: 200
contacts[].address	string	Max. length: 1000
contacts[].isPrimary	boolean
createdOn Creation Date	datetime-only

Inherits: object

Model

Parameter	Type	Description
name*	string
version*	string

Response object returned on successful upload of a dataset.

Inherits: object

Model

Parameter

Type

Description

datasetId*

string

Unique VDI Dataset identifier string.

Pattern: ^[a-zA-Z0-9_-]{14}$

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

Inherits: object

Model

Parameter	Type	Description
datasetId*	string	Unique VDI Dataset identifier string. Pattern: ^[a-zA-Z0-9_-]{14}$ Min. length: 14 Max. length: 14 Inherits: lib.VDI-ID
owner*	object	Details about the owner of a VDI dataset. Inherits: lib.DatasetOwner
owner.userId* Owner User ID	integer	VEuPathDB user ID of the owner of the dataset. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: lib.User-ID
owner.firstName Owner First Name	string
owner.lastName Owner Last Name	string
owner.email Owner Email	string
owner.organization Owner Organization	string
shareStatus*	string	Enum: open accepted rejected Inherits: lib.ShareOfferStatus
datasetType*	object	Information about a specific dataset type. Inherits: lib.DatasetTypeInfo
datasetType.name* Type Name	string
datasetType.displayName Type Display Name	string	Display name for the type. This field is ignored in requests and will always be present in responses.
datasetType.version* Type Version	string
projectIds*	array
projectIds[] Project ID	string	Name or ID of a target VEuPathDB project. Valid project IDs are: AmoebaDB ClinEpiDB CryptoDB FungiDB GiardiaDB HostDB MicrobiomeDB MicrosporidiaDB PiroplasmaDB PlasmoDB ToxoDB TrichDB TriTrypDB VectorBase VEuPathDB Inherits: lib.ProjectID

Enum:

open
accepted
rejected

Inherits: string

Inherits: object

Model

Parameter	Type	Description
upload*	object	Inherits: lib.DatasetZipDetails
upload.zipSize*	integer	Format: int64
upload.contents*	array
upload.contents[] Dataset File Details	object	Inherits: lib.DatasetFileDetails
upload.contents[].fileName* File Name	string
upload.contents[].fileSize* File Size	integer	Size of the file in bytes. Format: int64
install	object	Inherits: lib.DatasetZipDetails
install.zipSize*	integer	Format: int64
install.contents*	array
install.contents[] Dataset File Details	object	Inherits: lib.DatasetFileDetails
install.contents[].fileName* File Name	string
install.contents[].fileSize* File Size	integer	Size of the file in bytes. Format: int64

Inherits: object

Model

Parameter	Type	Description
zipSize*	integer	Format: int64
contents*	array
contents[] Dataset File Details	object	Inherits: lib.DatasetFileDetails
contents[].fileName* File Name	string
contents[].fileSize* File Size	integer	Size of the file in bytes. Format: int64

Inherits: object

Model

Parameter	Type	Description
fileName* File Name	string
fileSize* File Size	integer	Size of the file in bytes. Format: int64

Details about a specific singular dataset.

Inherits: object

Model

Parameter Type Description

datasetId* Dataset ID

string

Unique VDI Dataset identifier string.

Pattern: ^[a-zA-Z0-9_-]{14}$

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

owner* Owner Details

object

Details about the owner of a VDI dataset.

Inherits: lib.DatasetOwner

owner.userId* Owner User ID

integer

VEuPathDB user ID of the owner of the dataset.

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

owner.firstName Owner First Name string

owner.lastName Owner Last Name string

owner.email Owner Email string

owner.organization Owner Organization string

datasetType* Dataset Type Info

object

Information about a specific dataset type.

Inherits: lib.DatasetTypeInfo

datasetType.name* Type Name string

datasetType.displayName Type Display Name

string

Display name for the type. This field is ignored in requests and will always be present in responses.

datasetType.version* Type Version string

name* Dataset Name string

shortName string

shortAttribution string

category string

summary Dataset Summary string

description Dataset Description string

sourceUrl Source URL

string

URL of the dataset data source, if the dataset was uploaded via URL.

origin* Dataset Origin

string

String representing the origin of the dataset. Examples include direct-upload, nephele, or galaxy.

projectIds* Project IDs

array

Project IDs for projects the user dataset record was submitted to.

Unique items: Yes

projectIds[] Project ID

string

Name or ID of a target VEuPathDB project.

Valid project IDs are:

AmoebaDB
ClinEpiDB
CryptoDB
FungiDB
GiardiaDB
HostDB
MicrobiomeDB
MicrosporidiaDB
PiroplasmaDB
PlasmoDB
ToxoDB
TrichDB
TriTrypDB
VectorBase
VEuPathDB

Inherits: lib.ProjectID

visibility* Dataset Visibility

string

Enum:

private
protected
public

Inherits: lib.DatasetVisibility

importMessages Import Messages

array

Log lines from the import process.

These messages will be warnings and/or validation errors.

Default value: []

importMessages[] string

status* Dataset Status Info

object

Information about the import and install status of a dataset.

Inherits: lib.DatasetStatusInfo

status.import*

string

Import status of the dataset.

Value	Description
`queued`	The dataset has not yet been processed and is waiting in the queue.
`in-progress`	The dataset is currently being import processed.
`complete`	The dataset has been processed and imported for installation.
`invalid`	The dataset failed import validation.
`failed`	The dataset import failed due to an internal server error.

Enum:

queued
in-progress
complete
invalid
failed

Inherits: lib.DatasetImportStatus

status.install array

status.install[] Dataset Install Status Entry

object

Entry in a list of install statuses for a dataset.

Inherits: lib.DatasetInstallStatusEntry

status.install[].projectId*

string

Name or ID of a target VEuPathDB project.

Valid project IDs are:

AmoebaDB
ClinEpiDB
CryptoDB
FungiDB
GiardiaDB
HostDB
MicrobiomeDB
MicrosporidiaDB
PiroplasmaDB
PlasmoDB
ToxoDB
TrichDB
TriTrypDB
VectorBase
VEuPathDB

Inherits: lib.ProjectID

status.install[].metaStatus*

string

Enum:

running
complete
failed-validation
failed-installation
ready-for-reinstall
missing-dependency

Inherits: lib.DatasetInstallStatus

status.install[].metaMessage string

status.install[].dataStatus

string

Enum:

running
complete
failed-validation
failed-installation
ready-for-reinstall
missing-dependency

Inherits: lib.DatasetInstallStatus

status.install[].dataMessage string

shares Shares

array

Array of share offers that have been created by the owner of this dataset to share it with other users.

shares[] Share Offer

object

Inherits: lib.ShareOffer

shares[].recipient*

object

I AM A UNION!

Inherits: lib.ShareOfferRecipient

shares[].recipient.userId* User ID

integer

Format: int64

shares[].recipient.firstName First Name string

shares[].recipient.lastName Last Name string

shares[].recipient.organization Organization string

shares[].recipient.email Email string

shares[].status*

string

Enum:

grant
revoke

Inherits: lib.ShareOfferAction

created* Creation Timestamp

datetime

Timestamp for when this dataset was created.

dependencies* Dataset Dependencies

array

Unique items: Yes

dependencies[]

object

Inherits: lib.DatasetDependency

dependencies[].resourceIdentifier* string

dependencies[].resourceDisplayName* string

dependencies[].resourceVersion* string

publications Dataset Publications

array

Unique items: Yes

publications[]

object

Inherits: lib.DatasetPublication

publications[].pubMedId*

string

Min. length: 3

Max. length: 30

publications[].citation

string

Min. length: 3

Max. length: 2000

hyperlinks Dataset Hyperlinks

array

Unique items: Yes

hyperlinks[]

object

Inherits: lib.DatasetHyperlink

hyperlinks[].url*

string

Min. length: 3

Max. length: 200

hyperlinks[].text*

string

Min. length: 3

Max. length: 300

hyperlinks[].description

string

Max. length: 4000

hyperlinks[].isPublication boolean

organisms Dataset Organism Abbreviations

array

Unique items: Yes

organisms[]

string

Max. length: 20

contacts Dataset Contacts

array

Unique items: Yes

contacts[]

object

Inherits: lib.DatasetContact

contacts[].name*

string

Min. length: 3

Max. length: 300

contacts[].email

string

Min. length: 5

Max. length: 4000

contacts[].affiliation

string

Max. length: 4000

contacts[].city

string

Max. length: 200

contacts[].state

string

Max. length: 200

contacts[].country

string

Max. length: 200

contacts[].address

string

Max. length: 1000

contacts[].isPrimary boolean

Inherits: object

Model

Parameter	Type	Description
recipient*	object	I AM A UNION! Inherits: lib.ShareOfferRecipient
recipient.userId* User ID	integer	Format: int64
recipient.firstName First Name	string
recipient.lastName Last Name	string
recipient.organization Organization	string
recipient.email Email	string
status*	string	Enum: grant revoke Inherits: lib.ShareOfferAction

Examples

{
  "recipient": {
    "userId": 123456,
    "firstName": "Joe",
    "lastName": "User",
    "email": "juser@ujoe.edu",
    "organization": "University of Joe"
  },
  "status": "revoke"
}

I AM A UNION!

Inherits: object

Model

Parameter	Type	Description
userId* User ID	integer	Format: int64
firstName First Name	string
lastName Last Name	string
organization Organization	string
email Email	string

Examples

{
  "userId": 123456,
  "email": "myusername@someuniversity.edu"
}

Request to update the metadata for a dataset.

Inherits: object

Model

Parameter	Type	Description
visibility Dataset Visibility	string	Enum: private protected public Inherits: lib.DatasetVisibility
name Dataset Name	string	User provided name for a dataset.
shortName	string
shortAttribution	string
category	string
summary Dataset Summary	string	User provided summary for a dataset.
description Dataset Description	string	User provided description for a dataset.
publications Dataset Publications	array	Unique items: Yes
publications[]	object	Inherits: lib.DatasetPublication
publications[].pubMedId*	string	Min. length: 3 Max. length: 30
publications[].citation	string	Min. length: 3 Max. length: 2000
hyperlinks Dataset Hyperlinks	array	Unique items: Yes
hyperlinks[]	object	Inherits: lib.DatasetHyperlink
hyperlinks[].url*	string	Min. length: 3 Max. length: 200
hyperlinks[].text*	string	Min. length: 3 Max. length: 300
hyperlinks[].description	string	Max. length: 4000
hyperlinks[].isPublication	boolean
organisms Dataset Organism Abbreviations	array	Unique items: Yes
organisms[]	string	Max. length: 20
contacts Dataset Contacts	array	Unique items: Yes
contacts[]	object	Inherits: lib.DatasetContact
contacts[].name*	string	Min. length: 3 Max. length: 300
contacts[].email	string	Min. length: 5 Max. length: 4000
contacts[].affiliation	string	Max. length: 4000
contacts[].city	string	Max. length: 200
contacts[].state	string	Max. length: 200
contacts[].country	string	Max. length: 200
contacts[].address	string	Max. length: 1000
contacts[].isPrimary	boolean

An offer to share (or un-share) a dataset with a single target user.

Inherits: object

Model

Parameter	Type	Description
action* Offer Action	string	What action to take with the dataset share offer. Either `grant` or `revoke`. A value of `grant` means the share should be offered to the user if they do not already have the dataset, or continue to be allowed if they already have access to the dataset. A value of `revoke` means the share should not be offered to the target user if they do not already have the dataset, or the sharing should be stopped if the user did already have access to the dataset. Enum: grant revoke Inherits: lib.ShareOfferAction

A receipt or response to a share offer of a dataset to a single user.

Inherits: object

Model

Parameter	Type	Description
action* Acknowledgement Action	string	What action to take with acknowledging a dataset share offer. Either `accept` or `reject`. A value of `accept` means that the dataset that a share was offered for should become available to the accepting user. A value of `reject` means that the dataset that a share was offered for should become unavailable to the rejecting user. Enum: accept reject Inherits: lib.ShareReceiptAction

Inherits: object

Model

Parameter	Type	Description
displayName* Plugin Display Name	string
typeName* Dataset Type Name	string
typeVersion* Dataset Type Version	string
projects Relevant Projects	array	Projects that this plugin is restricted to. An empty or absent list indicates that the plugin has no project restrictions and may be used on any site.
projects[]	string

Inherits: object

Model

Parameter	Type	Description
quota*	object	Inherits: lib.UserQuotaDetails
quota.limit*	integer	Max number of bytes a user is allowed to upload. Format: int64
quota.usage*	integer	Current number of bytes counted against the user's quota. Format: int64

Inherits: object

Model

Parameter	Type	Description
limit*	integer	Max number of bytes a user is allowed to upload. Format: int64
usage*	integer	Current number of bytes counted against the user's quota. Format: int64

Unique VDI Dataset identifier string.

Pattern: ^[a-zA-Z0-9_-]{14}$

Min. length: 14

Max. length: 14

Inherits: string

Unique user identifier

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: integer

Name or ID of a target VEuPathDB project.

Valid project IDs are:

AmoebaDB
ClinEpiDB
CryptoDB
FungiDB
GiardiaDB
HostDB
MicrobiomeDB
MicrosporidiaDB
PiroplasmaDB
PlasmoDB
ToxoDB
TrichDB
TriTrypDB
VectorBase
VEuPathDB

Inherits: string

Details about the owner of a VDI dataset.

Inherits: object

Model

Parameter	Type	Description
userId* Owner User ID	integer	VEuPathDB user ID of the owner of the dataset. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
firstName Owner First Name	string
lastName Owner Last Name	string
email Owner Email	string
organization Owner Organization	string

Information about a specific dataset type.

Inherits: object

Model

Parameter	Type	Description
name* Type Name	string
displayName Type Display Name	string	Display name for the type. This field is ignored in requests and will always be present in responses.
version* Type Version	string

Enum:

grant
revoke

Inherits: string

Enum:

accept
reject

Inherits: string

Enum:

private
protected
public

Inherits: string

Information about the import and install status of a dataset.

Inherits: object

Model

Parameter Type Description

import*

string

Import status of the dataset.

Value	Description
`queued`	The dataset has not yet been processed and is waiting in the queue.
`in-progress`	The dataset is currently being import processed.
`complete`	The dataset has been processed and imported for installation.
`invalid`	The dataset failed import validation.
`failed`	The dataset import failed due to an internal server error.

Enum:

queued
in-progress
complete
invalid
failed

Inherits: lib.DatasetImportStatus

install array

install[] Dataset Install Status Entry

object

Entry in a list of install statuses for a dataset.

Inherits: lib.DatasetInstallStatusEntry

install[].projectId*

string

Name or ID of a target VEuPathDB project.

Valid project IDs are:

AmoebaDB
ClinEpiDB
CryptoDB
FungiDB
GiardiaDB
HostDB
MicrobiomeDB
MicrosporidiaDB
PiroplasmaDB
PlasmoDB
ToxoDB
TrichDB
TriTrypDB
VectorBase
VEuPathDB

Inherits: string

install[].metaStatus*

string

Enum:

running
complete
failed-validation
failed-installation
ready-for-reinstall
missing-dependency

Inherits: lib.DatasetInstallStatus

install[].metaMessage string

install[].dataStatus

string

Enum:

running
complete
failed-validation
failed-installation
ready-for-reinstall
missing-dependency

Inherits: lib.DatasetInstallStatus

install[].dataMessage string

Import status of the dataset.

Value	Description
`queued`	The dataset has not yet been processed and is waiting in the queue.
`in-progress`	The dataset is currently being import processed.
`complete`	The dataset has been processed and imported for installation.
`invalid`	The dataset failed import validation.
`failed`	The dataset import failed due to an internal server error.

Enum:

queued
in-progress
complete
invalid
failed

Inherits: string

Enum:

running
complete
failed-validation
failed-installation
ready-for-reinstall
missing-dependency

Inherits: string

Entry in a list of install statuses for a dataset.

Inherits: object

Model

Parameter	Type	Description
projectId*	string	Name or ID of a target VEuPathDB project. Valid project IDs are: AmoebaDB ClinEpiDB CryptoDB FungiDB GiardiaDB HostDB MicrobiomeDB MicrosporidiaDB PiroplasmaDB PlasmoDB ToxoDB TrichDB TriTrypDB VectorBase VEuPathDB Inherits: string
metaStatus*	string	Enum: running complete failed-validation failed-installation ready-for-reinstall missing-dependency Inherits: string
metaMessage	string
dataStatus	string	Enum: running complete failed-validation failed-installation ready-for-reinstall missing-dependency Inherits: string
dataMessage	string

Inherits: object

Model

Parameter	Type	Description
resourceIdentifier*	string
resourceDisplayName*	string
resourceVersion*	string

Inherits: object

Model

Parameter	Type	Description
name*	string	Min. length: 3 Max. length: 300
email	string	Min. length: 5 Max. length: 4000
affiliation	string	Max. length: 4000
city	string	Max. length: 200
state	string	Max. length: 200
country	string	Max. length: 200
address	string	Max. length: 1000
isPrimary	boolean

Inherits: object

Model

Parameter	Type	Description
url*	string	Min. length: 3 Max. length: 200
text*	string	Min. length: 3 Max. length: 300
description	string	Max. length: 4000
isPublication	boolean

Inherits: object

Model

Parameter

Type

Description

pubMedId*

string

Min. length: 3

Max. length: 30

citation

string

Min. length: 3

Max. length: 2000

Discriminator: status

Inherits: object

Model

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

Enum:

bad-request
unauthorized
forbidden
not-found
bad-method
conflict
gone
invalid-input
failed-dependency
server-error

Inherits: string

Request could not be parsed or was otherwise unusable.

Discriminator: status

Discriminator value: bad-request

Inherits: lib.Error

Model

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

Examples

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

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: lib.Error

Model

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method conflict gone invalid-input failed-dependency server-error Inherits: lib.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: lib.Error

Model

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method conflict gone invalid-input failed-dependency server-error Inherits: lib.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: lib.Error

Model

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method conflict gone invalid-input failed-dependency server-error Inherits: lib.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: lib.Error

Model

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

Examples

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

The request could not be completed due to a conflict with the current state of the resource.

If you submitted a resource, that resource may already exist.

Discriminator: status

Discriminator value: conflict

Inherits: lib.Error

Model

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

Examples

{
  "status": "conflict",
  "message": "Target resource already exists and cannot be overwritten."
}

The request could not be completed due to the requested resource or its underlying data no longer being present on the server.

Discriminator: status

Discriminator value: gone

Inherits: lib.Error

Model

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

Examples

{
  "status": "gone",
  "message": "The target resource or its dependencies no longer exists."
}

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

Discriminator: status

Discriminator value: invalid-input

Inherits: lib.Error

Model

Parameter	Type	Description
status*	string	Enum: bad-request unauthorized forbidden not-found bad-method conflict gone invalid-input failed-dependency server-error Inherits: lib.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: failed-dependency

Inherits: lib.Error

Model

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

Examples

{
  "status": "failed-dependency",
  "dependency": "google.com",
  "message": "unexpected status code 403 from google.com"
}

Discriminator: status

Discriminator value: server-error

Inherits: lib.Error

Model

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

Examples

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

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

VEuPathDB Dataset Installer v2.1.0

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Target Example

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200 OK

400 Bad Request

401 Unauthorized

500 Internal Server Error

Request Body

200 OK

400 Bad Request

401 Unauthorized

422 Unprocessable Entity

424 Failed Dependency

500 Internal Server Error

204 No Content

409 Conflict

Headers

Request Body

200 OK

400 Bad Request

401 Unauthorized

403 Forbidden

422 Unprocessable Entity

500 Internal Server Error

Parameters

200 OK

Parameters

200 OK

401 Unauthorized

500 Internal Server Error

Parameters

Request Body

204 No Content

400 Bad Request

401 Unauthorized

500 Internal Server Error

204 No Content

400 Bad Request

401 Unauthorized

500 Internal Server Error

Parameters

200 OK

200 OK

Parameters

200 OK

Request Body

204 No Content

400 Bad Request

401 Unauthorized

404 Not Found

500 Internal Server Error

200 OK

401 Unauthorized

500 Internal Server Error

Parameters

200 OK