VEuPathDB Dataset Installer v1.7.0

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

Parameter	Type	Description
install_target InstallTargetID	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. This is desirable for UI-based client use to improve request processing time by the service. Min. length: 5 Max. length: 32 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"

install_target InstallTargetID

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.

This is desirable for UI-based client use to improve request processing time by the service.

Min. length: 5

Max. length: 32

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 \
  https://veupathdb.org/vdi/datasets?InstallTargetID=<value>&ownership=<value>

Parameter Type Description

[] Dataset Listing Item

object

Short entry with basic details about a dataset.

Inherits: object

[].datasetId*

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: lib.VdiId

[].owner*

object

Details about the owner of a VDI dataset.

Inherits: lib.DatasetOwner

[].owner.userId*

integer

VEuPathDB User ID

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.UserId

[].owner.firstName string

[].owner.lastName string

[].owner.email string

[].owner.affiliation string

[].type*

object

Details about a specific dataset type.

Inherits: lib.DatasetTypeOutput

[].type.name*

string

Min. length: 3

[].type.version*

string

Min. length: 1

[].type.category*

string

Min. length: 3

[].visibility*

string

Enum:

private
protected
public

Inherits: lib.DatasetVisibility

[].name*

string

User-provided name for the dataset.

Min. length: 3

Max. length: 1024

Inherits: lib.DatasetName

[].origin*

string

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

Min. length: 3

Max. length: 256

Inherits: lib.DatasetOrigin

[].installTargets*

array

Project IDs for projects the dataset record was submitted to.

Unique items: Yes

[].installTargets[]

string

Name or ID of a target VEuPathDB project, such as "PlasmoDB".

Min. length: 5

Max. length: 32

Inherits: lib.InstallTargetID

[].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: string

[].status.install array

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

object

Entry in a list of install statuses for a dataset.

Inherits: object

[].status.install[].installTarget*

string

Name or ID of a target VEuPathDB project, such as "PlasmoDB".

Min. length: 5

Max. length: 32

Inherits: lib.InstallTargetID

[].status.install[].metaStatus*

string

Enum:

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

Inherits: string

[].status.install[].metaMessages array

[].status.install[].metaMessages[] string

[].status.install[].dataStatus

string

Enum:

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

Inherits: string

[].status.install[].dataMessages array

[].status.install[].dataMessages[] string

[].shares* array

[].shares[] Dataset Listing Share Info

object

Inherits: lib.DatasetListShareUser

[].shares[].userId*

integer

VEuPathDB User ID

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.UserId

[].shares[].firstName* string

[].shares[].lastName* string

[].shares[].affiliation* string

[].shares[].accepted* boolean

[].fileCount*

integer

Number of files uploaded for this dataset.

[].fileSizeTotal*

integer

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

Format: int64

[].created*

datetime

Timestamp of the creation of the dataset

Inherits: datetime

[].summary*

string

Brief summary of the dataset.

Min. length: 3

Max. length: 4000

Inherits: lib.DatasetSummary

[].description

string

Longform description of the dataset.

Inherits: string

[].originalId

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: lib.VdiId

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 too-early server-error Inherits: lib.ErrorType
message*	string

Response Body

{
  "status": "bad-request",
  "message": "Invalid install_target 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 too-early 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 too-early 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 root of the body description below is of the multipart form data fields and not of a literal JSON object.

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

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. Providing both fields will result in a 4xx range error response.

curl -X POST \
  -H "Content-type: multipart/form-data"
  -d @file \
  https://veupathdb.org/vdi/datasets

Dataset Post Request DatasetPostRequestBody

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
details*	object	Metadata about the dataset being submitted. Inherits: lib.DatasetMetaBase
details.installTargets*	array	IDs of the projects this dataset is being submitted to. Unique items: Yes
details.installTargets[]	string	Name or ID of a target VEuPathDB project, such as "PlasmoDB". Min. length: 5 Max. length: 32 Inherits: lib.InstallTargetID
details.name*	string	User-provided name for the dataset. Min. length: 3 Max. length: 1024 Inherits: lib.DatasetName
details.summary*	string	Brief summary of the dataset. Min. length: 3 Max. length: 4000 Inherits: lib.DatasetSummary
details.description	string	Longform description of the dataset. Inherits: string
details.origin*	string	String representing the origin of the dataset. Examples include `direct-upload`, `nephele`, or `galaxy`. Min. length: 3 Max. length: 256 Inherits: lib.DatasetOrigin
details.dependencies*	array	Unique items: Yes
details.dependencies[] Dataset Dependency	object	Inherits: object
details.dependencies[].resourceIdentifier*	string	Min. length: 3 Max. length: 50
details.dependencies[].resourceDisplayName*	string	Min. length: 3 Max. length: 100
details.dependencies[].resourceVersion*	string	Min. length: 1 Max. length: 50
details.publications	array	Unique items: Yes
details.publications[] Dataset Publication	object	Inherits: lib.DatasetPublication
details.publications[].identifier*	string	Min. length: 3 Max. length: 30 Inherits: lib.DatasetPublicationIdentifier
details.publications[].type	string	Default value: "pmid" Enum: pmid doi Inherits: lib.DatasetPublicationType
details.publications[].citation	string	Min. length: 3 Max. length: 2000
details.publications[].isPrimary	boolean	Only one publication may be marked as primary.
details.contacts	array	Unique items: Yes
details.contacts[] Dataset Contact	object	Inherits: object
details.contacts[].firstName	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 1 Max. length: 300
details.contacts[].middleName	string	Min. length: 1 Max. length: 300
details.contacts[].lastName	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 1 Max. length: 300
details.contacts[].isPrimary	boolean	Only one contact may be marked as primary.
details.contacts[].email	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 5 Max. length: 4000
details.contacts[].affiliation Organization	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Max. length: 4000
details.contacts[].country	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Max. length: 200
details.projectName	string	Required if: Install target is MBio or ClinEpi Min. length: 1 Max. length: 256 Inherits: lib.DatasetProjectName
details.programName	string	Required if: Install target is MBio or ClinEpi Min. length: 1 Max. length: 256 Inherits: lib.DatasetProgramName
details.linkedDatasets Explicitly Related Datasets	array	Other studies or datasets that the user is explicitly indicating are related to the dataset represented by this metadata object. Unique items: Yes
details.linkedDatasets[]	object	Inherits: lib.LinkedDataset
details.linkedDatasets[].datasetUri*	string
details.linkedDatasets[].sharesRecords*	boolean
details.experimentalOrganism	object	Required for Genomics, VectorBase, and Microbiome. Optional for ClinEpi. Inherits: lib.DatasetOrganism
details.experimentalOrganism.species*	string
details.experimentalOrganism.strain*	string
details.hostOrganism	object	Inherits: lib.DatasetOrganism
details.hostOrganism.species*	string
details.hostOrganism.strain*	string
details.characteristics	object	Inherits: object
details.characteristics.studyDesign	string	Required for ClinEpi
details.characteristics.studyType	string	Required for ClinEpi
details.characteristics.countries	array	Unique items: Yes
details.characteristics.countries[]	string	Min. length: 3 Max. length: 128
details.characteristics.years	object	Inherits: lib.SampleYearRange
details.characteristics.years.start*	integer	Min. value: 1500 Max. value: 2500 Format: int16
details.characteristics.years.end*	integer	Min. value: 1500 Max. value: 2500 Format: int16
details.characteristics.studySpecies	array	Unique items: Yes
details.characteristics.studySpecies[]	string	Min. length: 3 Max. length: 128
details.characteristics.diseases	array	Diseases or health conditions Unique items: Yes
details.characteristics.diseases[]	string	Min. length: 3 Max. length: 128
details.characteristics.associatedFactors	array	Unique items: Yes
details.characteristics.associatedFactors[]	string	Min. length: 3 Max. length: 128
details.characteristics.participantAges	string	Min. length: 1 Max. length: 128
details.characteristics.sampleTypes	array	Unique items: Yes
details.characteristics.sampleTypes[]	string	Min. length: 3 Max. length: 128
details.externalIdentifiers	object	Inherits: lib.ExternalIdentifiers
details.externalIdentifiers.dois	array	Unique items: Yes
details.externalIdentifiers.dois[]	object	Inherits: object
details.externalIdentifiers.dois[].doi*	string	Min. length: 6 Max. length: 128
details.externalIdentifiers.dois[].description	string
details.externalIdentifiers.hyperlinks	array	Unique items: Yes
details.externalIdentifiers.hyperlinks[] Dataset Hyperlink	object	Inherits: object
details.externalIdentifiers.hyperlinks[].url*	string	Min. length: 7 Max. length: 200
details.externalIdentifiers.hyperlinks[].description	string	Max. length: 4000
details.externalIdentifiers.bioprojectIds	array	Unique items: Yes
details.externalIdentifiers.bioprojectIds[]	object	Inherits: object
details.externalIdentifiers.bioprojectIds[].id*	string	Min. length: 4 Max. length: 64
details.externalIdentifiers.bioprojectIds[].description	string
details.funding	array	Unique items: Yes
details.funding[]	object	Inherits: object
details.funding[].agency*	string	Min. length: 3 Max. length: 256
details.funding[].awardNumber*	string	Min. length: 3 Max. length: 64
details.shortAttribution	string	Min. length: 3 Max. length: 40 Inherits: lib.ShortAttribution
details.type*	object	Inherits: lib.DatasetTypeInput
details.type.name*	string	Min. length: 3 Max. length: 128
details.type.version*	string	Min. length: 1 Max. length: 32
details.visibility	string	Default value: "private" Enum: private protected public Inherits: lib.DatasetVisibility
dataFiles	array	Dataset files to upload. This field is incompatible with the `url` field.
dataFiles[]	file
url	string	URL to a dataset file to upload. This field is incompatible with the `file` field.
docFiles	array	Files containing additional dataset documentation or meta info that is not part of the data itself.
docFiles[]	file

Parameter	Type	Description
Location*	string	URL to the new dataset resource.

Dataset Post Response DatasetPostResponseBody

application/json

Successful upload response.

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

Inherits: object

Parameter

Type

Description

datasetId*

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: lib.VdiId

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 too-early 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 too-early 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 too-early 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 too-early 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 too-early server-error Inherits: lib.ErrorType
message*	string
requestId*	string

Response Body

{
  "status": "server-error",
  "message": "Datastore connection lost",
  "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
vdi-id* VdiId	string	VDI dataset identifier Pattern: ^[a-zA-Z0-9_-]+$ Inherits: string

Parameter

Type

Description

Path

vdi-id* VdiId

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: string

curl -X GET \
  https://veupathdb.org/vdi/datasets/{vdi-id}

Dataset Details DatasetDetails

application/json

Details about a specific singular dataset.

Inherits: lib.DatasetMetaBase

Parameter Type Description

installTargets*

array

IDs of the projects this dataset is being submitted to.

Unique items: Yes

installTargets[]

string

Name or ID of a target VEuPathDB project, such as "PlasmoDB".

Min. length: 5

Max. length: 32

Inherits: lib.InstallTargetID

name*

string

User-provided name for the dataset.

Min. length: 3

Max. length: 1024

Inherits: lib.DatasetName

summary*

string

Brief summary of the dataset.

Min. length: 3

Max. length: 4000

Inherits: lib.DatasetSummary

description

string

Longform description of the dataset.

Inherits: string

origin*

string

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

Min. length: 3

Max. length: 256

Inherits: lib.DatasetOrigin

dependencies*

array

Unique items: Yes

dependencies[] Dataset Dependency

object

Inherits: object

dependencies[].resourceIdentifier*

string

Min. length: 3

Max. length: 50

dependencies[].resourceDisplayName*

string

Min. length: 3

Max. length: 100

dependencies[].resourceVersion*

string

Min. length: 1

Max. length: 50

publications

array

Unique items: Yes

publications[] Dataset Publication

object

Inherits: lib.DatasetPublication

publications[].identifier*

string

Min. length: 3

Max. length: 30

Inherits: lib.DatasetPublicationIdentifier

publications[].type

string

Default value: "pmid"

Enum:

pmid
doi

Inherits: lib.DatasetPublicationType

publications[].citation

string

Min. length: 3

Max. length: 2000

publications[].isPrimary

boolean

Only one publication may be marked as primary.

contacts

array

Unique items: Yes

contacts[] Dataset Contact

object

Inherits: object

contacts[].firstName

string

Required if:

isPrimary is true
Install target is MBio or ClinEpi
Dataset is public/community

Min. length: 1

Max. length: 300

contacts[].middleName

string

Min. length: 1

Max. length: 300

contacts[].lastName

string

Required if:

isPrimary is true
Install target is MBio or ClinEpi
Dataset is public/community

Min. length: 1

Max. length: 300

contacts[].isPrimary

boolean

Only one contact may be marked as primary.

contacts[].email

string

Required if:

isPrimary is true
Install target is MBio or ClinEpi
Dataset is public/community

Min. length: 5

Max. length: 4000

contacts[].affiliation Organization

string

Required if:

isPrimary is true
Install target is MBio or ClinEpi
Dataset is public/community

Max. length: 4000

contacts[].country

string

Required if:

isPrimary is true
Install target is MBio or ClinEpi
Dataset is public/community

Max. length: 200

projectName

string

Required if:

Install target is MBio or ClinEpi

Min. length: 1

Max. length: 256

Inherits: lib.DatasetProjectName

programName

string

Required if:

Install target is MBio or ClinEpi

Min. length: 1

Max. length: 256

Inherits: lib.DatasetProgramName

linkedDatasets Explicitly Related Datasets

array

Other studies or datasets that the user is explicitly indicating are related to the dataset represented by this metadata object.

Unique items: Yes

linkedDatasets[]

object

Inherits: lib.LinkedDataset

linkedDatasets[].datasetUri* string

linkedDatasets[].sharesRecords* boolean

experimentalOrganism

object

Required for Genomics, VectorBase, and Microbiome.

Optional for ClinEpi.

Inherits: lib.DatasetOrganism

experimentalOrganism.species* string

experimentalOrganism.strain* string

hostOrganism

object

Inherits: lib.DatasetOrganism

hostOrganism.species* string

hostOrganism.strain* string

characteristics

object

Inherits: object

characteristics.studyDesign

string

Required for ClinEpi

characteristics.studyType

string

Required for ClinEpi

characteristics.countries

array

Unique items: Yes

characteristics.countries[]

string

Min. length: 3

Max. length: 128

characteristics.years

object

Inherits: lib.SampleYearRange

characteristics.years.start*

integer

Min. value: 1500

Max. value: 2500

Format: int16

characteristics.years.end*

integer

Min. value: 1500

Max. value: 2500

Format: int16

characteristics.studySpecies

array

Unique items: Yes

characteristics.studySpecies[]

string

Min. length: 3

Max. length: 128

characteristics.diseases

array

Diseases or health conditions

Unique items: Yes

characteristics.diseases[]

string

Min. length: 3

Max. length: 128

characteristics.associatedFactors

array

Unique items: Yes

characteristics.associatedFactors[]

string

Min. length: 3

Max. length: 128

characteristics.participantAges

string

Min. length: 1

Max. length: 128

characteristics.sampleTypes

array

Unique items: Yes

characteristics.sampleTypes[]

string

Min. length: 3

Max. length: 128

externalIdentifiers

object

Inherits: lib.ExternalIdentifiers

externalIdentifiers.dois

array

Unique items: Yes

externalIdentifiers.dois[]

object

Inherits: object

externalIdentifiers.dois[].doi*

string

Min. length: 6

Max. length: 128

externalIdentifiers.dois[].description string

externalIdentifiers.hyperlinks

array

Unique items: Yes

externalIdentifiers.hyperlinks[] Dataset Hyperlink

object

Inherits: lib.DatasetHyperlink

externalIdentifiers.hyperlinks[].url*

string

Min. length: 7

Max. length: 200

externalIdentifiers.hyperlinks[].description

string

Max. length: 4000

externalIdentifiers.bioprojectIds

array

Unique items: Yes

externalIdentifiers.bioprojectIds[]

object

Inherits: object

externalIdentifiers.bioprojectIds[].id*

string

Min. length: 4

Max. length: 64

externalIdentifiers.bioprojectIds[].description string

funding

array

Unique items: Yes

funding[]

object

Inherits: lib.DatasetFundingAward

funding[].agency*

string

Min. length: 3

Max. length: 256

funding[].awardNumber*

string

Min. length: 3

Max. length: 64

shortAttribution

string

Min. length: 3

Max. length: 40

Inherits: lib.ShortAttribution

datasetId*

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: lib.VdiId

type*

object

Details about a specific dataset type.

Inherits: lib.DatasetTypeOutput

type.name*

string

Min. length: 3

type.version*

string

Min. length: 1

type.category*

string

Min. length: 3

visibility*

string

Enum:

private
protected
public

Inherits: lib.DatasetVisibility

owner*

object

Details about the owner of a VDI dataset.

Inherits: lib.DatasetOwner

owner.userId*

integer

VEuPathDB User ID

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.UserId

owner.firstName string

owner.lastName string

owner.email string

owner.affiliation string

created*

datetime

Timestamp of the creation of the dataset

Inherits: datetime

sourceUrl

string

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

Inherits: lib.DatasetSourceUrl

revisionHistory

object

Inherits: lib.RevisionHistory

revisionHistory.originalId*

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: lib.VdiId

revisionHistory.revisions* array

revisionHistory.revisions[] Dataset Revision

object

Dataset revision history entry.

Inherits: lib.DatasetRevision

revisionHistory.revisions[].action*

string

Enum:

create
extend
revise

Inherits: lib.DatasetRevisionAction

revisionHistory.revisions[].timestamp* datetime

revisionHistory.revisions[].revisionId*

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: lib.VdiId

revisionHistory.revisions[].revisionNote*

string

Note providing a reason and/or description for the revision.

Min. length: 10

Max. length: 4096

Inherits: lib.DatasetRevisionNote

revisionHistory.revisions[].fileListUrl*

string

URL to the file listing for the revision entry.

shortName*

string

Min. length: 3

Max. length: 20

Inherits: lib.ShortName

relatedDatasets Implicitly Related Datasets

array

Datasets that are implicitly related to the dataset represented by this object by way of sharing a common project name or program name, or by having one or more publications in common.

Unique items: Yes

relatedDatasets[]

object

Inherits: lib.RelatedDatasetInfo

relatedDatasets[].datasetId*

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: lib.VdiId

relatedDatasets[].type*

object

Details about a specific dataset type.

Inherits: lib.DatasetTypeOutput

relatedDatasets[].type.name*

string

Min. length: 3

relatedDatasets[].type.version*

string

Min. length: 1

relatedDatasets[].type.category*

string

Min. length: 3

relatedDatasets[].name*

string

User-provided name for the dataset.

Min. length: 3

Max. length: 1024

Inherits: lib.DatasetName

relatedDatasets[].summary*

string

Brief summary of the dataset.

Min. length: 3

Max. length: 4000

Inherits: lib.DatasetSummary

relatedDatasets[].created*

datetime

Timestamp of the creation of the dataset

Inherits: datetime

relatedDatasets[].relatedBy*

object

Discriminator: relationType

Inherits: lib.ImplicitRelation

relatedDatasets[].relatedBy.relationType*

string

Enum:

publication
program-name
project-name

Inherits: lib.ImplicitRelationType

importMessages

array

Log lines from the import process.

These messages will be warnings and/or validation errors.

importMessages[] string

array

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

shares[] Dataset Share Offer

object

Inherits: lib.ShareOffer

shares[].recipient*

object

Inherits: lib.ShareOfferRecipient

shares[].recipient.userId*

integer

VEuPathDB User ID

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.UserId

shares[].recipient.firstName string

shares[].recipient.lastName string

shares[].recipient.affiliation string

shares[].recipient.email string

shares[].status*

string

Enum:

grant
revoke

Inherits: lib.ShareOfferAction

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 Target Status

object

Entry in a list of install statuses for a dataset.

Inherits: lib.DatasetInstallStatusEntry

status.install[].installTarget*

string

Name or ID of a target VEuPathDB project, such as "PlasmoDB".

Min. length: 5

Max. length: 32

Inherits: lib.InstallTargetID

status.install[].metaStatus*

string

Enum:

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

Inherits: lib.DatasetInstallStatus

status.install[].metaMessages array

status.install[].metaMessages[] string

status.install[].dataStatus

string

Enum:

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

Inherits: lib.DatasetInstallStatus

status.install[].dataMessages array

status.install[].dataMessages[] string

files*

object

Inherits: lib.DatasetFileListing

files.upload*

object

Inherits: lib.DatasetZipDetails

files.upload.zipSize*

integer

Format: int64

files.upload.contents* array

files.upload.contents[] Decompressed File Info

object

Inherits: lib.DatasetFileDetails

files.upload.contents[].fileName* string

files.upload.contents[].fileSize*

integer

Size of the file in bytes.

Format: int64

files.install

object

Inherits: lib.DatasetZipDetails

files.install.zipSize*

integer

Format: int64

files.install.contents* array

files.install.contents[] Decompressed File Info

object

Inherits: lib.DatasetFileDetails

files.install.contents[].fileName* string

files.install.contents[].fileSize*

integer

Size of the file in bytes.

Format: int64

files.documents array

files.documents[] Decompressed File Info

object

Inherits: lib.DatasetFileDetails

files.documents[].fileName* string

files.documents[].fileSize*

integer

Size of the file in bytes.

Format: int64

Parameter	Type	Description
Location*	string	URL to the newest dataset revision.

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 too-early 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 too-early 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 too-early server-error Inherits: lib.ErrorType
message*	string
requestId*	string

Response Body

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

Updates the metadata for a target dataset.

If a field in the request body is null, the matching metadata 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
vdi-id* VdiId	string	VDI dataset identifier Pattern: ^[a-zA-Z0-9_-]+$ Inherits: string

Parameter

Type

Description

Path

vdi-id* VdiId

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: string

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

Dataset Patch Request DatasetPatchRequestBody

application/json

Request to update the metadata for a dataset.

Fields that are omitted will be ignored when updating the target dataset record.

Fields that are present, with a value of null indicate the intent to remove the field from the dataset metadata. All other values provided will be used to replace the existing dataset metadata value.

Inherits: object

Parameter	Type	Description
type	object	If present, the only valid action is `replace`. Only permitted when transitioning from a none-type dataset into an actual dataset type. Inherits: lib.DatasetTypePatch
type.value	object	Inherits: lib.DatasetTypeInput
type.value.name*	string	Min. length: 3 Max. length: 128
type.value.version*	string	Min. length: 1 Max. length: 32
visibility	object	If present, the only valid action is `replace`. Inherits: lib.VisibilityPatch
visibility.value	string	Enum: private protected public Inherits: lib.DatasetVisibility
name	object	Inherits: lib.StringPatch
name.value*	string
summary	object	Inherits: lib.StringPatch
summary.value*	string
description	object	Inherits: lib.OptionalStringPatch
description.value	string
publications	object	Inherits: lib.PublicationsPatch
publications.value	array	Unique items: Yes
publications.value[] Dataset Publication	object	Inherits: lib.DatasetPublication
publications.value[].identifier*	string	Min. length: 3 Max. length: 30 Inherits: lib.DatasetPublicationIdentifier
publications.value[].type	string	Default value: "pmid" Enum: pmid doi Inherits: lib.DatasetPublicationType
publications.value[].citation	string	Min. length: 3 Max. length: 2000
publications.value[].isPrimary	boolean	Only one publication may be marked as primary.
contacts	object	If the dataset visibility is not `private`, the only valid action is `replace`. Inherits: object
contacts.value	array	Unique items: Yes
contacts.value[] Dataset Contact	object	Inherits: lib.DatasetContact
contacts.value[].firstName	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 1 Max. length: 300
contacts.value[].middleName	string	Min. length: 1 Max. length: 300
contacts.value[].lastName	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 1 Max. length: 300
contacts.value[].isPrimary	boolean	Only one contact may be marked as primary.
contacts.value[].email	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 5 Max. length: 4000
contacts.value[].affiliation Organization	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Max. length: 4000
contacts.value[].country	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Max. length: 200
projectName	object	Inherits: lib.OptionalStringPatch
projectName.value	string
programName	object	Inherits: lib.OptionalStringPatch
programName.value	string
linkedDatasets	object	Inherits: lib.LinkedDatasetPatch
linkedDatasets.value	array	Unique items: Yes
linkedDatasets.value[]	object	Inherits: lib.LinkedDataset
linkedDatasets.value[].datasetUri*	string
linkedDatasets.value[].sharesRecords*	boolean
experimentalOrganism	object	Inherits: lib.OrganismPatch
experimentalOrganism.value	object	Inherits: object
experimentalOrganism.value.species*	string
experimentalOrganism.value.strain*	string
hostOrganism	object	Inherits: lib.OrganismPatch
hostOrganism.value	object	Inherits: object
hostOrganism.value.species*	string
hostOrganism.value.strain*	string
characteristics	object	Inherits: object
characteristics.studyDesign	object	Inherits: lib.OptionalStringPatch
characteristics.studyDesign.value	string
characteristics.studyType	object	Inherits: lib.OptionalStringPatch
characteristics.studyType.value	string
characteristics.countries	object
characteristics.countries.value	array	Unique items: Yes
characteristics.countries.value[]	string	Min. length: 3 Max. length: 128
characteristics.years	object
characteristics.years.value	object	Inherits: lib.SampleYearRange
characteristics.years.value.start*	integer	Min. value: 1500 Max. value: 2500 Format: int16
characteristics.years.value.end*	integer	Min. value: 1500 Max. value: 2500 Format: int16
characteristics.studySpecies	object
characteristics.studySpecies.value	array	Unique items: Yes
characteristics.studySpecies.value[]	string	Min. length: 3 Max. length: 128
characteristics.diseases	object
characteristics.diseases.value	array	Unique items: Yes
characteristics.diseases.value[]	string	Min. length: 3 Max. length: 128
characteristics.associatedFactors	object
characteristics.associatedFactors.value	array	Unique items: Yes
characteristics.associatedFactors.value[]	string	Min. length: 3 Max. length: 128
characteristics.participantAges	object	Inherits: lib.OptionalStringPatch
characteristics.participantAges.value	string
characteristics.sampleTypes	object
characteristics.sampleTypes.value	array	Unique items: Yes
characteristics.sampleTypes.value[]	string	Min. length: 3 Max. length: 128
externalIdentifiers	object	Inherits: lib.ExternalIdentifiersPatch
externalIdentifiers.dois	object
externalIdentifiers.dois.value	array	Unique items: Yes
externalIdentifiers.dois.value[]	object	Inherits: object
externalIdentifiers.dois.value[].doi*	string	Min. length: 6 Max. length: 128
externalIdentifiers.dois.value[].description	string
externalIdentifiers.hyperlinks	object
externalIdentifiers.hyperlinks.value	array	Unique items: Yes
externalIdentifiers.hyperlinks.value[] Dataset Hyperlink	object	Inherits: object
externalIdentifiers.hyperlinks.value[].url*	string	Min. length: 7 Max. length: 200
externalIdentifiers.hyperlinks.value[].description	string	Max. length: 4000
externalIdentifiers.bioprojectIds	object
externalIdentifiers.bioprojectIds.value	array	Unique items: Yes
externalIdentifiers.bioprojectIds.value[]	object	Inherits: object
externalIdentifiers.bioprojectIds.value[].id*	string	Min. length: 4 Max. length: 64
externalIdentifiers.bioprojectIds.value[].description	string
funding	object	Inherits: lib.FundingPatch
funding.value	array	Unique items: Yes
funding.value[]	object	Inherits: object
funding.value[].agency*	string	Min. length: 3 Max. length: 256
funding.value[].awardNumber*	string	Min. length: 3 Max. length: 64
shortAttribution	object	Inherits: lib.OptionalStringPatch
shortAttribution.value	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 too-early 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 too-early 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 too-early 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 too-early 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 too-early 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 too-early server-error Inherits: lib.ErrorType
message*	string
requestId*	string

Response Body

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

Uploads a new dataset data revision to replace the existing target dataset.

This method is effectively a modification of the PATCH request rules for the metadata body to add the required field revisionNote.

This means that omitting fields from the request or setting them to null will tell VDI to use the original dataset's values for those fields.

Parameters

Parameter	Type	Description
vdi-id* VdiId	string	VDI dataset identifier Pattern: ^[a-zA-Z0-9_-]+$ Inherits: string

Parameter

Type

Description

Path

vdi-id* VdiId

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: string

curl -X PUT \
  -H "Content-type: multipart/form-data"
  -d @file \
  https://veupathdb.org/vdi/datasets/{vdi-id}

Inherits: object

Parameter	Type	Description
details*	object	Metadata about the dataset being submitted. Inherits: lib.DatasetPatchRequestBody
details.type	object	If present, the only valid action is `replace`. Only permitted when transitioning from a none-type dataset into an actual dataset type. Inherits: lib.DatasetTypePatch
details.type.value	object	Inherits: lib.DatasetTypeInput
details.type.value.name*	string	Min. length: 3 Max. length: 128
details.type.value.version*	string	Min. length: 1 Max. length: 32
details.visibility	object	If present, the only valid action is `replace`. Inherits: lib.VisibilityPatch
details.visibility.value	string	Enum: private protected public Inherits: lib.DatasetVisibility
details.name	object	Inherits: lib.StringPatch
details.name.value*	string
details.summary	object	Inherits: lib.StringPatch
details.summary.value*	string
details.description	object	Inherits: lib.OptionalStringPatch
details.description.value	string
details.publications	object	Inherits: lib.PublicationsPatch
details.publications.value	array	Unique items: Yes
details.publications.value[] Dataset Publication	object	Inherits: lib.DatasetPublication
details.publications.value[].identifier*	string	Min. length: 3 Max. length: 30 Inherits: lib.DatasetPublicationIdentifier
details.publications.value[].type	string	Default value: "pmid" Enum: pmid doi Inherits: lib.DatasetPublicationType
details.publications.value[].citation	string	Min. length: 3 Max. length: 2000
details.publications.value[].isPrimary	boolean	Only one publication may be marked as primary.
details.contacts	object	If the dataset visibility is not `private`, the only valid action is `replace`. Inherits: object
details.contacts.value	array	Unique items: Yes
details.contacts.value[] Dataset Contact	object	Inherits: lib.DatasetContact
details.contacts.value[].firstName	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 1 Max. length: 300
details.contacts.value[].middleName	string	Min. length: 1 Max. length: 300
details.contacts.value[].lastName	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 1 Max. length: 300
details.contacts.value[].isPrimary	boolean	Only one contact may be marked as primary.
details.contacts.value[].email	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 5 Max. length: 4000
details.contacts.value[].affiliation Organization	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Max. length: 4000
details.contacts.value[].country	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Max. length: 200
details.projectName	object	Inherits: lib.OptionalStringPatch
details.projectName.value	string
details.programName	object	Inherits: lib.OptionalStringPatch
details.programName.value	string
details.linkedDatasets	object	Inherits: lib.LinkedDatasetPatch
details.linkedDatasets.value	array	Unique items: Yes
details.linkedDatasets.value[]	object	Inherits: lib.LinkedDataset
details.linkedDatasets.value[].datasetUri*	string
details.linkedDatasets.value[].sharesRecords*	boolean
details.experimentalOrganism	object	Inherits: lib.OrganismPatch
details.experimentalOrganism.value	object	Inherits: object
details.experimentalOrganism.value.species*	string
details.experimentalOrganism.value.strain*	string
details.hostOrganism	object	Inherits: lib.OrganismPatch
details.hostOrganism.value	object	Inherits: object
details.hostOrganism.value.species*	string
details.hostOrganism.value.strain*	string
details.characteristics	object	Inherits: object
details.characteristics.studyDesign	object	Inherits: lib.OptionalStringPatch
details.characteristics.studyDesign.value	string
details.characteristics.studyType	object	Inherits: lib.OptionalStringPatch
details.characteristics.studyType.value	string
details.characteristics.countries	object
details.characteristics.countries.value	array	Unique items: Yes
details.characteristics.countries.value[]	string	Min. length: 3 Max. length: 128
details.characteristics.years	object
details.characteristics.years.value	object	Inherits: lib.SampleYearRange
details.characteristics.years.value.start*	integer	Min. value: 1500 Max. value: 2500 Format: int16
details.characteristics.years.value.end*	integer	Min. value: 1500 Max. value: 2500 Format: int16
details.characteristics.studySpecies	object
details.characteristics.studySpecies.value	array	Unique items: Yes
details.characteristics.studySpecies.value[]	string	Min. length: 3 Max. length: 128
details.characteristics.diseases	object
details.characteristics.diseases.value	array	Unique items: Yes
details.characteristics.diseases.value[]	string	Min. length: 3 Max. length: 128
details.characteristics.associatedFactors	object
details.characteristics.associatedFactors.value	array	Unique items: Yes
details.characteristics.associatedFactors.value[]	string	Min. length: 3 Max. length: 128
details.characteristics.participantAges	object	Inherits: lib.OptionalStringPatch
details.characteristics.participantAges.value	string
details.characteristics.sampleTypes	object
details.characteristics.sampleTypes.value	array	Unique items: Yes
details.characteristics.sampleTypes.value[]	string	Min. length: 3 Max. length: 128
details.externalIdentifiers	object	Inherits: lib.ExternalIdentifiersPatch
details.externalIdentifiers.dois	object
details.externalIdentifiers.dois.value	array	Unique items: Yes
details.externalIdentifiers.dois.value[]	object	Inherits: object
details.externalIdentifiers.dois.value[].doi*	string	Min. length: 6 Max. length: 128
details.externalIdentifiers.dois.value[].description	string
details.externalIdentifiers.hyperlinks	object
details.externalIdentifiers.hyperlinks.value	array	Unique items: Yes
details.externalIdentifiers.hyperlinks.value[] Dataset Hyperlink	object	Inherits: object
details.externalIdentifiers.hyperlinks.value[].url*	string	Min. length: 7 Max. length: 200
details.externalIdentifiers.hyperlinks.value[].description	string	Max. length: 4000
details.externalIdentifiers.bioprojectIds	object
details.externalIdentifiers.bioprojectIds.value	array	Unique items: Yes
details.externalIdentifiers.bioprojectIds.value[]	object	Inherits: object
details.externalIdentifiers.bioprojectIds.value[].id*	string	Min. length: 4 Max. length: 64
details.externalIdentifiers.bioprojectIds.value[].description	string
details.funding	object	Inherits: lib.FundingPatch
details.funding.value	array	Unique items: Yes
details.funding.value[]	object	Inherits: object
details.funding.value[].agency*	string	Min. length: 3 Max. length: 256
details.funding.value[].awardNumber*	string	Min. length: 3 Max. length: 64
details.shortAttribution	object	Inherits: lib.OptionalStringPatch
details.shortAttribution.value	string
details.origin*	string	String representing the origin of the dataset. Examples include `direct-upload`, `nephele`, or `galaxy`. Min. length: 3 Max. length: 256 Inherits: string
details.revisionNote*	string	Note providing a reason and/or description for the revision. Min. length: 10 Max. length: 4096 Inherits: lib.DatasetRevisionNote
dataFiles	array	Dataset files to upload. This field is incompatible with the `url` field.
dataFiles[]	file
url	string	URL to a dataset file to upload. This field is incompatible with the `file` field.
docFiles	array	Files containing additional dataset documentation or meta info that is not part of the data itself.
docFiles[]	file

Parameter	Type	Description
Location*	string	URL to the new dataset resource.

Inherits: object

Parameter

Type

Description

datasetId*

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: lib.VdiId

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 too-early 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 too-early 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 too-early 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 too-early 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 too-early 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 too-early server-error Inherits: lib.ErrorType
message*	string
requestId*	string

Response Body

{
  "status": "server-error",
  "message": "Datastore connection lost",
  "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
vdi-id* VdiId	string	VDI dataset identifier Pattern: ^[a-zA-Z0-9_-]+$ Inherits: string

Parameter

Type

Description

Path

vdi-id* VdiId

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: string

curl -X DELETE \
  https://veupathdb.org/vdi/datasets/{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 too-early 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 too-early 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 too-early 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 too-early server-error Inherits: lib.ErrorType
message*	string
requestId*	string

Response Body

{
  "status": "server-error",
  "message": "Datastore connection lost",
  "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
vdi-id* VdiId	string	VDI dataset identifier Pattern: ^[a-zA-Z0-9_-]+$ Inherits: string

Parameter

Type

Description

Path

vdi-id* VdiId

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: string

curl -X GET \
  https://veupathdb.org/vdi/datasets/{vdi-id}/files

Inherits: object

Parameter	Type	Description
upload*	object	Inherits: lib.DatasetZipDetails
upload.zipSize*	integer	Format: int64
upload.contents*	array
upload.contents[] Decompressed File Info	object	Inherits: object
upload.contents[].fileName*	string
upload.contents[].fileSize*	integer	Size of the file in bytes. Format: int64
install	object	Inherits: lib.DatasetZipDetails
install.zipSize*	integer	Format: int64
install.contents*	array
install.contents[] Decompressed File Info	object	Inherits: object
install.contents[].fileName*	string
install.contents[].fileSize*	integer	Size of the file in bytes. Format: int64
documents	array
documents[] Decompressed File Info	object	Inherits: object
documents[].fileName*	string
documents[].fileSize*	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 too-early 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 too-early 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 too-early 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
vdi-id* VdiId	string	VDI dataset identifier Pattern: ^[a-zA-Z0-9_-]+$ Inherits: string

Parameter

Type

Description

Path

vdi-id* VdiId

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: string

curl -X GET \
  https://veupathdb.org/vdi/datasets/{vdi-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 too-early 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 too-early 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 too-early 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 processed files that were/would be installed into the VEuPathDB project site on successful installation processing.

Parameters

Parameter

Type

Description

Path

vdi-id* VdiId

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: string

curl -X GET \
  https://veupathdb.org/vdi/datasets/{vdi-id}/files/install

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 too-early 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 too-early 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 too-early 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

vdi-id* VdiId

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: string

file-name*

string

curl -X GET \
  https://veupathdb.org/vdi/datasets/{vdi-id}/files/documents/{file-name}

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 too-early 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 too-early 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 too-early 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

vdi-id* VdiId

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: string

file-name*

string

curl -X PUT \
  -H "Content-type: application/octet-stream"
  -d @file \
  https://veupathdb.org/vdi/datasets/{vdi-id}/files/documents/{file-name}

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 too-early 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 too-early 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 too-early 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 too-early 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

vdi-id* VdiId

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: string

recipient-user-id* UserId

integer

VEuPathDB User ID

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: integer

curl -X PUT \
  -H "Content-type: application/json"
  -d @body.json \
  https://veupathdb.org/vdi/datasets/{vdi-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*	string	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 too-early 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 too-early 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 too-early 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 too-early 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 too-early 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 too-early 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

vdi-id* VdiId

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: string

recipient-user-id* UserId

integer

VEuPathDB User ID

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: integer

curl -X PUT \
  -H "Content-type: application/json"
  -d @body.json \
  https://veupathdb.org/vdi/datasets/{vdi-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*	string	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

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

curl -X GET \
  https://veupathdb.org/vdi/datasets/community

Parameter Type Description

[] Dataset Listing Item

object

Short entry with basic details about a dataset.

Inherits: object

[].datasetId*

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: lib.VdiId

[].owner*

object

Details about the owner of a VDI dataset.

Inherits: lib.DatasetOwner

[].owner.userId*

integer

VEuPathDB User ID

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.UserId

[].owner.firstName string

[].owner.lastName string

[].owner.email string

[].owner.affiliation string

[].type*

object

Details about a specific dataset type.

Inherits: lib.DatasetTypeOutput

[].type.name*

string

Min. length: 3

[].type.version*

string

Min. length: 1

[].type.category*

string

Min. length: 3

[].visibility*

string

Enum:

private
protected
public

Inherits: lib.DatasetVisibility

[].name*

string

User-provided name for the dataset.

Min. length: 3

Max. length: 1024

Inherits: lib.DatasetName

[].origin*

string

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

Min. length: 3

Max. length: 256

Inherits: lib.DatasetOrigin

[].installTargets*

array

Project IDs for projects the dataset record was submitted to.

Unique items: Yes

[].installTargets[]

string

Name or ID of a target VEuPathDB project, such as "PlasmoDB".

Min. length: 5

Max. length: 32

Inherits: lib.InstallTargetID

[].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: string

[].status.install array

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

object

Entry in a list of install statuses for a dataset.

Inherits: object

[].status.install[].installTarget*

string

Name or ID of a target VEuPathDB project, such as "PlasmoDB".

Min. length: 5

Max. length: 32

Inherits: lib.InstallTargetID

[].status.install[].metaStatus*

string

Enum:

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

Inherits: string

[].status.install[].metaMessages array

[].status.install[].metaMessages[] string

[].status.install[].dataStatus

string

Enum:

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

Inherits: string

[].status.install[].dataMessages array

[].status.install[].dataMessages[] string

[].shares* array

[].shares[] Dataset Listing Share Info

object

Inherits: lib.DatasetListShareUser

[].shares[].userId*

integer

VEuPathDB User ID

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.UserId

[].shares[].firstName* string

[].shares[].lastName* string

[].shares[].affiliation* string

[].shares[].accepted* boolean

[].fileCount*

integer

Number of files uploaded for this dataset.

[].fileSizeTotal*

integer

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

Format: int64

[].created*

datetime

Timestamp of the creation of the dataset

Inherits: datetime

[].summary*

string

Brief summary of the dataset.

Min. length: 3

Max. length: 4000

Inherits: lib.DatasetSummary

[].description

string

Longform description of the dataset.

Inherits: string

[].originalId

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: lib.VdiId

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 too-early 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 too-early 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 \
  https://veupathdb.org/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 too-early 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 too-early 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"

Enum:

open
accepted
rejected
all

curl -X GET \
  https://veupathdb.org/vdi/users/self/share-offers?status=<value>

Parameter	Type	Description
[] Share Offer Details	object	Inherits: object
[].datasetId*	string	VDI dataset identifier Pattern: ^[a-zA-Z0-9_-]+$ Inherits: lib.VdiId
[].owner*	object	Details about the owner of a VDI dataset. Inherits: object
[].owner.userId*	integer	VEuPathDB User ID Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: lib.UserId
[].owner.firstName	string
[].owner.lastName	string
[].owner.email	string
[].owner.affiliation	string
[].shareStatus*	string	Enum: open accepted rejected Inherits: lib.ShareOfferStatus
[].type*	object	Details about a specific dataset type. Inherits: object
[].type.name*	string	Min. length: 3
[].type.version*	string	Min. length: 1
[].type.category*	string	Min. length: 3
[].installTargets*	array	Unique items: Yes
[].installTargets[]	string	Name or ID of a target VEuPathDB project, such as "PlasmoDB". Min. length: 5 Max. length: 32 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 too-early 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 too-early 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 too-early 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

installTarget InstallTargetID

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.

Min. length: 5

Max. length: 32

Inherits: string

curl -X GET \
  https://veupathdb.org/vdi/plugins?InstallTargetID=<value>

Parameter	Type	Description
[] Plugin Info	object	Inherits: object
[].pluginName*	string
[].type*	object	Details about a specific dataset type. Inherits: object
[].type.name*	string	Min. length: 3
[].type.version*	string	Min. length: 1
[].type.category*	string	Min. length: 3
[].maxFileSize*	integer	Format: int64
[].allowedFileExtensions*	array
[].allowedFileExtensions[]	string
[].installTargets	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.
[].installTargets[]	string	Name or ID of a target VEuPathDB project, such as "PlasmoDB". Min. length: 5 Max. length: 32 Inherits: string

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 too-early 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 too-early server-error Inherits: lib.ErrorType
message*	string
requestId*	string

Response Body

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

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

Providing a limit query param value of -1 indicates that ALL records should be returned. In this case, the offset parameter will be ignored.

Example - List All Live Datasets

curl --header "Admin-Token: ${VDI_ADMIN_TOKEN}" \
"${VDI_INSTANCE}/admin/reports/datasets/list-all?limit=-1" \
> results.json

Example - Paginated by Project

curl --header "Admin-Token: ${VDI_ADMIN_TOKEN}" \
"${VDI_INSTANCE}/admin/reports/datasets/list-all?offset=100&install_target=PlasmoDB" \
> results.json

Parameters

Parameter	Type	Description
Query
install_target	string	Filter results by install target project ID. This field is not case-sensitive.
include_deleted	boolean	Controls whether datasets that have been marked as deleted should be included in the results.
limit	integer	Result count limit. If set to `-1`, no limit is applied. Default value: 100
offset	integer	Pagination offset. Ignored if `limit < 0`.

Secured By

Admin Token AdminToken

Per-service admin token header.

curl -X GET \
  https://veupathdb.org/vdi/admin/reports/datasets/list-all?install_target=<value>&include_deleted=<value>&limit=<value>&offset=<value>

Inherits: object

Parameter Type Description

meta*

object

Inherits: object

meta.count* integer

meta.offset* integer

meta.limit* integer

meta.total* integer

results* array

results[]

object

Inherits: object

results[].datasetId*

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: lib.VdiId

results[].owner*

integer

VEuPathDB User ID

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.UserId

results[].datasetType*

object

Details about a specific dataset type.

Inherits: lib.DatasetTypeOutput

results[].datasetType.name*

string

Min. length: 3

results[].datasetType.version*

string

Min. length: 1

results[].datasetType.category*

string

Min. length: 3

results[].visibility*

string

Enum:

private
protected
public

Inherits: lib.DatasetVisibility

results[].name*

string

User-provided name for the dataset.

Min. length: 3

Max. length: 1024

Inherits: lib.DatasetName

results[].origin*

string

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

Min. length: 3

Max. length: 256

Inherits: lib.DatasetOrigin

results[].installTargets*

array

Unique items: Yes

results[].installTargets[]

string

Name or ID of a target VEuPathDB project, such as "PlasmoDB".

Min. length: 5

Max. length: 32

Inherits: lib.InstallTargetID

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 Target Status

object

Entry in a list of install statuses for a dataset.

Inherits: lib.DatasetInstallStatusEntry

results[].status.install[].installTarget*

string

Name or ID of a target VEuPathDB project, such as "PlasmoDB".

Min. length: 5

Max. length: 32

Inherits: lib.InstallTargetID

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

string

Enum:

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

Inherits: lib.DatasetInstallStatus

results[].status.install[].metaMessages array

results[].status.install[].metaMessages[] string

results[].status.install[].dataStatus

string

Enum:

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

Inherits: lib.DatasetInstallStatus

results[].status.install[].dataMessages array

results[].status.install[].dataMessages[] string

results[].created*

datetime

Timestamp of the creation of the dataset

Inherits: lib.DatasetCreationDate

results[].isDeleted* boolean

results[].summary*

string

Brief summary of the dataset.

Min. length: 3

Max. length: 4000

Inherits: lib.DatasetSummary

results[].description

string

Longform description of the dataset.

Inherits: lib.DatasetDescription

results[].programName string

results[].projectName string

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 too-early server-error Inherits: lib.ErrorType
message*	string
requestId*	string

Response Body

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

Example

curl --header "Admin-Token: ${VDI_ADMIN_TOKEN}" \
"${VDI_INSTANCE}/admin/reports/datasets/123dk37h" \
> details.json

Parameters

Parameter

Type

Description

Path

vdi-id* VdiId

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: string

Secured By

Admin Token AdminToken

Per-service admin token header.

curl -X GET \
  https://veupathdb.org/vdi/admin/reports/datasets/{vdi-id}

Inherits: object

Parameter	Type	Description
datasetType*	object	Details about a specific dataset type. Inherits: object
datasetType.name*	string	Min. length: 3
datasetType.version*	string	Min. length: 1
datasetType.category*	string	Min. length: 3
owner*	integer	VEuPathDB User ID Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: lib.UserId
isDeleted*	boolean
origin*	string	String representing the origin of the dataset. Examples include `direct-upload`, `nephele`, or `galaxy`. Min. length: 3 Max. length: 256 Inherits: string
created*	datetime	Timestamp of the creation of the dataset Inherits: datetime
inserted*	datetime
name*	string	User-provided name for the dataset. Min. length: 3 Max. length: 1024 Inherits: string
installTargets*	array	Unique items: Yes
installTargets[]	string	Name or ID of a target VEuPathDB project, such as "PlasmoDB". Min. length: 5 Max. length: 32 Inherits: string
status*	string
importMessages*	array
importMessages[]	string
visibility*	string	Enum: private protected public Inherits: string
summary*	string	Brief summary of the dataset. Min. length: 3 Max. length: 4000 Inherits: string
description	string	Longform description of the dataset. Inherits: string
syncControl	object	Inherits: lib.SyncControlRecord
syncControl.sharesUpdateTime*	datetime
syncControl.dataUpdateTime*	datetime
syncControl.metaUpdateTime*	datetime
uploadFiles	array
uploadFiles[]	string
installFiles	array
installFiles[]	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 too-early server-error Inherits: lib.ErrorType
message*	string

Response Body

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

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 too-early 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 too-early server-error Inherits: lib.ErrorType
message*	string
requestId*	string

Response Body

{
  "status": "server-error",
  "message": "Datastore connection lost",
  "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.

Example - List All

curl --header "Admin-Token: ${VDI_ADMIN_TOKEN}" \
"${VDI_INSTANCE}/admin/reports/imports/failed?limit=-1" \
> failed-imports.json

Parameters

Parameter	Type	Description
Query
user UserId	integer	Filters results to only records owned by the target user. Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: integer
before Partial Datetime	string	Filters results to only records created before the given datetime. Min. length: 4 Inherits: string
after Partial Datetime	string	Filter results to only records created after the given datetime. Min. length: 4 Inherits: string
sort	string	Sorting field. Default value: "date" Enum: date
order	string	Sort order. Default value: "desc" Enum: asc desc
limit	integer	Result count limit. If set to `-1`, no limit is applied. Default value: 100
offset	integer	Pagination offset. Ignored if `limit < 0`.

Secured By

Admin Token AdminToken

Per-service admin token header.

curl -X GET \
  https://veupathdb.org/vdi/admin/reports/imports/failed?UserId=<value>&PartialDate=<value>&PartialDate=<value>&sort=<value>&order=<value>&limit=<value>&offset=<value>

Inherits: object

Parameter	Type	Description
meta*	object	Inherits: lib.BrokenImportListingMeta
meta.count*	integer	Number of records in the result
meta.before	string
meta.after	string
meta.user	integer	VEuPathDB User ID Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: lib.UserId
meta.limit*	integer
meta.offset*	integer
results*	array
results[] Broken Import Details	object	Inherits: object
results[].datasetId*	string	VDI dataset identifier Pattern: ^[a-zA-Z0-9_-]+$ Inherits: lib.VdiId
results[].owner*	integer	VEuPathDB User ID Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: lib.UserId
results[].datasetType*	object	Details about a specific dataset type. Inherits: lib.DatasetTypeOutput
results[].datasetType.name*	string	Min. length: 3
results[].datasetType.version*	string	Min. length: 1
results[].datasetType.category*	string	Min. length: 3
results[].installTargets*	array	Unique items: Yes
results[].installTargets[]	string	Name or ID of a target VEuPathDB project, such as "PlasmoDB". Min. length: 5 Max. length: 32 Inherits: lib.InstallTargetID
results[].messages*	array
results[].messages[]	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 too-early server-error Inherits: lib.ErrorType
message*	string

Response Body

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

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 too-early server-error Inherits: lib.ErrorType
message*	string
requestId*	string

Response Body

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

Lists datasets that failed installation due to a non-user error, such as a system outage or service bug.

The returned report may be either a list of dataset ID strings, or a list of dataset detail objects depending on the provided expanded query parameter value. By default, dataset detail objects are returned.

Example - Dataset ID List

curl --header "Admin-Token: ${VDI_ADMIN_TOKEN}" \
"${VDI_INSTANCE}/admin/reports/installs/failed?expanded=false" \
> failed-installs.json

Example - Detailed Dataset List

curl --header "Admin-Token: ${VDI_ADMIN_TOKEN}" \
"${VDI_INSTANCE}/admin/reports/installs/failed" \
> failed-installs.json

Parameters

Parameter	Type	Description
Query
expanded	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

Secured By

Admin Token AdminToken

Per-service admin token header.

curl -X GET \
  https://veupathdb.org/vdi/admin/reports/installs/failed?expanded=<value>

Inherits: object

Parameter Type Description

details array

details[]

object

Inherits: object

details[].datasetId*

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: lib.VdiId

details[].owner*

integer

VEuPathDB User ID

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.UserId

details[].datasetType*

object

Details about a specific dataset type.

Inherits: lib.DatasetTypeOutput

details[].datasetType.name*

string

Min. length: 3

details[].datasetType.version*

string

Min. length: 1

details[].datasetType.category*

string

Min. length: 3

details[].installTargets*

array

Unique items: Yes

details[].installTargets[]

string

Name or ID of a target VEuPathDB project, such as "PlasmoDB".

Min. length: 5

Max. length: 32

Inherits: lib.InstallTargetID

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 Target Status

object

Entry in a list of install statuses for a dataset.

Inherits: lib.DatasetInstallStatusEntry

details[].status.install[].installTarget*

string

Name or ID of a target VEuPathDB project, such as "PlasmoDB".

Min. length: 5

Max. length: 32

Inherits: lib.InstallTargetID

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

string

Enum:

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

Inherits: lib.DatasetInstallStatus

details[].status.install[].metaMessages array

details[].status.install[].metaMessages[] string

details[].status.install[].dataStatus

string

Enum:

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

Inherits: lib.DatasetInstallStatus

details[].status.install[].dataMessages array

details[].status.install[].dataMessages[] string

ids array

ids[]

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: lib.VdiId

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 too-early server-error Inherits: lib.ErrorType
message*	string
requestId*	string

Response Body

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

Lists all the objects currently in the 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

Example

curl --header "Admin-Token: ${VDI_ADMIN_TOKEN}" \
"${VDI_INSTANCE}/admin/reports/object-store/list-all" \
> minio-objects.tsv

Secured By

Admin Token AdminToken

Per-service admin token header.

curl -X GET \
  https://veupathdb.org/vdi/admin/reports/object-store/list-all

Response Body

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

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 too-early server-error Inherits: lib.ErrorType
message*	string
requestId*	string

Response Body

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

Upload a dataset on behalf of a target user.

Usage: This endpoint functions the same as the normal create dataset endpoint with the additional requirement of a target User ID provided as a header.

Example File Upload:

curl --header "Admin-Token: ${VDI_ADMIN_TOKEN}" \
--header "User-ID: ${TARGET_USER_ID}" \
--form meta=@dataset-metadata.json \
--form file=@dataset-contents.zip \
"${VDI_INSTANCE}/admin/rpc/datasets/proxy-upload"

Example URL Upload:

curl --header "Admin-Token: ${VDI_ADMIN_TOKEN}" \
--header "User-ID: ${TARGET_USER_ID}" \
--form meta=@dataset-metadata.json \
--form url='https://some.website.com/path/to/file' \
"${VDI_INSTANCE}/admin/rpc/datasets/proxy-upload"

Headers

Parameter

Type

Description

User-ID* UserId

integer

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

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: integer

Secured By

Admin Token AdminToken

Per-service admin token header.

curl -X POST \
  -H "UserId: <value>" \
  -H "Content-type: multipart/form-data"
  -d @file \
  https://veupathdb.org/vdi/admin/rpc/datasets/proxy-upload

Dataset Proxy Post Request DatasetProxyPostRequestBody

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
details*	object	Metadata about the dataset being submitted. Inherits: lib.DatasetPostMeta
details.installTargets*	array	IDs of the projects this dataset is being submitted to. Unique items: Yes
details.installTargets[]	string	Name or ID of a target VEuPathDB project, such as "PlasmoDB". Min. length: 5 Max. length: 32 Inherits: lib.InstallTargetID
details.name*	string	User-provided name for the dataset. Min. length: 3 Max. length: 1024 Inherits: lib.DatasetName
details.summary*	string	Brief summary of the dataset. Min. length: 3 Max. length: 4000 Inherits: lib.DatasetSummary
details.description	string	Longform description of the dataset. Inherits: string
details.origin*	string	String representing the origin of the dataset. Examples include `direct-upload`, `nephele`, or `galaxy`. Min. length: 3 Max. length: 256 Inherits: lib.DatasetOrigin
details.dependencies*	array	Unique items: Yes
details.dependencies[] Dataset Dependency	object	Inherits: object
details.dependencies[].resourceIdentifier*	string	Min. length: 3 Max. length: 50
details.dependencies[].resourceDisplayName*	string	Min. length: 3 Max. length: 100
details.dependencies[].resourceVersion*	string	Min. length: 1 Max. length: 50
details.publications	array	Unique items: Yes
details.publications[] Dataset Publication	object	Inherits: lib.DatasetPublication
details.publications[].identifier*	string	Min. length: 3 Max. length: 30 Inherits: lib.DatasetPublicationIdentifier
details.publications[].type	string	Default value: "pmid" Enum: pmid doi Inherits: lib.DatasetPublicationType
details.publications[].citation	string	Min. length: 3 Max. length: 2000
details.publications[].isPrimary	boolean	Only one publication may be marked as primary.
details.contacts	array	Unique items: Yes
details.contacts[] Dataset Contact	object	Inherits: object
details.contacts[].firstName	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 1 Max. length: 300
details.contacts[].middleName	string	Min. length: 1 Max. length: 300
details.contacts[].lastName	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 1 Max. length: 300
details.contacts[].isPrimary	boolean	Only one contact may be marked as primary.
details.contacts[].email	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 5 Max. length: 4000
details.contacts[].affiliation Organization	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Max. length: 4000
details.contacts[].country	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Max. length: 200
details.projectName	string	Required if: Install target is MBio or ClinEpi Min. length: 1 Max. length: 256 Inherits: lib.DatasetProjectName
details.programName	string	Required if: Install target is MBio or ClinEpi Min. length: 1 Max. length: 256 Inherits: lib.DatasetProgramName
details.linkedDatasets Explicitly Related Datasets	array	Other studies or datasets that the user is explicitly indicating are related to the dataset represented by this metadata object. Unique items: Yes
details.linkedDatasets[]	object	Inherits: lib.LinkedDataset
details.linkedDatasets[].datasetUri*	string
details.linkedDatasets[].sharesRecords*	boolean
details.experimentalOrganism	object	Required for Genomics, VectorBase, and Microbiome. Optional for ClinEpi. Inherits: lib.DatasetOrganism
details.experimentalOrganism.species*	string
details.experimentalOrganism.strain*	string
details.hostOrganism	object	Inherits: lib.DatasetOrganism
details.hostOrganism.species*	string
details.hostOrganism.strain*	string
details.characteristics	object	Inherits: object
details.characteristics.studyDesign	string	Required for ClinEpi
details.characteristics.studyType	string	Required for ClinEpi
details.characteristics.countries	array	Unique items: Yes
details.characteristics.countries[]	string	Min. length: 3 Max. length: 128
details.characteristics.years	object	Inherits: lib.SampleYearRange
details.characteristics.years.start*	integer	Min. value: 1500 Max. value: 2500 Format: int16
details.characteristics.years.end*	integer	Min. value: 1500 Max. value: 2500 Format: int16
details.characteristics.studySpecies	array	Unique items: Yes
details.characteristics.studySpecies[]	string	Min. length: 3 Max. length: 128
details.characteristics.diseases	array	Diseases or health conditions Unique items: Yes
details.characteristics.diseases[]	string	Min. length: 3 Max. length: 128
details.characteristics.associatedFactors	array	Unique items: Yes
details.characteristics.associatedFactors[]	string	Min. length: 3 Max. length: 128
details.characteristics.participantAges	string	Min. length: 1 Max. length: 128
details.characteristics.sampleTypes	array	Unique items: Yes
details.characteristics.sampleTypes[]	string	Min. length: 3 Max. length: 128
details.externalIdentifiers	object	Inherits: lib.ExternalIdentifiers
details.externalIdentifiers.dois	array	Unique items: Yes
details.externalIdentifiers.dois[]	object	Inherits: object
details.externalIdentifiers.dois[].doi*	string	Min. length: 6 Max. length: 128
details.externalIdentifiers.dois[].description	string
details.externalIdentifiers.hyperlinks	array	Unique items: Yes
details.externalIdentifiers.hyperlinks[] Dataset Hyperlink	object	Inherits: object
details.externalIdentifiers.hyperlinks[].url*	string	Min. length: 7 Max. length: 200
details.externalIdentifiers.hyperlinks[].description	string	Max. length: 4000
details.externalIdentifiers.bioprojectIds	array	Unique items: Yes
details.externalIdentifiers.bioprojectIds[]	object	Inherits: object
details.externalIdentifiers.bioprojectIds[].id*	string	Min. length: 4 Max. length: 64
details.externalIdentifiers.bioprojectIds[].description	string
details.funding	array	Unique items: Yes
details.funding[]	object	Inherits: object
details.funding[].agency*	string	Min. length: 3 Max. length: 256
details.funding[].awardNumber*	string	Min. length: 3 Max. length: 64
details.shortAttribution	string	Min. length: 3 Max. length: 40 Inherits: lib.ShortAttribution
details.type*	object	Inherits: lib.DatasetTypeInput
details.type.name*	string	Min. length: 3 Max. length: 128
details.type.version*	string	Min. length: 1 Max. length: 32
details.visibility	string	Default value: "private" Enum: private protected public Inherits: lib.DatasetVisibility
details.createdOn Creation Date	datetime
dataFiles	array	Dataset files to upload. This field is incompatible with the `url` field.
dataFiles[]	file
url	string	URL to a dataset file to upload. This field is incompatible with the `file` field.
docFiles	array	Files containing additional dataset documentation or meta info that is not part of the data itself.
docFiles[]	file

Dataset Post Response DatasetPostResponseBody

application/json

Successful upload response.

Inherits: object

Parameter

Type

Description

datasetId*

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: lib.VdiId

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 too-early server-error Inherits: lib.ErrorType
message*	string

Response Body

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

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 too-early 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 too-early 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 too-early server-error Inherits: lib.ErrorType
message*	string
requestId*	string

Response Body

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

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

Example

curl --request POST \
--header "Admin-Token: ${VDI_ADMIN_TOKEN}" \
"${VDI_INSTANCE}/admin/rpc/datasets/prune?age_cutoff=2022-03-15"

Parameters

Parameter	Type	Description
Query
age_cutoff Retention Window Override	string	When given, overrides the configured dataset retention duration, and instead prunes all datasets that were soft-deleted before this timestamp. Expected date format is a subset of the RFC3336 format, requiring at least `yyyy-MM-dd`, but may be given additional precision part by part. Examples: `2022-03-15` - Day (assumes time 00:00) `2022-03-15T16` - Hour `2022-03-15T16:30` - Minute

Secured By

Admin Token AdminToken

Per-service admin token header.

curl -X POST \
  https://veupathdb.org/vdi/admin/rpc/datasets/prune?age_cutoff=<value>

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 too-early server-error Inherits: lib.ErrorType
message*	string

Response Body

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

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 too-early server-error Inherits: lib.ErrorType
message*	string
requestId*	string

Response Body

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

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

Example

curl --request POST \
--header "Admin-Token: ${VDI_ADMIN_TOKEN}" \
"${VDI_INSTANCE}/admin/rpc/datasets/reconcile"

Secured By

Admin Token AdminToken

Per-service admin token header.

curl -X POST \
  https://veupathdb.org/vdi/admin/rpc/datasets/reconcile

Conflict ConflictError

application/json

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

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

Response Body

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

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 too-early server-error Inherits: lib.ErrorType
message*	string
requestId*	string

Response Body

{
  "status": "server-error",
  "message": "Datastore connection lost",
  "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.

Single Run Example

curl --header "Admin-Token: ${VDI_ADMIN_TOKEN}" \
--data '{"all":true}'
"${VDI_INSTANCE}/admin/rpc/datasets/reconcile"

Batch Run Example

# Mark datasets as ready for reinstall, but don't start reinstaller yet
curl --header "Admin-Token: ${VDI_ADMIN_TOKEN}" \
--data '{"targets":["datasetId": "1235asf", "installTarget": "PlasmoDB"]}'
"${VDI_INSTANCE}/admin/rpc/datasets/reconcile?skip-run=true"

curl ...
curl ...
curl ...

# After all datasets have been marked, start the reinstaller.
curl --request POST \
--header "Admin-Token: ${VDI_ADMIN_TOKEN}" \
"${VDI_INSTANCE}/admin/rpc/datasets/reconcile"

Parameters

Parameter	Type	Description
Query
skip-run	boolean

Secured By

Admin Token AdminToken

Per-service admin token header.

curl -X POST \
  -H "Content-type: application/json"
  -d @body.json \
  https://veupathdb.org/vdi/admin/rpc/installs/clear-failed?skip-run=<value>

Install Cleanup Request InstallCleanupRequestBody

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 just run the reinstaller, unless skip-run is set, in which case 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	VDI dataset identifier Pattern: ^[a-zA-Z0-9_-]+$ Inherits: lib.VdiId
targets[].installTarget*	string	Name or ID of a target VEuPathDB project, such as "PlasmoDB". Min. length: 5 Max. length: 32 Inherits: lib.InstallTargetID

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 too-early server-error Inherits: lib.ErrorType
message*	string

Response Body

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

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 too-early server-error Inherits: lib.ErrorType
message*	string
requestId*	string

Response Body

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

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.

Secured By

Admin Token AdminToken

Per-service admin token header.

curl -X POST \
  -H "Content-type: application/json"
  -d @body.json \
  https://veupathdb.org/vdi/admin/rpc/object-store/purge-dataset

Inherits: object

Parameter

Type

Description

userId*

integer

VEuPathDB User ID

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.UserId

datasetId*

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: lib.VdiId

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 too-early server-error Inherits: lib.ErrorType
message*	string

Response Body

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

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 too-early server-error Inherits: lib.ErrorType
message*	string
requestId*	string

Response Body

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

Inherits: object

Parameter	Type	Description
buildInfo*	object	Inherits: object
buildInfo.gitTag*	string
buildInfo.gitCommit*	string
buildInfo.gitBranch*	string
buildInfo.gitUrl*	string
buildInfo.buildId*	string
buildInfo.buildNumber*	string
buildInfo.buildTime*	string
configuration*	object	Inherits: object
configuration.api*	object	Inherits: object
configuration.api.maxUploadSize*	integer	Format: int64
configuration.api.userMaxStorageSize*	integer	Format: int64
configuration.daemons*	object	Inherits: object
configuration.daemons.reconciler*	object	Inherits: lib.ReconcilerConfig
configuration.daemons.reconciler.enabled*	boolean
configuration.daemons.reconciler.fullRunInterval*	string
configuration.daemons.reconciler.slimRunInterval*	string
configuration.daemons.reconciler.performDeletes*	boolean
features*	object	Inherits: object
features.supportedArchiveTypes*	array
features.supportedArchiveTypes[]	string

Renders the API documentation for this service.

curl -X GET \
  https://veupathdb.org/vdi/api

Prints information about the overall service health.

curl -X GET \
  https://veupathdb.org/vdi/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 \
  https://veupathdb.org/vdi/metrics

Security Schemes

Per-service admin token header.

curl -X <method> \
  https://veupathdb.org/vdi/<path>

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 too-early server-error Inherits: lib.ErrorType
message*	string

Response Body

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

curl -X <method> \
  https://veupathdb.org/vdi/<path>

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 too-early server-error Inherits: lib.ErrorType
message*	string

Response Body

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

Types

Inherits: object

Model

Parameter	Type	Description
maxUploadSize*	integer	Format: int64
userMaxStorageSize*	integer	Format: int64

Inherits: object

Model

Parameter Type Description

datasetId*

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: lib.VdiId

owner*

integer

VEuPathDB User ID

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.UserId

datasetType*

object

Details about a specific dataset type.

Inherits: lib.DatasetTypeOutput

datasetType.name*

string

Min. length: 3

datasetType.version*

string

Min. length: 1

datasetType.category*

string

Min. length: 3

visibility*

string

Enum:

private
protected
public

Inherits: lib.DatasetVisibility

name*

string

User-provided name for the dataset.

Min. length: 3

Max. length: 1024

Inherits: lib.DatasetName

origin*

string

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

Min. length: 3

Max. length: 256

Inherits: lib.DatasetOrigin

installTargets*

array

Unique items: Yes

installTargets[]

string

Name or ID of a target VEuPathDB project, such as "PlasmoDB".

Min. length: 5

Max. length: 32

Inherits: lib.InstallTargetID

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 Target Status

object

Entry in a list of install statuses for a dataset.

Inherits: lib.DatasetInstallStatusEntry

status.install[].installTarget*

string

Name or ID of a target VEuPathDB project, such as "PlasmoDB".

Min. length: 5

Max. length: 32

Inherits: lib.InstallTargetID

status.install[].metaStatus*

string

Enum:

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

Inherits: lib.DatasetInstallStatus

status.install[].metaMessages array

status.install[].metaMessages[] string

status.install[].dataStatus

string

Enum:

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

Inherits: lib.DatasetInstallStatus

status.install[].dataMessages array

status.install[].dataMessages[] string

created*

datetime

Timestamp of the creation of the dataset

Inherits: lib.DatasetCreationDate

isDeleted* boolean

summary*

string

Brief summary of the dataset.

Min. length: 3

Max. length: 4000

Inherits: lib.DatasetSummary

description

string

Longform description of the dataset.

Inherits: lib.DatasetDescription

programName string

projectName string

Inherits: object

Model

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

Inherits: object

Model

Parameter Type Description

meta*

object

Inherits: object

meta.count* integer

meta.offset* integer

meta.limit* integer

meta.total* integer

results* array

results[]

object

Inherits: object

results[].datasetId*

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: lib.VdiId

results[].owner*

integer

VEuPathDB User ID

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.UserId

results[].datasetType*

object

Details about a specific dataset type.

Inherits: lib.DatasetTypeOutput

results[].datasetType.name*

string

Min. length: 3

results[].datasetType.version*

string

Min. length: 1

results[].datasetType.category*

string

Min. length: 3

results[].visibility*

string

Enum:

private
protected
public

Inherits: lib.DatasetVisibility

results[].name*

string

User-provided name for the dataset.

Min. length: 3

Max. length: 1024

Inherits: lib.DatasetName

results[].origin*

string

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

Min. length: 3

Max. length: 256

Inherits: lib.DatasetOrigin

results[].installTargets*

array

Unique items: Yes

results[].installTargets[]

string

Name or ID of a target VEuPathDB project, such as "PlasmoDB".

Min. length: 5

Max. length: 32

Inherits: lib.InstallTargetID

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 Target Status

object

Entry in a list of install statuses for a dataset.

Inherits: lib.DatasetInstallStatusEntry

results[].status.install[].installTarget*

string

Name or ID of a target VEuPathDB project, such as "PlasmoDB".

Min. length: 5

Max. length: 32

Inherits: lib.InstallTargetID

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

string

Enum:

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

Inherits: lib.DatasetInstallStatus

results[].status.install[].metaMessages array

results[].status.install[].metaMessages[] string

results[].status.install[].dataStatus

string

Enum:

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

Inherits: lib.DatasetInstallStatus

results[].status.install[].dataMessages array

results[].status.install[].dataMessages[] string

results[].created*

datetime

Timestamp of the creation of the dataset

Inherits: lib.DatasetCreationDate

results[].isDeleted* boolean

results[].summary*

string

Brief summary of the dataset.

Min. length: 3

Max. length: 4000

Inherits: lib.DatasetSummary

results[].description

string

Longform description of the dataset.

Inherits: lib.DatasetDescription

results[].programName string

results[].projectName 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 too-early server-error Inherits: lib.ErrorType
message*	string

Examples

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

Inherits: object

Model

Parameter

Type

Description

id*

string

Min. length: 4

Max. length: 64

description

string

Inherits: object

Model

Parameter Type Description

datasetId*

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: lib.VdiId

owner*

integer

VEuPathDB User ID

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.UserId

datasetType*

object

Details about a specific dataset type.

Inherits: lib.DatasetTypeOutput

datasetType.name*

string

Min. length: 3

datasetType.version*

string

Min. length: 1

datasetType.category*

string

Min. length: 3

installTargets*

array

Unique items: Yes

installTargets[]

string

Name or ID of a target VEuPathDB project, such as "PlasmoDB".

Min. length: 5

Max. length: 32

Inherits: lib.InstallTargetID

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 Target Status

object

Entry in a list of install statuses for a dataset.

Inherits: lib.DatasetInstallStatusEntry

status.install[].installTarget*

string

Name or ID of a target VEuPathDB project, such as "PlasmoDB".

Min. length: 5

Max. length: 32

Inherits: lib.InstallTargetID

status.install[].metaStatus*

string

Enum:

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

Inherits: lib.DatasetInstallStatus

status.install[].metaMessages array

status.install[].metaMessages[] string

status.install[].dataStatus

string

Enum:

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

Inherits: lib.DatasetInstallStatus

status.install[].dataMessages array

status.install[].dataMessages[] string

Inherits: object

Model

Parameter Type Description

details array

details[]

object

Inherits: object

details[].datasetId*

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: lib.VdiId

details[].owner*

integer

VEuPathDB User ID

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.UserId

details[].datasetType*

object

Details about a specific dataset type.

Inherits: lib.DatasetTypeOutput

details[].datasetType.name*

string

Min. length: 3

details[].datasetType.version*

string

Min. length: 1

details[].datasetType.category*

string

Min. length: 3

details[].installTargets*

array

Unique items: Yes

details[].installTargets[]

string

Name or ID of a target VEuPathDB project, such as "PlasmoDB".

Min. length: 5

Max. length: 32

Inherits: lib.InstallTargetID

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 Target Status

object

Entry in a list of install statuses for a dataset.

Inherits: lib.DatasetInstallStatusEntry

details[].status.install[].installTarget*

string

Name or ID of a target VEuPathDB project, such as "PlasmoDB".

Min. length: 5

Max. length: 32

Inherits: lib.InstallTargetID

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

string

Enum:

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

Inherits: lib.DatasetInstallStatus

details[].status.install[].metaMessages array

details[].status.install[].metaMessages[] string

details[].status.install[].dataStatus

string

Enum:

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

Inherits: lib.DatasetInstallStatus

details[].status.install[].dataMessages array

details[].status.install[].dataMessages[] string

ids array

ids[]

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: lib.VdiId

Inherits: object

Model

Parameter	Type	Description
datasetId*	string	VDI dataset identifier Pattern: ^[a-zA-Z0-9_-]+$ Inherits: lib.VdiId
owner*	integer	VEuPathDB User ID Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: lib.UserId
datasetType*	object	Details about a specific dataset type. Inherits: lib.DatasetTypeOutput
datasetType.name*	string	Min. length: 3
datasetType.version*	string	Min. length: 1
datasetType.category*	string	Min. length: 3
installTargets*	array	Unique items: Yes
installTargets[]	string	Name or ID of a target VEuPathDB project, such as "PlasmoDB". Min. length: 5 Max. length: 32 Inherits: lib.InstallTargetID
messages*	array
messages[]	string

Inherits: object

Model

Parameter	Type	Description
meta*	object	Inherits: lib.BrokenImportListingMeta
meta.count*	integer	Number of records in the result
meta.before	string
meta.after	string
meta.user	integer	VEuPathDB User ID Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: lib.UserId
meta.limit*	integer
meta.offset*	integer
results*	array
results[] Broken Import Details	object	Inherits: object
results[].datasetId*	string	VDI dataset identifier Pattern: ^[a-zA-Z0-9_-]+$ Inherits: lib.VdiId
results[].owner*	integer	VEuPathDB User ID Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: lib.UserId
results[].datasetType*	object	Details about a specific dataset type. Inherits: lib.DatasetTypeOutput
results[].datasetType.name*	string	Min. length: 3
results[].datasetType.version*	string	Min. length: 1
results[].datasetType.category*	string	Min. length: 3
results[].installTargets*	array	Unique items: Yes
results[].installTargets[]	string	Name or ID of a target VEuPathDB project, such as "PlasmoDB". Min. length: 5 Max. length: 32 Inherits: lib.InstallTargetID
results[].messages*	array
results[].messages[]	string

Inherits: object

Model

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

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 too-early server-error Inherits: lib.ErrorType
message*	string

Examples

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

If the dataset visibility is not private, the only valid action is replace.

Inherits: object

Model

Parameter	Type	Description
value	array	Unique items: Yes
value[] Dataset Contact	object	Inherits: lib.DatasetContact
value[].firstName	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 1 Max. length: 300
value[].middleName	string	Min. length: 1 Max. length: 300
value[].lastName	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 1 Max. length: 300
value[].isPrimary	boolean	Only one contact may be marked as primary.
value[].email	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 5 Max. length: 4000
value[].affiliation Organization	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Max. length: 4000
value[].country	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Max. length: 200

Inherits: object

Model

Parameter

Type

Description

doi*

string

Min. length: 6

Max. length: 128

description

string

Inherits: object

Model

Parameter	Type	Description
reconciler*	object	Inherits: lib.ReconcilerConfig
reconciler.enabled*	boolean
reconciler.fullRunInterval*	string
reconciler.slimRunInterval*	string
reconciler.performDeletes*	boolean

Inherits: object

Model

Parameter	Type	Description
studyDesign	string	Required for ClinEpi
studyType	string	Required for ClinEpi
countries	array	Unique items: Yes
countries[]	string	Min. length: 3 Max. length: 128
years	object	Inherits: lib.SampleYearRange
years.start*	integer	Min. value: 1500 Max. value: 2500 Format: int16
years.end*	integer	Min. value: 1500 Max. value: 2500 Format: int16
studySpecies	array	Unique items: Yes
studySpecies[]	string	Min. length: 3 Max. length: 128
diseases	array	Diseases or health conditions Unique items: Yes
diseases[]	string	Min. length: 3 Max. length: 128
associatedFactors	array	Unique items: Yes
associatedFactors[]	string	Min. length: 3 Max. length: 128
participantAges	string	Min. length: 1 Max. length: 128
sampleTypes	array	Unique items: Yes
sampleTypes[]	string	Min. length: 3 Max. length: 128

Inherits: object

Model

Parameter	Type	Description
studyDesign	object	Inherits: lib.OptionalStringPatch
studyDesign.value	string
studyType	object	Inherits: lib.OptionalStringPatch
studyType.value	string
countries	object
countries.value	array	Unique items: Yes
countries.value[]	string	Min. length: 3 Max. length: 128
years	object
years.value	object	Inherits: lib.SampleYearRange
years.value.start*	integer	Min. value: 1500 Max. value: 2500 Format: int16
years.value.end*	integer	Min. value: 1500 Max. value: 2500 Format: int16
studySpecies	object
studySpecies.value	array	Unique items: Yes
studySpecies.value[]	string	Min. length: 3 Max. length: 128
diseases	object
diseases.value	array	Unique items: Yes
diseases.value[]	string	Min. length: 3 Max. length: 128
associatedFactors	object
associatedFactors.value	array	Unique items: Yes
associatedFactors.value[]	string	Min. length: 3 Max. length: 128
participantAges	object	Inherits: lib.OptionalStringPatch
participantAges.value	string
sampleTypes	object
sampleTypes.value	array	Unique items: Yes
sampleTypes.value[]	string	Min. length: 3 Max. length: 128

Inherits: object

Model

Parameter	Type	Description
firstName	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 1 Max. length: 300
middleName	string	Min. length: 1 Max. length: 300
lastName	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 1 Max. length: 300
isPrimary	boolean	Only one contact may be marked as primary.
email	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 5 Max. length: 4000
affiliation Organization	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Max. length: 4000
country	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Max. length: 200

Timestamp of the creation of the dataset

Inherits: datetime

Inherits: object

Model

Parameter

Type

Description

resourceIdentifier*

string

Min. length: 3

Max. length: 50

resourceDisplayName*

string

Min. length: 3

Max. length: 100

resourceVersion*

string

Min. length: 1

Max. length: 50

Longform description of the dataset.

Inherits: string

Details about a specific singular dataset.

Inherits: lib.DatasetMetaBase

Model

Parameter Type Description

installTargets*

array

IDs of the projects this dataset is being submitted to.

Unique items: Yes

installTargets[]

string

Name or ID of a target VEuPathDB project, such as "PlasmoDB".

Min. length: 5

Max. length: 32

Inherits: lib.InstallTargetID

name*

string

User-provided name for the dataset.

Min. length: 3

Max. length: 1024

Inherits: lib.DatasetName

summary*

string

Brief summary of the dataset.

Min. length: 3

Max. length: 4000

Inherits: lib.DatasetSummary

description

string

Longform description of the dataset.

Inherits: string

origin*

string

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

Min. length: 3

Max. length: 256

Inherits: lib.DatasetOrigin

dependencies*

array

Unique items: Yes

dependencies[] Dataset Dependency

object

Inherits: object

dependencies[].resourceIdentifier*

string

Min. length: 3

Max. length: 50

dependencies[].resourceDisplayName*

string

Min. length: 3

Max. length: 100

dependencies[].resourceVersion*

string

Min. length: 1

Max. length: 50

publications

array

Unique items: Yes

publications[] Dataset Publication

object

Inherits: lib.DatasetPublication

publications[].identifier*

string

Min. length: 3

Max. length: 30

Inherits: lib.DatasetPublicationIdentifier

publications[].type

string

Default value: "pmid"

Enum:

pmid
doi

Inherits: lib.DatasetPublicationType

publications[].citation

string

Min. length: 3

Max. length: 2000

publications[].isPrimary

boolean

Only one publication may be marked as primary.

contacts

array

Unique items: Yes

contacts[] Dataset Contact

object

Inherits: object

contacts[].firstName

string

Required if:

isPrimary is true
Install target is MBio or ClinEpi
Dataset is public/community

Min. length: 1

Max. length: 300

contacts[].middleName

string

Min. length: 1

Max. length: 300

contacts[].lastName

string

Required if:

isPrimary is true
Install target is MBio or ClinEpi
Dataset is public/community

Min. length: 1

Max. length: 300

contacts[].isPrimary

boolean

Only one contact may be marked as primary.

contacts[].email

string

Required if:

isPrimary is true
Install target is MBio or ClinEpi
Dataset is public/community

Min. length: 5

Max. length: 4000

contacts[].affiliation Organization

string

Required if:

isPrimary is true
Install target is MBio or ClinEpi
Dataset is public/community

Max. length: 4000

contacts[].country

string

Required if:

isPrimary is true
Install target is MBio or ClinEpi
Dataset is public/community

Max. length: 200

projectName

string

Required if:

Install target is MBio or ClinEpi

Min. length: 1

Max. length: 256

Inherits: lib.DatasetProjectName

programName

string

Required if:

Install target is MBio or ClinEpi

Min. length: 1

Max. length: 256

Inherits: lib.DatasetProgramName

linkedDatasets Explicitly Related Datasets

array

Other studies or datasets that the user is explicitly indicating are related to the dataset represented by this metadata object.

Unique items: Yes

linkedDatasets[]

object

Inherits: lib.LinkedDataset

linkedDatasets[].datasetUri* string

linkedDatasets[].sharesRecords* boolean

experimentalOrganism

object

Required for Genomics, VectorBase, and Microbiome.

Optional for ClinEpi.

Inherits: lib.DatasetOrganism

experimentalOrganism.species* string

experimentalOrganism.strain* string

hostOrganism

object

Inherits: lib.DatasetOrganism

hostOrganism.species* string

hostOrganism.strain* string

characteristics

object

Inherits: object

characteristics.studyDesign

string

Required for ClinEpi

characteristics.studyType

string

Required for ClinEpi

characteristics.countries

array

Unique items: Yes

characteristics.countries[]

string

Min. length: 3

Max. length: 128

characteristics.years

object

Inherits: lib.SampleYearRange

characteristics.years.start*

integer

Min. value: 1500

Max. value: 2500

Format: int16

characteristics.years.end*

integer

Min. value: 1500

Max. value: 2500

Format: int16

characteristics.studySpecies

array

Unique items: Yes

characteristics.studySpecies[]

string

Min. length: 3

Max. length: 128

characteristics.diseases

array

Diseases or health conditions

Unique items: Yes

characteristics.diseases[]

string

Min. length: 3

Max. length: 128

characteristics.associatedFactors

array

Unique items: Yes

characteristics.associatedFactors[]

string

Min. length: 3

Max. length: 128

characteristics.participantAges

string

Min. length: 1

Max. length: 128

characteristics.sampleTypes

array

Unique items: Yes

characteristics.sampleTypes[]

string

Min. length: 3

Max. length: 128

externalIdentifiers

object

Inherits: lib.ExternalIdentifiers

externalIdentifiers.dois

array

Unique items: Yes

externalIdentifiers.dois[]

object

Inherits: object

externalIdentifiers.dois[].doi*

string

Min. length: 6

Max. length: 128

externalIdentifiers.dois[].description string

externalIdentifiers.hyperlinks

array

Unique items: Yes

externalIdentifiers.hyperlinks[] Dataset Hyperlink

object

Inherits: lib.DatasetHyperlink

externalIdentifiers.hyperlinks[].url*

string

Min. length: 7

Max. length: 200

externalIdentifiers.hyperlinks[].description

string

Max. length: 4000

externalIdentifiers.bioprojectIds

array

Unique items: Yes

externalIdentifiers.bioprojectIds[]

object

Inherits: object

externalIdentifiers.bioprojectIds[].id*

string

Min. length: 4

Max. length: 64

externalIdentifiers.bioprojectIds[].description string

funding

array

Unique items: Yes

funding[]

object

Inherits: lib.DatasetFundingAward

funding[].agency*

string

Min. length: 3

Max. length: 256

funding[].awardNumber*

string

Min. length: 3

Max. length: 64

shortAttribution

string

Min. length: 3

Max. length: 40

Inherits: lib.ShortAttribution

datasetId*

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: lib.VdiId

type*

object

Details about a specific dataset type.

Inherits: lib.DatasetTypeOutput

type.name*

string

Min. length: 3

type.version*

string

Min. length: 1

type.category*

string

Min. length: 3

visibility*

string

Enum:

private
protected
public

Inherits: lib.DatasetVisibility

owner*

object

Details about the owner of a VDI dataset.

Inherits: lib.DatasetOwner

owner.userId*

integer

VEuPathDB User ID

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.UserId

owner.firstName string

owner.lastName string

owner.email string

owner.affiliation string

created*

datetime

Timestamp of the creation of the dataset

Inherits: datetime

sourceUrl

string

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

Inherits: lib.DatasetSourceUrl

revisionHistory

object

Inherits: lib.RevisionHistory

revisionHistory.originalId*

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: lib.VdiId

revisionHistory.revisions* array

revisionHistory.revisions[] Dataset Revision

object

Dataset revision history entry.

Inherits: lib.DatasetRevision

revisionHistory.revisions[].action*

string

Enum:

create
extend
revise

Inherits: lib.DatasetRevisionAction

revisionHistory.revisions[].timestamp* datetime

revisionHistory.revisions[].revisionId*

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: lib.VdiId

revisionHistory.revisions[].revisionNote*

string

Note providing a reason and/or description for the revision.

Min. length: 10

Max. length: 4096

Inherits: lib.DatasetRevisionNote

revisionHistory.revisions[].fileListUrl*

string

URL to the file listing for the revision entry.

shortName*

string

Min. length: 3

Max. length: 20

Inherits: lib.ShortName

relatedDatasets Implicitly Related Datasets

array

Datasets that are implicitly related to the dataset represented by this object by way of sharing a common project name or program name, or by having one or more publications in common.

Unique items: Yes

relatedDatasets[]

object

Inherits: lib.RelatedDatasetInfo

relatedDatasets[].datasetId*

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: lib.VdiId

relatedDatasets[].type*

object

Details about a specific dataset type.

Inherits: lib.DatasetTypeOutput

relatedDatasets[].type.name*

string

Min. length: 3

relatedDatasets[].type.version*

string

Min. length: 1

relatedDatasets[].type.category*

string

Min. length: 3

relatedDatasets[].name*

string

User-provided name for the dataset.

Min. length: 3

Max. length: 1024

Inherits: lib.DatasetName

relatedDatasets[].summary*

string

Brief summary of the dataset.

Min. length: 3

Max. length: 4000

Inherits: lib.DatasetSummary

relatedDatasets[].created*

datetime

Timestamp of the creation of the dataset

Inherits: datetime

relatedDatasets[].relatedBy*

object

Discriminator: relationType

Inherits: lib.ImplicitRelation

relatedDatasets[].relatedBy.relationType*

string

Enum:

publication
program-name
project-name

Inherits: lib.ImplicitRelationType

importMessages

array

Log lines from the import process.

These messages will be warnings and/or validation errors.

importMessages[] string

array

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

shares[] Dataset Share Offer

object

Inherits: lib.ShareOffer

shares[].recipient*

object

Inherits: lib.ShareOfferRecipient

shares[].recipient.userId*

integer

VEuPathDB User ID

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.UserId

shares[].recipient.firstName string

shares[].recipient.lastName string

shares[].recipient.affiliation string

shares[].recipient.email string

shares[].status*

string

Enum:

grant
revoke

Inherits: lib.ShareOfferAction

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 Target Status

object

Entry in a list of install statuses for a dataset.

Inherits: lib.DatasetInstallStatusEntry

status.install[].installTarget*

string

Name or ID of a target VEuPathDB project, such as "PlasmoDB".

Min. length: 5

Max. length: 32

Inherits: lib.InstallTargetID

status.install[].metaStatus*

string

Enum:

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

Inherits: lib.DatasetInstallStatus

status.install[].metaMessages array

status.install[].metaMessages[] string

status.install[].dataStatus

string

Enum:

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

Inherits: lib.DatasetInstallStatus

status.install[].dataMessages array

status.install[].dataMessages[] string

files*

object

Inherits: lib.DatasetFileListing

files.upload*

object

Inherits: lib.DatasetZipDetails

files.upload.zipSize*

integer

Format: int64

files.upload.contents* array

files.upload.contents[] Decompressed File Info

object

Inherits: lib.DatasetFileDetails

files.upload.contents[].fileName* string

files.upload.contents[].fileSize*

integer

Size of the file in bytes.

Format: int64

files.install

object

Inherits: lib.DatasetZipDetails

files.install.zipSize*

integer

Format: int64

files.install.contents* array

files.install.contents[] Decompressed File Info

object

Inherits: lib.DatasetFileDetails

files.install.contents[].fileName* string

files.install.contents[].fileSize*

integer

Size of the file in bytes.

Format: int64

files.documents array

files.documents[] Decompressed File Info

object

Inherits: lib.DatasetFileDetails

files.documents[].fileName* string

files.documents[].fileSize*

integer

Size of the file in bytes.

Format: int64

Inherits: object

Model

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

Inherits: object

Model

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

Inherits: object

Model

Parameter

Type

Description

agency*

string

Min. length: 3

Max. length: 256

awardNumber*

string

Min. length: 3

Max. length: 64

Inherits: object

Model

Parameter

Type

Description

url*

string

Min. length: 7

Max. length: 200

description

string

Max. length: 4000

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
installTarget*	string	Name or ID of a target VEuPathDB project, such as "PlasmoDB". Min. length: 5 Max. length: 32 Inherits: lib.InstallTargetID
metaStatus*	string	Enum: running complete failed-validation failed-installation ready-for-reinstall missing-dependency Inherits: string
metaMessages	array
metaMessages[]	string
dataStatus	string	Enum: running complete failed-validation failed-installation ready-for-reinstall missing-dependency Inherits: string
dataMessages	array
dataMessages[]	string

Short entry with basic details about a dataset.

Inherits: object

Model

Parameter Type Description

datasetId*

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: lib.VdiId

owner*

object

Details about the owner of a VDI dataset.

Inherits: lib.DatasetOwner

owner.userId*

integer

VEuPathDB User ID

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.UserId

owner.firstName string

owner.lastName string

owner.email string

owner.affiliation string

type*

object

Details about a specific dataset type.

Inherits: lib.DatasetTypeOutput

type.name*

string

Min. length: 3

type.version*

string

Min. length: 1

type.category*

string

Min. length: 3

visibility*

string

Enum:

private
protected
public

Inherits: lib.DatasetVisibility

name*

string

User-provided name for the dataset.

Min. length: 3

Max. length: 1024

Inherits: lib.DatasetName

origin*

string

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

Min. length: 3

Max. length: 256

Inherits: lib.DatasetOrigin

installTargets*

array

Project IDs for projects the dataset record was submitted to.

Unique items: Yes

installTargets[]

string

Name or ID of a target VEuPathDB project, such as "PlasmoDB".

Min. length: 5

Max. length: 32

Inherits: lib.InstallTargetID

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: string

status.install array

status.install[] Dataset Install Target Status

object

Entry in a list of install statuses for a dataset.

Inherits: object

status.install[].installTarget*

string

Name or ID of a target VEuPathDB project, such as "PlasmoDB".

Min. length: 5

Max. length: 32

Inherits: lib.InstallTargetID

status.install[].metaStatus*

string

Enum:

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

Inherits: string

status.install[].metaMessages array

status.install[].metaMessages[] string

status.install[].dataStatus

string

Enum:

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

Inherits: string

status.install[].dataMessages array

status.install[].dataMessages[] string

shares* array

shares[] Dataset Listing Share Info

object

Inherits: lib.DatasetListShareUser

shares[].userId*

integer

VEuPathDB User ID

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.UserId

shares[].firstName* string

shares[].lastName* string

shares[].affiliation* string

shares[].accepted* boolean

fileCount*

integer

Number of files uploaded for this dataset.

fileSizeTotal*

integer

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

Format: int64

created*

datetime

Timestamp of the creation of the dataset

Inherits: datetime

summary*

string

Brief summary of the dataset.

Min. length: 3

Max. length: 4000

Inherits: lib.DatasetSummary

description

string

Longform description of the dataset.

Inherits: string

originalId

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: lib.VdiId

Inherits: object

Model

Parameter	Type	Description
userId*	integer	VEuPathDB User ID Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: lib.UserId
firstName*	string
lastName*	string
affiliation*	string
accepted*	boolean

Field definitions common to all dataset metadata representations throughout the VDI REST API endpoints.

Metadata fields that are omitted from this type are subtype dependent on API context.

Inherits: object

Model

Parameter	Type	Description
installTargets*	array	IDs of the projects this dataset is being submitted to. Unique items: Yes
installTargets[]	string	Name or ID of a target VEuPathDB project, such as "PlasmoDB". Min. length: 5 Max. length: 32 Inherits: lib.InstallTargetID
name*	string	User-provided name for the dataset. Min. length: 3 Max. length: 1024 Inherits: lib.DatasetName
summary*	string	Brief summary of the dataset. Min. length: 3 Max. length: 4000 Inherits: lib.DatasetSummary
description	string	Longform description of the dataset. Inherits: string
origin*	string	String representing the origin of the dataset. Examples include `direct-upload`, `nephele`, or `galaxy`. Min. length: 3 Max. length: 256 Inherits: lib.DatasetOrigin
dependencies*	array	Unique items: Yes
dependencies[] Dataset Dependency	object	Inherits: object
dependencies[].resourceIdentifier*	string	Min. length: 3 Max. length: 50
dependencies[].resourceDisplayName*	string	Min. length: 3 Max. length: 100
dependencies[].resourceVersion*	string	Min. length: 1 Max. length: 50
publications	array	Unique items: Yes
publications[] Dataset Publication	object	Inherits: lib.DatasetPublication
publications[].identifier*	string	Min. length: 3 Max. length: 30 Inherits: lib.DatasetPublicationIdentifier
publications[].type	string	Default value: "pmid" Enum: pmid doi Inherits: lib.DatasetPublicationType
publications[].citation	string	Min. length: 3 Max. length: 2000
publications[].isPrimary	boolean	Only one publication may be marked as primary.
contacts	array	Unique items: Yes
contacts[] Dataset Contact	object	Inherits: object
contacts[].firstName	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 1 Max. length: 300
contacts[].middleName	string	Min. length: 1 Max. length: 300
contacts[].lastName	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 1 Max. length: 300
contacts[].isPrimary	boolean	Only one contact may be marked as primary.
contacts[].email	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 5 Max. length: 4000
contacts[].affiliation Organization	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Max. length: 4000
contacts[].country	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Max. length: 200
projectName	string	Required if: Install target is MBio or ClinEpi Min. length: 1 Max. length: 256 Inherits: lib.DatasetProjectName
programName	string	Required if: Install target is MBio or ClinEpi Min. length: 1 Max. length: 256 Inherits: lib.DatasetProgramName
linkedDatasets Explicitly Related Datasets	array	Other studies or datasets that the user is explicitly indicating are related to the dataset represented by this metadata object. Unique items: Yes
linkedDatasets[]	object	Inherits: lib.LinkedDataset
linkedDatasets[].datasetUri*	string
linkedDatasets[].sharesRecords*	boolean
experimentalOrganism	object	Required for Genomics, VectorBase, and Microbiome. Optional for ClinEpi. Inherits: lib.DatasetOrganism
experimentalOrganism.species*	string
experimentalOrganism.strain*	string
hostOrganism	object	Inherits: lib.DatasetOrganism
hostOrganism.species*	string
hostOrganism.strain*	string
characteristics	object	Inherits: object
characteristics.studyDesign	string	Required for ClinEpi
characteristics.studyType	string	Required for ClinEpi
characteristics.countries	array	Unique items: Yes
characteristics.countries[]	string	Min. length: 3 Max. length: 128
characteristics.years	object	Inherits: lib.SampleYearRange
characteristics.years.start*	integer	Min. value: 1500 Max. value: 2500 Format: int16
characteristics.years.end*	integer	Min. value: 1500 Max. value: 2500 Format: int16
characteristics.studySpecies	array	Unique items: Yes
characteristics.studySpecies[]	string	Min. length: 3 Max. length: 128
characteristics.diseases	array	Diseases or health conditions Unique items: Yes
characteristics.diseases[]	string	Min. length: 3 Max. length: 128
characteristics.associatedFactors	array	Unique items: Yes
characteristics.associatedFactors[]	string	Min. length: 3 Max. length: 128
characteristics.participantAges	string	Min. length: 1 Max. length: 128
characteristics.sampleTypes	array	Unique items: Yes
characteristics.sampleTypes[]	string	Min. length: 3 Max. length: 128
externalIdentifiers	object	Inherits: lib.ExternalIdentifiers
externalIdentifiers.dois	array	Unique items: Yes
externalIdentifiers.dois[]	object	Inherits: object
externalIdentifiers.dois[].doi*	string	Min. length: 6 Max. length: 128
externalIdentifiers.dois[].description	string
externalIdentifiers.hyperlinks	array	Unique items: Yes
externalIdentifiers.hyperlinks[] Dataset Hyperlink	object	Inherits: object
externalIdentifiers.hyperlinks[].url*	string	Min. length: 7 Max. length: 200
externalIdentifiers.hyperlinks[].description	string	Max. length: 4000
externalIdentifiers.bioprojectIds	array	Unique items: Yes
externalIdentifiers.bioprojectIds[]	object	Inherits: object
externalIdentifiers.bioprojectIds[].id*	string	Min. length: 4 Max. length: 64
externalIdentifiers.bioprojectIds[].description	string
funding	array	Unique items: Yes
funding[]	object	Inherits: object
funding[].agency*	string	Min. length: 3 Max. length: 256
funding[].awardNumber*	string	Min. length: 3 Max. length: 64
shortAttribution	string	Min. length: 3 Max. length: 40 Inherits: lib.ShortAttribution

User-provided name for the dataset.

Min. length: 3

Max. length: 1024

Inherits: string

Inherits: object

Model

Parameter

Type

Description

userId*

integer

VEuPathDB User ID

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.UserId

datasetId*

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: lib.VdiId

Inherits: object

Model

Parameter	Type	Description
species*	string
strain*	string

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

Min. length: 3

Max. length: 256

Inherits: string

Details about the owner of a VDI dataset.

Inherits: object

Model

Parameter	Type	Description
userId*	integer	VEuPathDB User ID Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: lib.UserId
firstName	string
lastName	string
email	string
affiliation	string

Request to update the metadata for a dataset.

Fields that are omitted will be ignored when updating the target dataset record.

Inherits: object

Model

Parameter	Type	Description
type	object	If present, the only valid action is `replace`. Only permitted when transitioning from a none-type dataset into an actual dataset type. Inherits: lib.DatasetTypePatch
type.value	object	Inherits: lib.DatasetTypeInput
type.value.name*	string	Min. length: 3 Max. length: 128
type.value.version*	string	Min. length: 1 Max. length: 32
visibility	object	If present, the only valid action is `replace`. Inherits: lib.VisibilityPatch
visibility.value	string	Enum: private protected public Inherits: lib.DatasetVisibility
name	object	Inherits: lib.StringPatch
name.value*	string
summary	object	Inherits: lib.StringPatch
summary.value*	string
description	object	Inherits: lib.OptionalStringPatch
description.value	string
publications	object	Inherits: lib.PublicationsPatch
publications.value	array	Unique items: Yes
publications.value[] Dataset Publication	object	Inherits: lib.DatasetPublication
publications.value[].identifier*	string	Min. length: 3 Max. length: 30 Inherits: lib.DatasetPublicationIdentifier
publications.value[].type	string	Default value: "pmid" Enum: pmid doi Inherits: lib.DatasetPublicationType
publications.value[].citation	string	Min. length: 3 Max. length: 2000
publications.value[].isPrimary	boolean	Only one publication may be marked as primary.
contacts	object	If the dataset visibility is not `private`, the only valid action is `replace`. Inherits: object
contacts.value	array	Unique items: Yes
contacts.value[] Dataset Contact	object	Inherits: lib.DatasetContact
contacts.value[].firstName	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 1 Max. length: 300
contacts.value[].middleName	string	Min. length: 1 Max. length: 300
contacts.value[].lastName	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 1 Max. length: 300
contacts.value[].isPrimary	boolean	Only one contact may be marked as primary.
contacts.value[].email	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 5 Max. length: 4000
contacts.value[].affiliation Organization	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Max. length: 4000
contacts.value[].country	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Max. length: 200
projectName	object	Inherits: lib.OptionalStringPatch
projectName.value	string
programName	object	Inherits: lib.OptionalStringPatch
programName.value	string
linkedDatasets	object	Inherits: lib.LinkedDatasetPatch
linkedDatasets.value	array	Unique items: Yes
linkedDatasets.value[]	object	Inherits: lib.LinkedDataset
linkedDatasets.value[].datasetUri*	string
linkedDatasets.value[].sharesRecords*	boolean
experimentalOrganism	object	Inherits: lib.OrganismPatch
experimentalOrganism.value	object	Inherits: object
experimentalOrganism.value.species*	string
experimentalOrganism.value.strain*	string
hostOrganism	object	Inherits: lib.OrganismPatch
hostOrganism.value	object	Inherits: object
hostOrganism.value.species*	string
hostOrganism.value.strain*	string
characteristics	object	Inherits: object
characteristics.studyDesign	object	Inherits: lib.OptionalStringPatch
characteristics.studyDesign.value	string
characteristics.studyType	object	Inherits: lib.OptionalStringPatch
characteristics.studyType.value	string
characteristics.countries	object
characteristics.countries.value	array	Unique items: Yes
characteristics.countries.value[]	string	Min. length: 3 Max. length: 128
characteristics.years	object
characteristics.years.value	object	Inherits: lib.SampleYearRange
characteristics.years.value.start*	integer	Min. value: 1500 Max. value: 2500 Format: int16
characteristics.years.value.end*	integer	Min. value: 1500 Max. value: 2500 Format: int16
characteristics.studySpecies	object
characteristics.studySpecies.value	array	Unique items: Yes
characteristics.studySpecies.value[]	string	Min. length: 3 Max. length: 128
characteristics.diseases	object
characteristics.diseases.value	array	Unique items: Yes
characteristics.diseases.value[]	string	Min. length: 3 Max. length: 128
characteristics.associatedFactors	object
characteristics.associatedFactors.value	array	Unique items: Yes
characteristics.associatedFactors.value[]	string	Min. length: 3 Max. length: 128
characteristics.participantAges	object	Inherits: lib.OptionalStringPatch
characteristics.participantAges.value	string
characteristics.sampleTypes	object
characteristics.sampleTypes.value	array	Unique items: Yes
characteristics.sampleTypes.value[]	string	Min. length: 3 Max. length: 128
externalIdentifiers	object	Inherits: lib.ExternalIdentifiersPatch
externalIdentifiers.dois	object
externalIdentifiers.dois.value	array	Unique items: Yes
externalIdentifiers.dois.value[]	object	Inherits: object
externalIdentifiers.dois.value[].doi*	string	Min. length: 6 Max. length: 128
externalIdentifiers.dois.value[].description	string
externalIdentifiers.hyperlinks	object
externalIdentifiers.hyperlinks.value	array	Unique items: Yes
externalIdentifiers.hyperlinks.value[] Dataset Hyperlink	object	Inherits: object
externalIdentifiers.hyperlinks.value[].url*	string	Min. length: 7 Max. length: 200
externalIdentifiers.hyperlinks.value[].description	string	Max. length: 4000
externalIdentifiers.bioprojectIds	object
externalIdentifiers.bioprojectIds.value	array	Unique items: Yes
externalIdentifiers.bioprojectIds.value[]	object	Inherits: object
externalIdentifiers.bioprojectIds.value[].id*	string	Min. length: 4 Max. length: 64
externalIdentifiers.bioprojectIds.value[].description	string
funding	object	Inherits: lib.FundingPatch
funding.value	array	Unique items: Yes
funding.value[]	object	Inherits: object
funding.value[].agency*	string	Min. length: 3 Max. length: 256
funding.value[].awardNumber*	string	Min. length: 3 Max. length: 64
shortAttribution	object	Inherits: lib.OptionalStringPatch
shortAttribution.value	string

Field definitions common to all dataset metadata representations throughout the VDI REST API endpoints.

Metadata fields that are omitted from this type are subtype dependent on API context.

Inherits: lib.DatasetMetaBase

Model

Parameter	Type	Description
installTargets*	array	IDs of the projects this dataset is being submitted to. Unique items: Yes
installTargets[]	string	Name or ID of a target VEuPathDB project, such as "PlasmoDB". Min. length: 5 Max. length: 32 Inherits: lib.InstallTargetID
name*	string	User-provided name for the dataset. Min. length: 3 Max. length: 1024 Inherits: lib.DatasetName
summary*	string	Brief summary of the dataset. Min. length: 3 Max. length: 4000 Inherits: lib.DatasetSummary
description	string	Longform description of the dataset. Inherits: string
origin*	string	String representing the origin of the dataset. Examples include `direct-upload`, `nephele`, or `galaxy`. Min. length: 3 Max. length: 256 Inherits: lib.DatasetOrigin
dependencies*	array	Unique items: Yes
dependencies[] Dataset Dependency	object	Inherits: object
dependencies[].resourceIdentifier*	string	Min. length: 3 Max. length: 50
dependencies[].resourceDisplayName*	string	Min. length: 3 Max. length: 100
dependencies[].resourceVersion*	string	Min. length: 1 Max. length: 50
publications	array	Unique items: Yes
publications[] Dataset Publication	object	Inherits: lib.DatasetPublication
publications[].identifier*	string	Min. length: 3 Max. length: 30 Inherits: lib.DatasetPublicationIdentifier
publications[].type	string	Default value: "pmid" Enum: pmid doi Inherits: lib.DatasetPublicationType
publications[].citation	string	Min. length: 3 Max. length: 2000
publications[].isPrimary	boolean	Only one publication may be marked as primary.
contacts	array	Unique items: Yes
contacts[] Dataset Contact	object	Inherits: object
contacts[].firstName	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 1 Max. length: 300
contacts[].middleName	string	Min. length: 1 Max. length: 300
contacts[].lastName	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 1 Max. length: 300
contacts[].isPrimary	boolean	Only one contact may be marked as primary.
contacts[].email	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 5 Max. length: 4000
contacts[].affiliation Organization	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Max. length: 4000
contacts[].country	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Max. length: 200
projectName	string	Required if: Install target is MBio or ClinEpi Min. length: 1 Max. length: 256 Inherits: lib.DatasetProjectName
programName	string	Required if: Install target is MBio or ClinEpi Min. length: 1 Max. length: 256 Inherits: lib.DatasetProgramName
linkedDatasets Explicitly Related Datasets	array	Other studies or datasets that the user is explicitly indicating are related to the dataset represented by this metadata object. Unique items: Yes
linkedDatasets[]	object	Inherits: lib.LinkedDataset
linkedDatasets[].datasetUri*	string
linkedDatasets[].sharesRecords*	boolean
experimentalOrganism	object	Required for Genomics, VectorBase, and Microbiome. Optional for ClinEpi. Inherits: lib.DatasetOrganism
experimentalOrganism.species*	string
experimentalOrganism.strain*	string
hostOrganism	object	Inherits: lib.DatasetOrganism
hostOrganism.species*	string
hostOrganism.strain*	string
characteristics	object	Inherits: object
characteristics.studyDesign	string	Required for ClinEpi
characteristics.studyType	string	Required for ClinEpi
characteristics.countries	array	Unique items: Yes
characteristics.countries[]	string	Min. length: 3 Max. length: 128
characteristics.years	object	Inherits: lib.SampleYearRange
characteristics.years.start*	integer	Min. value: 1500 Max. value: 2500 Format: int16
characteristics.years.end*	integer	Min. value: 1500 Max. value: 2500 Format: int16
characteristics.studySpecies	array	Unique items: Yes
characteristics.studySpecies[]	string	Min. length: 3 Max. length: 128
characteristics.diseases	array	Diseases or health conditions Unique items: Yes
characteristics.diseases[]	string	Min. length: 3 Max. length: 128
characteristics.associatedFactors	array	Unique items: Yes
characteristics.associatedFactors[]	string	Min. length: 3 Max. length: 128
characteristics.participantAges	string	Min. length: 1 Max. length: 128
characteristics.sampleTypes	array	Unique items: Yes
characteristics.sampleTypes[]	string	Min. length: 3 Max. length: 128
externalIdentifiers	object	Inherits: lib.ExternalIdentifiers
externalIdentifiers.dois	array	Unique items: Yes
externalIdentifiers.dois[]	object	Inherits: object
externalIdentifiers.dois[].doi*	string	Min. length: 6 Max. length: 128
externalIdentifiers.dois[].description	string
externalIdentifiers.hyperlinks	array	Unique items: Yes
externalIdentifiers.hyperlinks[] Dataset Hyperlink	object	Inherits: object
externalIdentifiers.hyperlinks[].url*	string	Min. length: 7 Max. length: 200
externalIdentifiers.hyperlinks[].description	string	Max. length: 4000
externalIdentifiers.bioprojectIds	array	Unique items: Yes
externalIdentifiers.bioprojectIds[]	object	Inherits: object
externalIdentifiers.bioprojectIds[].id*	string	Min. length: 4 Max. length: 64
externalIdentifiers.bioprojectIds[].description	string
funding	array	Unique items: Yes
funding[]	object	Inherits: object
funding[].agency*	string	Min. length: 3 Max. length: 256
funding[].awardNumber*	string	Min. length: 3 Max. length: 64
shortAttribution	string	Min. length: 3 Max. length: 40 Inherits: lib.ShortAttribution
type*	object	Inherits: lib.DatasetTypeInput
type.name*	string	Min. length: 3 Max. length: 128
type.version*	string	Min. length: 1 Max. length: 32
visibility	string	Default value: "private" Enum: private protected public Inherits: lib.DatasetVisibility

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

Inherits: object

Model

Parameter	Type	Description
details*	object	Metadata about the dataset being submitted. Inherits: lib.DatasetMetaBase
details.installTargets*	array	IDs of the projects this dataset is being submitted to. Unique items: Yes
details.installTargets[]	string	Name or ID of a target VEuPathDB project, such as "PlasmoDB". Min. length: 5 Max. length: 32 Inherits: lib.InstallTargetID
details.name*	string	User-provided name for the dataset. Min. length: 3 Max. length: 1024 Inherits: lib.DatasetName
details.summary*	string	Brief summary of the dataset. Min. length: 3 Max. length: 4000 Inherits: lib.DatasetSummary
details.description	string	Longform description of the dataset. Inherits: string
details.origin*	string	String representing the origin of the dataset. Examples include `direct-upload`, `nephele`, or `galaxy`. Min. length: 3 Max. length: 256 Inherits: lib.DatasetOrigin
details.dependencies*	array	Unique items: Yes
details.dependencies[] Dataset Dependency	object	Inherits: object
details.dependencies[].resourceIdentifier*	string	Min. length: 3 Max. length: 50
details.dependencies[].resourceDisplayName*	string	Min. length: 3 Max. length: 100
details.dependencies[].resourceVersion*	string	Min. length: 1 Max. length: 50
details.publications	array	Unique items: Yes
details.publications[] Dataset Publication	object	Inherits: lib.DatasetPublication
details.publications[].identifier*	string	Min. length: 3 Max. length: 30 Inherits: lib.DatasetPublicationIdentifier
details.publications[].type	string	Default value: "pmid" Enum: pmid doi Inherits: lib.DatasetPublicationType
details.publications[].citation	string	Min. length: 3 Max. length: 2000
details.publications[].isPrimary	boolean	Only one publication may be marked as primary.
details.contacts	array	Unique items: Yes
details.contacts[] Dataset Contact	object	Inherits: object
details.contacts[].firstName	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 1 Max. length: 300
details.contacts[].middleName	string	Min. length: 1 Max. length: 300
details.contacts[].lastName	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 1 Max. length: 300
details.contacts[].isPrimary	boolean	Only one contact may be marked as primary.
details.contacts[].email	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 5 Max. length: 4000
details.contacts[].affiliation Organization	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Max. length: 4000
details.contacts[].country	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Max. length: 200
details.projectName	string	Required if: Install target is MBio or ClinEpi Min. length: 1 Max. length: 256 Inherits: lib.DatasetProjectName
details.programName	string	Required if: Install target is MBio or ClinEpi Min. length: 1 Max. length: 256 Inherits: lib.DatasetProgramName
details.linkedDatasets Explicitly Related Datasets	array	Other studies or datasets that the user is explicitly indicating are related to the dataset represented by this metadata object. Unique items: Yes
details.linkedDatasets[]	object	Inherits: lib.LinkedDataset
details.linkedDatasets[].datasetUri*	string
details.linkedDatasets[].sharesRecords*	boolean
details.experimentalOrganism	object	Required for Genomics, VectorBase, and Microbiome. Optional for ClinEpi. Inherits: lib.DatasetOrganism
details.experimentalOrganism.species*	string
details.experimentalOrganism.strain*	string
details.hostOrganism	object	Inherits: lib.DatasetOrganism
details.hostOrganism.species*	string
details.hostOrganism.strain*	string
details.characteristics	object	Inherits: object
details.characteristics.studyDesign	string	Required for ClinEpi
details.characteristics.studyType	string	Required for ClinEpi
details.characteristics.countries	array	Unique items: Yes
details.characteristics.countries[]	string	Min. length: 3 Max. length: 128
details.characteristics.years	object	Inherits: lib.SampleYearRange
details.characteristics.years.start*	integer	Min. value: 1500 Max. value: 2500 Format: int16
details.characteristics.years.end*	integer	Min. value: 1500 Max. value: 2500 Format: int16
details.characteristics.studySpecies	array	Unique items: Yes
details.characteristics.studySpecies[]	string	Min. length: 3 Max. length: 128
details.characteristics.diseases	array	Diseases or health conditions Unique items: Yes
details.characteristics.diseases[]	string	Min. length: 3 Max. length: 128
details.characteristics.associatedFactors	array	Unique items: Yes
details.characteristics.associatedFactors[]	string	Min. length: 3 Max. length: 128
details.characteristics.participantAges	string	Min. length: 1 Max. length: 128
details.characteristics.sampleTypes	array	Unique items: Yes
details.characteristics.sampleTypes[]	string	Min. length: 3 Max. length: 128
details.externalIdentifiers	object	Inherits: lib.ExternalIdentifiers
details.externalIdentifiers.dois	array	Unique items: Yes
details.externalIdentifiers.dois[]	object	Inherits: object
details.externalIdentifiers.dois[].doi*	string	Min. length: 6 Max. length: 128
details.externalIdentifiers.dois[].description	string
details.externalIdentifiers.hyperlinks	array	Unique items: Yes
details.externalIdentifiers.hyperlinks[] Dataset Hyperlink	object	Inherits: object
details.externalIdentifiers.hyperlinks[].url*	string	Min. length: 7 Max. length: 200
details.externalIdentifiers.hyperlinks[].description	string	Max. length: 4000
details.externalIdentifiers.bioprojectIds	array	Unique items: Yes
details.externalIdentifiers.bioprojectIds[]	object	Inherits: object
details.externalIdentifiers.bioprojectIds[].id*	string	Min. length: 4 Max. length: 64
details.externalIdentifiers.bioprojectIds[].description	string
details.funding	array	Unique items: Yes
details.funding[]	object	Inherits: object
details.funding[].agency*	string	Min. length: 3 Max. length: 256
details.funding[].awardNumber*	string	Min. length: 3 Max. length: 64
details.shortAttribution	string	Min. length: 3 Max. length: 40 Inherits: lib.ShortAttribution
details.type*	object	Inherits: lib.DatasetTypeInput
details.type.name*	string	Min. length: 3 Max. length: 128
details.type.version*	string	Min. length: 1 Max. length: 32
details.visibility	string	Default value: "private" Enum: private protected public Inherits: lib.DatasetVisibility
dataFiles	array	Dataset files to upload. This field is incompatible with the `url` field.
dataFiles[]	file
url	string	URL to a dataset file to upload. This field is incompatible with the `file` field.
docFiles	array	Files containing additional dataset documentation or meta info that is not part of the data itself.
docFiles[]	file

Successful upload response.

Inherits: object

Model

Parameter

Type

Description

datasetId*

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: lib.VdiId

Min. length: 1

Max. length: 256

Inherits: string

Min. length: 1

Max. length: 256

Inherits: string

Field definitions common to all dataset metadata representations throughout the VDI REST API endpoints.

Metadata fields that are omitted from this type are subtype dependent on API context.

Inherits: lib.DatasetPostMeta

Model

Parameter	Type	Description
installTargets*	array	IDs of the projects this dataset is being submitted to. Unique items: Yes
installTargets[]	string	Name or ID of a target VEuPathDB project, such as "PlasmoDB". Min. length: 5 Max. length: 32 Inherits: lib.InstallTargetID
name*	string	User-provided name for the dataset. Min. length: 3 Max. length: 1024 Inherits: lib.DatasetName
summary*	string	Brief summary of the dataset. Min. length: 3 Max. length: 4000 Inherits: lib.DatasetSummary
description	string	Longform description of the dataset. Inherits: string
origin*	string	String representing the origin of the dataset. Examples include `direct-upload`, `nephele`, or `galaxy`. Min. length: 3 Max. length: 256 Inherits: lib.DatasetOrigin
dependencies*	array	Unique items: Yes
dependencies[] Dataset Dependency	object	Inherits: object
dependencies[].resourceIdentifier*	string	Min. length: 3 Max. length: 50
dependencies[].resourceDisplayName*	string	Min. length: 3 Max. length: 100
dependencies[].resourceVersion*	string	Min. length: 1 Max. length: 50
publications	array	Unique items: Yes
publications[] Dataset Publication	object	Inherits: lib.DatasetPublication
publications[].identifier*	string	Min. length: 3 Max. length: 30 Inherits: lib.DatasetPublicationIdentifier
publications[].type	string	Default value: "pmid" Enum: pmid doi Inherits: lib.DatasetPublicationType
publications[].citation	string	Min. length: 3 Max. length: 2000
publications[].isPrimary	boolean	Only one publication may be marked as primary.
contacts	array	Unique items: Yes
contacts[] Dataset Contact	object	Inherits: object
contacts[].firstName	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 1 Max. length: 300
contacts[].middleName	string	Min. length: 1 Max. length: 300
contacts[].lastName	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 1 Max. length: 300
contacts[].isPrimary	boolean	Only one contact may be marked as primary.
contacts[].email	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 5 Max. length: 4000
contacts[].affiliation Organization	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Max. length: 4000
contacts[].country	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Max. length: 200
projectName	string	Required if: Install target is MBio or ClinEpi Min. length: 1 Max. length: 256 Inherits: lib.DatasetProjectName
programName	string	Required if: Install target is MBio or ClinEpi Min. length: 1 Max. length: 256 Inherits: lib.DatasetProgramName
linkedDatasets Explicitly Related Datasets	array	Other studies or datasets that the user is explicitly indicating are related to the dataset represented by this metadata object. Unique items: Yes
linkedDatasets[]	object	Inherits: lib.LinkedDataset
linkedDatasets[].datasetUri*	string
linkedDatasets[].sharesRecords*	boolean
experimentalOrganism	object	Required for Genomics, VectorBase, and Microbiome. Optional for ClinEpi. Inherits: lib.DatasetOrganism
experimentalOrganism.species*	string
experimentalOrganism.strain*	string
hostOrganism	object	Inherits: lib.DatasetOrganism
hostOrganism.species*	string
hostOrganism.strain*	string
characteristics	object	Inherits: object
characteristics.studyDesign	string	Required for ClinEpi
characteristics.studyType	string	Required for ClinEpi
characteristics.countries	array	Unique items: Yes
characteristics.countries[]	string	Min. length: 3 Max. length: 128
characteristics.years	object	Inherits: lib.SampleYearRange
characteristics.years.start*	integer	Min. value: 1500 Max. value: 2500 Format: int16
characteristics.years.end*	integer	Min. value: 1500 Max. value: 2500 Format: int16
characteristics.studySpecies	array	Unique items: Yes
characteristics.studySpecies[]	string	Min. length: 3 Max. length: 128
characteristics.diseases	array	Diseases or health conditions Unique items: Yes
characteristics.diseases[]	string	Min. length: 3 Max. length: 128
characteristics.associatedFactors	array	Unique items: Yes
characteristics.associatedFactors[]	string	Min. length: 3 Max. length: 128
characteristics.participantAges	string	Min. length: 1 Max. length: 128
characteristics.sampleTypes	array	Unique items: Yes
characteristics.sampleTypes[]	string	Min. length: 3 Max. length: 128
externalIdentifiers	object	Inherits: lib.ExternalIdentifiers
externalIdentifiers.dois	array	Unique items: Yes
externalIdentifiers.dois[]	object	Inherits: object
externalIdentifiers.dois[].doi*	string	Min. length: 6 Max. length: 128
externalIdentifiers.dois[].description	string
externalIdentifiers.hyperlinks	array	Unique items: Yes
externalIdentifiers.hyperlinks[] Dataset Hyperlink	object	Inherits: object
externalIdentifiers.hyperlinks[].url*	string	Min. length: 7 Max. length: 200
externalIdentifiers.hyperlinks[].description	string	Max. length: 4000
externalIdentifiers.bioprojectIds	array	Unique items: Yes
externalIdentifiers.bioprojectIds[]	object	Inherits: object
externalIdentifiers.bioprojectIds[].id*	string	Min. length: 4 Max. length: 64
externalIdentifiers.bioprojectIds[].description	string
funding	array	Unique items: Yes
funding[]	object	Inherits: object
funding[].agency*	string	Min. length: 3 Max. length: 256
funding[].awardNumber*	string	Min. length: 3 Max. length: 64
shortAttribution	string	Min. length: 3 Max. length: 40 Inherits: lib.ShortAttribution
type*	object	Inherits: lib.DatasetTypeInput
type.name*	string	Min. length: 3 Max. length: 128
type.version*	string	Min. length: 1 Max. length: 32
visibility	string	Default value: "private" Enum: private protected public Inherits: lib.DatasetVisibility
createdOn Creation Date	datetime

Inherits: object

Model

Parameter	Type	Description
details*	object	Metadata about the dataset being submitted. Inherits: lib.DatasetPostMeta
details.installTargets*	array	IDs of the projects this dataset is being submitted to. Unique items: Yes
details.installTargets[]	string	Name or ID of a target VEuPathDB project, such as "PlasmoDB". Min. length: 5 Max. length: 32 Inherits: lib.InstallTargetID
details.name*	string	User-provided name for the dataset. Min. length: 3 Max. length: 1024 Inherits: lib.DatasetName
details.summary*	string	Brief summary of the dataset. Min. length: 3 Max. length: 4000 Inherits: lib.DatasetSummary
details.description	string	Longform description of the dataset. Inherits: string
details.origin*	string	String representing the origin of the dataset. Examples include `direct-upload`, `nephele`, or `galaxy`. Min. length: 3 Max. length: 256 Inherits: lib.DatasetOrigin
details.dependencies*	array	Unique items: Yes
details.dependencies[] Dataset Dependency	object	Inherits: object
details.dependencies[].resourceIdentifier*	string	Min. length: 3 Max. length: 50
details.dependencies[].resourceDisplayName*	string	Min. length: 3 Max. length: 100
details.dependencies[].resourceVersion*	string	Min. length: 1 Max. length: 50
details.publications	array	Unique items: Yes
details.publications[] Dataset Publication	object	Inherits: lib.DatasetPublication
details.publications[].identifier*	string	Min. length: 3 Max. length: 30 Inherits: lib.DatasetPublicationIdentifier
details.publications[].type	string	Default value: "pmid" Enum: pmid doi Inherits: lib.DatasetPublicationType
details.publications[].citation	string	Min. length: 3 Max. length: 2000
details.publications[].isPrimary	boolean	Only one publication may be marked as primary.
details.contacts	array	Unique items: Yes
details.contacts[] Dataset Contact	object	Inherits: object
details.contacts[].firstName	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 1 Max. length: 300
details.contacts[].middleName	string	Min. length: 1 Max. length: 300
details.contacts[].lastName	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 1 Max. length: 300
details.contacts[].isPrimary	boolean	Only one contact may be marked as primary.
details.contacts[].email	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 5 Max. length: 4000
details.contacts[].affiliation Organization	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Max. length: 4000
details.contacts[].country	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Max. length: 200
details.projectName	string	Required if: Install target is MBio or ClinEpi Min. length: 1 Max. length: 256 Inherits: lib.DatasetProjectName
details.programName	string	Required if: Install target is MBio or ClinEpi Min. length: 1 Max. length: 256 Inherits: lib.DatasetProgramName
details.linkedDatasets Explicitly Related Datasets	array	Other studies or datasets that the user is explicitly indicating are related to the dataset represented by this metadata object. Unique items: Yes
details.linkedDatasets[]	object	Inherits: lib.LinkedDataset
details.linkedDatasets[].datasetUri*	string
details.linkedDatasets[].sharesRecords*	boolean
details.experimentalOrganism	object	Required for Genomics, VectorBase, and Microbiome. Optional for ClinEpi. Inherits: lib.DatasetOrganism
details.experimentalOrganism.species*	string
details.experimentalOrganism.strain*	string
details.hostOrganism	object	Inherits: lib.DatasetOrganism
details.hostOrganism.species*	string
details.hostOrganism.strain*	string
details.characteristics	object	Inherits: object
details.characteristics.studyDesign	string	Required for ClinEpi
details.characteristics.studyType	string	Required for ClinEpi
details.characteristics.countries	array	Unique items: Yes
details.characteristics.countries[]	string	Min. length: 3 Max. length: 128
details.characteristics.years	object	Inherits: lib.SampleYearRange
details.characteristics.years.start*	integer	Min. value: 1500 Max. value: 2500 Format: int16
details.characteristics.years.end*	integer	Min. value: 1500 Max. value: 2500 Format: int16
details.characteristics.studySpecies	array	Unique items: Yes
details.characteristics.studySpecies[]	string	Min. length: 3 Max. length: 128
details.characteristics.diseases	array	Diseases or health conditions Unique items: Yes
details.characteristics.diseases[]	string	Min. length: 3 Max. length: 128
details.characteristics.associatedFactors	array	Unique items: Yes
details.characteristics.associatedFactors[]	string	Min. length: 3 Max. length: 128
details.characteristics.participantAges	string	Min. length: 1 Max. length: 128
details.characteristics.sampleTypes	array	Unique items: Yes
details.characteristics.sampleTypes[]	string	Min. length: 3 Max. length: 128
details.externalIdentifiers	object	Inherits: lib.ExternalIdentifiers
details.externalIdentifiers.dois	array	Unique items: Yes
details.externalIdentifiers.dois[]	object	Inherits: object
details.externalIdentifiers.dois[].doi*	string	Min. length: 6 Max. length: 128
details.externalIdentifiers.dois[].description	string
details.externalIdentifiers.hyperlinks	array	Unique items: Yes
details.externalIdentifiers.hyperlinks[] Dataset Hyperlink	object	Inherits: object
details.externalIdentifiers.hyperlinks[].url*	string	Min. length: 7 Max. length: 200
details.externalIdentifiers.hyperlinks[].description	string	Max. length: 4000
details.externalIdentifiers.bioprojectIds	array	Unique items: Yes
details.externalIdentifiers.bioprojectIds[]	object	Inherits: object
details.externalIdentifiers.bioprojectIds[].id*	string	Min. length: 4 Max. length: 64
details.externalIdentifiers.bioprojectIds[].description	string
details.funding	array	Unique items: Yes
details.funding[]	object	Inherits: object
details.funding[].agency*	string	Min. length: 3 Max. length: 256
details.funding[].awardNumber*	string	Min. length: 3 Max. length: 64
details.shortAttribution	string	Min. length: 3 Max. length: 40 Inherits: lib.ShortAttribution
details.type*	object	Inherits: lib.DatasetTypeInput
details.type.name*	string	Min. length: 3 Max. length: 128
details.type.version*	string	Min. length: 1 Max. length: 32
details.visibility	string	Default value: "private" Enum: private protected public Inherits: lib.DatasetVisibility
details.createdOn Creation Date	datetime
dataFiles	array	Dataset files to upload. This field is incompatible with the `url` field.
dataFiles[]	file
url	string	URL to a dataset file to upload. This field is incompatible with the `file` field.
docFiles	array	Files containing additional dataset documentation or meta info that is not part of the data itself.
docFiles[]	file

Inherits: object

Model

Parameter	Type	Description
identifier*	string	Min. length: 3 Max. length: 30 Inherits: lib.DatasetPublicationIdentifier
type	string	Default value: "pmid" Enum: pmid doi Inherits: lib.DatasetPublicationType
citation	string	Min. length: 3 Max. length: 2000
isPrimary	boolean	Only one publication may be marked as primary.

Min. length: 3

Max. length: 30

Inherits: string

Default value: "pmid"

Enum:

pmid
doi

Inherits: string

Request to update the metadata for a dataset.

Fields that are omitted will be ignored when updating the target dataset record.

Inherits: lib.DatasetPatchRequestBody

Model

Parameter	Type	Description
type	object	If present, the only valid action is `replace`. Only permitted when transitioning from a none-type dataset into an actual dataset type. Inherits: lib.DatasetTypePatch
type.value	object	Inherits: lib.DatasetTypeInput
type.value.name*	string	Min. length: 3 Max. length: 128
type.value.version*	string	Min. length: 1 Max. length: 32
visibility	object	If present, the only valid action is `replace`. Inherits: lib.VisibilityPatch
visibility.value	string	Enum: private protected public Inherits: lib.DatasetVisibility
name	object	Inherits: lib.StringPatch
name.value*	string
summary	object	Inherits: lib.StringPatch
summary.value*	string
description	object	Inherits: lib.OptionalStringPatch
description.value	string
publications	object	Inherits: lib.PublicationsPatch
publications.value	array	Unique items: Yes
publications.value[] Dataset Publication	object	Inherits: lib.DatasetPublication
publications.value[].identifier*	string	Min. length: 3 Max. length: 30 Inherits: lib.DatasetPublicationIdentifier
publications.value[].type	string	Default value: "pmid" Enum: pmid doi Inherits: lib.DatasetPublicationType
publications.value[].citation	string	Min. length: 3 Max. length: 2000
publications.value[].isPrimary	boolean	Only one publication may be marked as primary.
contacts	object	If the dataset visibility is not `private`, the only valid action is `replace`. Inherits: object
contacts.value	array	Unique items: Yes
contacts.value[] Dataset Contact	object	Inherits: lib.DatasetContact
contacts.value[].firstName	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 1 Max. length: 300
contacts.value[].middleName	string	Min. length: 1 Max. length: 300
contacts.value[].lastName	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 1 Max. length: 300
contacts.value[].isPrimary	boolean	Only one contact may be marked as primary.
contacts.value[].email	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 5 Max. length: 4000
contacts.value[].affiliation Organization	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Max. length: 4000
contacts.value[].country	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Max. length: 200
projectName	object	Inherits: lib.OptionalStringPatch
projectName.value	string
programName	object	Inherits: lib.OptionalStringPatch
programName.value	string
linkedDatasets	object	Inherits: lib.LinkedDatasetPatch
linkedDatasets.value	array	Unique items: Yes
linkedDatasets.value[]	object	Inherits: lib.LinkedDataset
linkedDatasets.value[].datasetUri*	string
linkedDatasets.value[].sharesRecords*	boolean
experimentalOrganism	object	Inherits: lib.OrganismPatch
experimentalOrganism.value	object	Inherits: object
experimentalOrganism.value.species*	string
experimentalOrganism.value.strain*	string
hostOrganism	object	Inherits: lib.OrganismPatch
hostOrganism.value	object	Inherits: object
hostOrganism.value.species*	string
hostOrganism.value.strain*	string
characteristics	object	Inherits: object
characteristics.studyDesign	object	Inherits: lib.OptionalStringPatch
characteristics.studyDesign.value	string
characteristics.studyType	object	Inherits: lib.OptionalStringPatch
characteristics.studyType.value	string
characteristics.countries	object
characteristics.countries.value	array	Unique items: Yes
characteristics.countries.value[]	string	Min. length: 3 Max. length: 128
characteristics.years	object
characteristics.years.value	object	Inherits: lib.SampleYearRange
characteristics.years.value.start*	integer	Min. value: 1500 Max. value: 2500 Format: int16
characteristics.years.value.end*	integer	Min. value: 1500 Max. value: 2500 Format: int16
characteristics.studySpecies	object
characteristics.studySpecies.value	array	Unique items: Yes
characteristics.studySpecies.value[]	string	Min. length: 3 Max. length: 128
characteristics.diseases	object
characteristics.diseases.value	array	Unique items: Yes
characteristics.diseases.value[]	string	Min. length: 3 Max. length: 128
characteristics.associatedFactors	object
characteristics.associatedFactors.value	array	Unique items: Yes
characteristics.associatedFactors.value[]	string	Min. length: 3 Max. length: 128
characteristics.participantAges	object	Inherits: lib.OptionalStringPatch
characteristics.participantAges.value	string
characteristics.sampleTypes	object
characteristics.sampleTypes.value	array	Unique items: Yes
characteristics.sampleTypes.value[]	string	Min. length: 3 Max. length: 128
externalIdentifiers	object	Inherits: lib.ExternalIdentifiersPatch
externalIdentifiers.dois	object
externalIdentifiers.dois.value	array	Unique items: Yes
externalIdentifiers.dois.value[]	object	Inherits: object
externalIdentifiers.dois.value[].doi*	string	Min. length: 6 Max. length: 128
externalIdentifiers.dois.value[].description	string
externalIdentifiers.hyperlinks	object
externalIdentifiers.hyperlinks.value	array	Unique items: Yes
externalIdentifiers.hyperlinks.value[] Dataset Hyperlink	object	Inherits: object
externalIdentifiers.hyperlinks.value[].url*	string	Min. length: 7 Max. length: 200
externalIdentifiers.hyperlinks.value[].description	string	Max. length: 4000
externalIdentifiers.bioprojectIds	object
externalIdentifiers.bioprojectIds.value	array	Unique items: Yes
externalIdentifiers.bioprojectIds.value[]	object	Inherits: object
externalIdentifiers.bioprojectIds.value[].id*	string	Min. length: 4 Max. length: 64
externalIdentifiers.bioprojectIds.value[].description	string
funding	object	Inherits: lib.FundingPatch
funding.value	array	Unique items: Yes
funding.value[]	object	Inherits: object
funding.value[].agency*	string	Min. length: 3 Max. length: 256
funding.value[].awardNumber*	string	Min. length: 3 Max. length: 64
shortAttribution	object	Inherits: lib.OptionalStringPatch
shortAttribution.value	string
origin*	string	String representing the origin of the dataset. Examples include `direct-upload`, `nephele`, or `galaxy`. Min. length: 3 Max. length: 256 Inherits: string
revisionNote*	string	Note providing a reason and/or description for the revision. Min. length: 10 Max. length: 4096 Inherits: lib.DatasetRevisionNote

Inherits: object

Model

Parameter	Type	Description
details*	object	Metadata about the dataset being submitted. Inherits: lib.DatasetPatchRequestBody
details.type	object	If present, the only valid action is `replace`. Only permitted when transitioning from a none-type dataset into an actual dataset type. Inherits: lib.DatasetTypePatch
details.type.value	object	Inherits: lib.DatasetTypeInput
details.type.value.name*	string	Min. length: 3 Max. length: 128
details.type.value.version*	string	Min. length: 1 Max. length: 32
details.visibility	object	If present, the only valid action is `replace`. Inherits: lib.VisibilityPatch
details.visibility.value	string	Enum: private protected public Inherits: lib.DatasetVisibility
details.name	object	Inherits: lib.StringPatch
details.name.value*	string
details.summary	object	Inherits: lib.StringPatch
details.summary.value*	string
details.description	object	Inherits: lib.OptionalStringPatch
details.description.value	string
details.publications	object	Inherits: lib.PublicationsPatch
details.publications.value	array	Unique items: Yes
details.publications.value[] Dataset Publication	object	Inherits: lib.DatasetPublication
details.publications.value[].identifier*	string	Min. length: 3 Max. length: 30 Inherits: lib.DatasetPublicationIdentifier
details.publications.value[].type	string	Default value: "pmid" Enum: pmid doi Inherits: lib.DatasetPublicationType
details.publications.value[].citation	string	Min. length: 3 Max. length: 2000
details.publications.value[].isPrimary	boolean	Only one publication may be marked as primary.
details.contacts	object	If the dataset visibility is not `private`, the only valid action is `replace`. Inherits: object
details.contacts.value	array	Unique items: Yes
details.contacts.value[] Dataset Contact	object	Inherits: lib.DatasetContact
details.contacts.value[].firstName	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 1 Max. length: 300
details.contacts.value[].middleName	string	Min. length: 1 Max. length: 300
details.contacts.value[].lastName	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 1 Max. length: 300
details.contacts.value[].isPrimary	boolean	Only one contact may be marked as primary.
details.contacts.value[].email	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Min. length: 5 Max. length: 4000
details.contacts.value[].affiliation Organization	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Max. length: 4000
details.contacts.value[].country	string	Required if: `isPrimary` is `true` Install target is MBio or ClinEpi Dataset is public/community Max. length: 200
details.projectName	object	Inherits: lib.OptionalStringPatch
details.projectName.value	string
details.programName	object	Inherits: lib.OptionalStringPatch
details.programName.value	string
details.linkedDatasets	object	Inherits: lib.LinkedDatasetPatch
details.linkedDatasets.value	array	Unique items: Yes
details.linkedDatasets.value[]	object	Inherits: lib.LinkedDataset
details.linkedDatasets.value[].datasetUri*	string
details.linkedDatasets.value[].sharesRecords*	boolean
details.experimentalOrganism	object	Inherits: lib.OrganismPatch
details.experimentalOrganism.value	object	Inherits: object
details.experimentalOrganism.value.species*	string
details.experimentalOrganism.value.strain*	string
details.hostOrganism	object	Inherits: lib.OrganismPatch
details.hostOrganism.value	object	Inherits: object
details.hostOrganism.value.species*	string
details.hostOrganism.value.strain*	string
details.characteristics	object	Inherits: object
details.characteristics.studyDesign	object	Inherits: lib.OptionalStringPatch
details.characteristics.studyDesign.value	string
details.characteristics.studyType	object	Inherits: lib.OptionalStringPatch
details.characteristics.studyType.value	string
details.characteristics.countries	object
details.characteristics.countries.value	array	Unique items: Yes
details.characteristics.countries.value[]	string	Min. length: 3 Max. length: 128
details.characteristics.years	object
details.characteristics.years.value	object	Inherits: lib.SampleYearRange
details.characteristics.years.value.start*	integer	Min. value: 1500 Max. value: 2500 Format: int16
details.characteristics.years.value.end*	integer	Min. value: 1500 Max. value: 2500 Format: int16
details.characteristics.studySpecies	object
details.characteristics.studySpecies.value	array	Unique items: Yes
details.characteristics.studySpecies.value[]	string	Min. length: 3 Max. length: 128
details.characteristics.diseases	object
details.characteristics.diseases.value	array	Unique items: Yes
details.characteristics.diseases.value[]	string	Min. length: 3 Max. length: 128
details.characteristics.associatedFactors	object
details.characteristics.associatedFactors.value	array	Unique items: Yes
details.characteristics.associatedFactors.value[]	string	Min. length: 3 Max. length: 128
details.characteristics.participantAges	object	Inherits: lib.OptionalStringPatch
details.characteristics.participantAges.value	string
details.characteristics.sampleTypes	object
details.characteristics.sampleTypes.value	array	Unique items: Yes
details.characteristics.sampleTypes.value[]	string	Min. length: 3 Max. length: 128
details.externalIdentifiers	object	Inherits: lib.ExternalIdentifiersPatch
details.externalIdentifiers.dois	object
details.externalIdentifiers.dois.value	array	Unique items: Yes
details.externalIdentifiers.dois.value[]	object	Inherits: object
details.externalIdentifiers.dois.value[].doi*	string	Min. length: 6 Max. length: 128
details.externalIdentifiers.dois.value[].description	string
details.externalIdentifiers.hyperlinks	object
details.externalIdentifiers.hyperlinks.value	array	Unique items: Yes
details.externalIdentifiers.hyperlinks.value[] Dataset Hyperlink	object	Inherits: object
details.externalIdentifiers.hyperlinks.value[].url*	string	Min. length: 7 Max. length: 200
details.externalIdentifiers.hyperlinks.value[].description	string	Max. length: 4000
details.externalIdentifiers.bioprojectIds	object
details.externalIdentifiers.bioprojectIds.value	array	Unique items: Yes
details.externalIdentifiers.bioprojectIds.value[]	object	Inherits: object
details.externalIdentifiers.bioprojectIds.value[].id*	string	Min. length: 4 Max. length: 64
details.externalIdentifiers.bioprojectIds.value[].description	string
details.funding	object	Inherits: lib.FundingPatch
details.funding.value	array	Unique items: Yes
details.funding.value[]	object	Inherits: object
details.funding.value[].agency*	string	Min. length: 3 Max. length: 256
details.funding.value[].awardNumber*	string	Min. length: 3 Max. length: 64
details.shortAttribution	object	Inherits: lib.OptionalStringPatch
details.shortAttribution.value	string
details.origin*	string	String representing the origin of the dataset. Examples include `direct-upload`, `nephele`, or `galaxy`. Min. length: 3 Max. length: 256 Inherits: string
details.revisionNote*	string	Note providing a reason and/or description for the revision. Min. length: 10 Max. length: 4096 Inherits: lib.DatasetRevisionNote
dataFiles	array	Dataset files to upload. This field is incompatible with the `url` field.
dataFiles[]	file
url	string	URL to a dataset file to upload. This field is incompatible with the `file` field.
docFiles	array	Files containing additional dataset documentation or meta info that is not part of the data itself.
docFiles[]	file

Inherits: object

Model

Parameter

Type

Description

datasetId*

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: lib.VdiId

Dataset revision history entry.

Inherits: object

Model

Parameter	Type	Description
action*	string	Enum: create extend revise Inherits: lib.DatasetRevisionAction
timestamp*	datetime
revisionId*	string	VDI dataset identifier Pattern: ^[a-zA-Z0-9_-]+$ Inherits: lib.VdiId
revisionNote*	string	Note providing a reason and/or description for the revision. Min. length: 10 Max. length: 4096 Inherits: lib.DatasetRevisionNote
fileListUrl*	string	URL to the file listing for the revision entry.

Enum:

create
extend
revise

Inherits: string

Note providing a reason and/or description for the revision.

Min. length: 10

Max. length: 4096

Inherits: string

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

Inherits: object

Model

Parameter	Type	Description
action*	string	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*	string	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

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

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: string

install array

install[] Dataset Install Target Status

object

Entry in a list of install statuses for a dataset.

Inherits: object

install[].installTarget*

string

Name or ID of a target VEuPathDB project, such as "PlasmoDB".

Min. length: 5

Max. length: 32

Inherits: lib.InstallTargetID

install[].metaStatus*

string

Enum:

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

Inherits: string

install[].metaMessages array

install[].metaMessages[] string

install[].dataStatus

string

Enum:

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

Inherits: string

install[].dataMessages array

install[].dataMessages[] string

Brief summary of the dataset.

Min. length: 3

Max. length: 4000

Inherits: string

Inherits: object

Model

Parameter

Type

Description

name*

string

Min. length: 3

Max. length: 128

version*

string

Min. length: 1

Max. length: 32

Details about a specific dataset type.

Inherits: object

Model

Parameter	Type	Description
name*	string	Min. length: 3
version*	string	Min. length: 1
category*	string	Min. length: 3

If present, the only valid action is replace.

Only permitted when transitioning from a none-type dataset into an actual dataset type.

Inherits: object

Model

Parameter

Type

Description

value

object

Inherits: object

value.name*

string

Min. length: 3

Max. length: 128

value.version*

string

Min. length: 1

Max. length: 32

Enum:

private
protected
public

Inherits: string

Inherits: object

Model

Parameter	Type	Description
zipSize*	integer	Format: int64
contents*	array
contents[] Decompressed File Info	object	Inherits: object
contents[].fileName*	string
contents[].fileSize*	integer	Size of the file in bytes. Format: int64

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 too-early server-error Inherits: lib.ErrorType
message*	string

Enum:

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

Inherits: string

Inherits: object

Model

Parameter	Type	Description
dois	array	Unique items: Yes
dois[]	object	Inherits: object
dois[].doi*	string	Min. length: 6 Max. length: 128
dois[].description	string
hyperlinks	array	Unique items: Yes
hyperlinks[] Dataset Hyperlink	object	Inherits: object
hyperlinks[].url*	string	Min. length: 7 Max. length: 200
hyperlinks[].description	string	Max. length: 4000
bioprojectIds	array	Unique items: Yes
bioprojectIds[]	object	Inherits: object
bioprojectIds[].id*	string	Min. length: 4 Max. length: 64
bioprojectIds[].description	string

Inherits: object

Model

Parameter	Type	Description
dois	object
dois.value	array	Unique items: Yes
dois.value[]	object	Inherits: object
dois.value[].doi*	string	Min. length: 6 Max. length: 128
dois.value[].description	string
hyperlinks	object
hyperlinks.value	array	Unique items: Yes
hyperlinks.value[] Dataset Hyperlink	object	Inherits: object
hyperlinks.value[].url*	string	Min. length: 7 Max. length: 200
hyperlinks.value[].description	string	Max. length: 4000
bioprojectIds	object
bioprojectIds.value	array	Unique items: Yes
bioprojectIds.value[]	object	Inherits: object
bioprojectIds.value[].id*	string	Min. length: 4 Max. length: 64
bioprojectIds.value[].description	string

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 too-early server-error Inherits: lib.ErrorType
message*	string
dependency*	string

Examples

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

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 too-early server-error Inherits: lib.ErrorType
message*	string

Examples

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

Inherits: object

Model

Parameter	Type	Description
value	array	Unique items: Yes
value[]	object	Inherits: object
value[].agency*	string	Min. length: 3 Max. length: 256
value[].awardNumber*	string	Min. length: 3 Max. length: 64

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 too-early server-error Inherits: lib.ErrorType
message*	string

Examples

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

Discriminator: relationType

Inherits: object

Model

Parameter	Type	Description
relationType*	string	Enum: publication program-name project-name Inherits: lib.ImplicitRelationType

Enum:

publication
program-name
project-name

Inherits: string

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

Inherits: object

Model

Parameter	Type	Description
all	boolean
targets	array	Unique items: Yes
targets[] Install Cleanup Target	object	Inherits: lib.InstallCleanupTarget
targets[].datasetId*	string	VDI dataset identifier Pattern: ^[a-zA-Z0-9_-]+$ Inherits: lib.VdiId
targets[].installTarget*	string	Name or ID of a target VEuPathDB project, such as "PlasmoDB". Min. length: 5 Max. length: 32 Inherits: lib.InstallTargetID

Inherits: object

Model

Parameter

Type

Description

datasetId*

string

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: lib.VdiId

installTarget*

string

Name or ID of a target VEuPathDB project, such as "PlasmoDB".

Min. length: 5

Max. length: 32

Inherits: lib.InstallTargetID

Name or ID of a target VEuPathDB project, such as "PlasmoDB".

Min. length: 5

Max. length: 32

Inherits: string

Inherits: object

Model

Parameter	Type	Description
datasetType*	object	Details about a specific dataset type. Inherits: object
datasetType.name*	string	Min. length: 3
datasetType.version*	string	Min. length: 1
datasetType.category*	string	Min. length: 3
owner*	integer	VEuPathDB User ID Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: lib.UserId
isDeleted*	boolean
origin*	string	String representing the origin of the dataset. Examples include `direct-upload`, `nephele`, or `galaxy`. Min. length: 3 Max. length: 256 Inherits: string
created*	datetime	Timestamp of the creation of the dataset Inherits: datetime
inserted*	datetime
name*	string	User-provided name for the dataset. Min. length: 3 Max. length: 1024 Inherits: string
installTargets*	array	Unique items: Yes
installTargets[]	string	Name or ID of a target VEuPathDB project, such as "PlasmoDB". Min. length: 5 Max. length: 32 Inherits: string
status*	string
importMessages*	array
importMessages[]	string
visibility*	string	Enum: private protected public Inherits: string
summary*	string	Brief summary of the dataset. Min. length: 3 Max. length: 4000 Inherits: string
description	string	Longform description of the dataset. Inherits: string
syncControl	object	Inherits: lib.SyncControlRecord
syncControl.sharesUpdateTime*	datetime
syncControl.dataUpdateTime*	datetime
syncControl.metaUpdateTime*	datetime
uploadFiles	array
uploadFiles[]	string
installFiles	array
installFiles[]	string

Inherits: object

Model

Parameter	Type	Description
datasetUri*	string
sharesRecords*	boolean

Inherits: object

Model

Parameter	Type	Description
value	array	Unique items: Yes
value[]	object	Inherits: object
value[].datasetUri*	string
value[].sharesRecords*	boolean

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 too-early server-error Inherits: lib.ErrorType
message*	string

Examples

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

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 too-early server-error Inherits: lib.ErrorType
message*	string

Examples

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

Inherits: object

Model

Parameter	Type	Description
value	string

Inherits: object

Model

Parameter	Type	Description
value	object	Inherits: object
value.species*	string
value.strain*	string

Subset of the RFC3339 format, requiring at least the 4 digit year, and may include additional precision, part by part. Each part must be 'complete' and include standard preceding segment delimiters.

Date segments that are omitted will be defaulted to the minimum valid value for that segment. For example, If only the year value is provided, the assumed remainder is -01-01T00:00:00.000Z.

Examples:

2022
2022-03
2022-03-15
2022-03-15T16
2022-03-15T16:30
2022-03-15T16:30:12
2022-03-15T16:30:12Z
2022-03-15T16:30:12+04:00
2022-03-15T16:30:12.123Z
2022-03-15T16:30:12.123-06:00

Min. length: 4

Inherits: string

Inherits: object

Model

Parameter	Type	Description
pluginName*	string
type*	object	Details about a specific dataset type. Inherits: object
type.name*	string	Min. length: 3
type.version*	string	Min. length: 1
type.category*	string	Min. length: 3
maxFileSize*	integer	Format: int64
allowedFileExtensions*	array
allowedFileExtensions[]	string
installTargets	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.
installTargets[]	string	Name or ID of a target VEuPathDB project, such as "PlasmoDB". Min. length: 5 Max. length: 32 Inherits: string

Inherits: object

Model

Parameter	Type	Description
value	array	Unique items: Yes
value[] Dataset Publication	object	Inherits: object
value[].identifier*	string	Min. length: 3 Max. length: 30 Inherits: lib.DatasetPublicationIdentifier
value[].type	string	Default value: "pmid" Enum: pmid doi Inherits: lib.DatasetPublicationType
value[].citation	string	Min. length: 3 Max. length: 2000
value[].isPrimary	boolean	Only one publication may be marked as primary.

Inherits: object

Model

Parameter	Type	Description
enabled*	boolean
fullRunInterval*	string
slimRunInterval*	string
performDeletes*	boolean

Inherits: object

Model

Parameter	Type	Description
datasetId*	string	VDI dataset identifier Pattern: ^[a-zA-Z0-9_-]+$ Inherits: lib.VdiId
type*	object	Details about a specific dataset type. Inherits: object
type.name*	string	Min. length: 3
type.version*	string	Min. length: 1
type.category*	string	Min. length: 3
name*	string	User-provided name for the dataset. Min. length: 3 Max. length: 1024 Inherits: string
summary*	string	Brief summary of the dataset. Min. length: 3 Max. length: 4000 Inherits: string
created*	datetime	Timestamp of the creation of the dataset Inherits: datetime
relatedBy*	object	Discriminator: relationType Inherits: object
relatedBy.relationType*	string	Enum: publication program-name project-name Inherits: lib.ImplicitRelationType

Discriminator: relationType

Discriminator value: program-name

Inherits: lib.ImplicitRelation

Model

Parameter	Type	Description
relationType*	string	Enum: publication program-name project-name Inherits: lib.ImplicitRelationType

Discriminator: relationType

Discriminator value: project-name

Inherits: lib.ImplicitRelation

Model

Parameter	Type	Description
relationType*	string	Enum: publication program-name project-name Inherits: lib.ImplicitRelationType

Discriminator: relationType

Discriminator value: publication

Inherits: lib.ImplicitRelation

Model

Parameter

Type

Description

relationType*

string

Enum:

publication
program-name
project-name

Inherits: lib.ImplicitRelationType

identifier*

string

Min. length: 3

Max. length: 30

Inherits: string

type*

string

Default value: "pmid"

Enum:

pmid
doi

Inherits: string

Inherits: object

Model

Parameter	Type	Description
originalId*	string	VDI dataset identifier Pattern: ^[a-zA-Z0-9_-]+$ Inherits: lib.VdiId
revisions*	array
revisions[] Dataset Revision	object	Dataset revision history entry. Inherits: object
revisions[].action*	string	Enum: create extend revise Inherits: lib.DatasetRevisionAction
revisions[].timestamp*	datetime
revisions[].revisionId*	string	VDI dataset identifier Pattern: ^[a-zA-Z0-9_-]+$ Inherits: lib.VdiId
revisions[].revisionNote*	string	Note providing a reason and/or description for the revision. Min. length: 10 Max. length: 4096 Inherits: lib.DatasetRevisionNote
revisions[].fileListUrl*	string	URL to the file listing for the revision entry.

Inherits: object

Model

Parameter

Type

Description

start*

integer

Min. value: 1500

Max. value: 2500

Format: int16

end*

integer

Min. value: 1500

Max. value: 2500

Format: int16

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 too-early server-error Inherits: lib.ErrorType
message*	string
requestId*	string

Examples

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

Inherits: object

Model

Parameter	Type	Description
api*	object	Inherits: object
api.maxUploadSize*	integer	Format: int64
api.userMaxStorageSize*	integer	Format: int64
daemons*	object	Inherits: object
daemons.reconciler*	object	Inherits: lib.ReconcilerConfig
daemons.reconciler.enabled*	boolean
daemons.reconciler.fullRunInterval*	string
daemons.reconciler.slimRunInterval*	string
daemons.reconciler.performDeletes*	boolean

Inherits: object

Model

Parameter	Type	Description
supportedArchiveTypes*	array
supportedArchiveTypes[]	string

Inherits: object

Model

Parameter	Type	Description
gitTag*	string
gitCommit*	string
gitBranch*	string
gitUrl*	string
buildId*	string
buildNumber*	string
buildTime*	string

Inherits: object

Model

Parameter	Type	Description
buildInfo*	object	Inherits: object
buildInfo.gitTag*	string
buildInfo.gitCommit*	string
buildInfo.gitBranch*	string
buildInfo.gitUrl*	string
buildInfo.buildId*	string
buildInfo.buildNumber*	string
buildInfo.buildTime*	string
configuration*	object	Inherits: object
configuration.api*	object	Inherits: object
configuration.api.maxUploadSize*	integer	Format: int64
configuration.api.userMaxStorageSize*	integer	Format: int64
configuration.daemons*	object	Inherits: object
configuration.daemons.reconciler*	object	Inherits: lib.ReconcilerConfig
configuration.daemons.reconciler.enabled*	boolean
configuration.daemons.reconciler.fullRunInterval*	string
configuration.daemons.reconciler.slimRunInterval*	string
configuration.daemons.reconciler.performDeletes*	boolean
features*	object	Inherits: object
features.supportedArchiveTypes*	array
features.supportedArchiveTypes[]	string

Inherits: object

Model

Parameter	Type	Description
recipient*	object	Inherits: lib.ShareOfferRecipient
recipient.userId*	integer	VEuPathDB User ID Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: lib.UserId
recipient.firstName	string
recipient.lastName	string
recipient.affiliation	string
recipient.email	string
status*	string	Enum: grant revoke Inherits: lib.ShareOfferAction

Enum:

grant
revoke

Inherits: string

Inherits: object

Model

Parameter	Type	Description
datasetId*	string	VDI dataset identifier Pattern: ^[a-zA-Z0-9_-]+$ Inherits: lib.VdiId
owner*	object	Details about the owner of a VDI dataset. Inherits: object
owner.userId*	integer	VEuPathDB User ID Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: lib.UserId
owner.firstName	string
owner.lastName	string
owner.email	string
owner.affiliation	string
shareStatus*	string	Enum: open accepted rejected Inherits: lib.ShareOfferStatus
type*	object	Details about a specific dataset type. Inherits: object
type.name*	string	Min. length: 3
type.version*	string	Min. length: 1
type.category*	string	Min. length: 3
installTargets*	array	Unique items: Yes
installTargets[]	string	Name or ID of a target VEuPathDB project, such as "PlasmoDB". Min. length: 5 Max. length: 32 Inherits: string

Inherits: object

Model

Parameter	Type	Description
userId*	integer	VEuPathDB User ID Min. value: 1 Max. value: 9223372036854776000 Format: int64 Inherits: lib.UserId
firstName	string
lastName	string
affiliation	string
email	string

Enum:

open
accepted
rejected

Inherits: string

Enum:

accept
reject

Inherits: string

Min. length: 3

Max. length: 40

Inherits: string

Min. length: 3

Max. length: 20

Inherits: string

Inherits: object

Model

Parameter	Type	Description
value*	string

Inherits: object

Model

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

Discriminator: status

Discriminator value: too-early

Inherits: lib.Error

Model

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

Examples

{
  "status": "too-early",
  "message": "The requested resource is not yet available."
}

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 too-early server-error Inherits: lib.ErrorType
message*	string

Examples

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

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 too-early 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."
      ]
    }
  }
}

VEuPathDB User ID

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: integer

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

VDI dataset identifier

Pattern: ^[a-zA-Z0-9_-]+$

Inherits: string

If present, the only valid action is replace.

Inherits: object

Model

Parameter	Type	Description
value	string	Enum: private protected public Inherits: string

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 v1.7.0

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200 OK chevron_right expand_more

400 Bad Request chevron_right expand_more

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422 Unprocessable Entity chevron_right expand_more

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424 Failed Dependency chevron_right expand_more

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500 Internal Server Error chevron_right expand_more

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404 Not Found chevron_right expand_more

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425 chevron_right expand_more

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204 No Content chevron_right expand_more

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200 OK chevron_right expand_more

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Parameters

200 OK

400 Bad Request

401 Unauthorized

500 Internal Server Error

Request Body

202 Accepted

400 Bad Request

401 Unauthorized

422 Unprocessable Entity

424 Failed Dependency

500 Internal Server Error

Parameters

200 OK

301 Moved Permanently

401 Unauthorized

404 Not Found

425

500 Internal Server Error

Parameters

Request Body

204 No Content

400 Bad Request

401 Unauthorized

403 Forbidden

404 Not Found

422 Unprocessable Entity

500 Internal Server Error

Parameters

Request Body

202 Accepted

400 Bad Request

401 Unauthorized

403 Forbidden

404 Not Found

422 Unprocessable Entity

500 Internal Server Error

Parameters

204 No Content

401 Unauthorized

403 Forbidden

404 Not Found

500 Internal Server Error

Parameters

200 OK

401 Unauthorized

404 Not Found

500 Internal Server Error

Parameters

200 OK

401 Unauthorized

404 Not Found

500 Internal Server Error

Parameters