VEuPathDB Dataset Installer v1.0.0

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Resources

get /vdi-datasets

List Datasets  

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 chevron_right expand_more

ParameterTypeDescription
Query
project_id Project IDstring

ID of the VEuPathDB project that results should be filtered to.

This means only datasets that are relevant to the project ID given will be returned.

Additionally, this controls the sites on which the dataset installation status will be checked. Meaning, if this parameter is specified and set to, for example, PlasmoDB, the status block in the response objects will only include installation status details for PlasmoDB and not any other sites that the dataset may have been installed into.

Inherits: string

ownership Dataset Ownership Filterstring

Ownership status filter.

Enum of:

  • any
  • owned
  • shared

If set to any the results are not filtered.

If set to owned, the results will be filtered to only results that are owned by the requesting user.

If set to shared, the results will be filtered to only results that are shared with the requesting user.

Default value: "any"

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

200 OK chevron_right expand_more

Success.

This response means that all checks passed and zero or more dataset records were found for the requesting user.

application/json

application/json

ParameterTypeDescription
[] Dataset List Itemobject

Short entry with basic details about a dataset.

Inherits: object

[].datasetId* Dataset IDstring

Unique VDI Dataset identifier string.

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

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

[].owner* Owner Detailsobject

Details about the owner of a VDI dataset.

Inherits: lib.DatasetOwner

[].owner.userId* Owner User IDinteger

VEuPathDB user ID of the owner of the dataset.

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

[].owner.firstName Owner First Namestring
[].owner.lastName Owner Last Namestring
[].owner.email Owner Emailstring
[].owner.organization Owner Organizationstring
[].datasetType* Dataset Typeobject

Information about a specific dataset type.

Inherits: lib.DatasetTypeInfo

[].datasetType.name* Type Namestring
[].datasetType.displayName Type Display Namestring

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

[].datasetType.version* Type Versionstring
[].visibility* Dataset Visibilitystring
Enum:
  • private
  • protected
  • public

Inherits: lib.DatasetVisibility

[].name* Dataset Namestring

User provided name for the dataset.

[].summary Dataset Summarystring

User provided summary of the dataset.

[].description Dataset Descriptionstring

User provided description of the dataset.

[].sourceUrl Source URLstring

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

[].origin* Dataset Originstring

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

[].projectIds* Project IDsarray

Project IDs for projects the dataset record was submitted to.

[].projectIds[] Project IDstring

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: lib.ProjectID

[].status* Status Infoobject

Information about the import and install status of a dataset.

Inherits: lib.DatasetStatusInfo

[].status.import*string

Import status of the dataset.

ValueDescription
queuedThe dataset has not yet been processed and is waiting in the queue.
in-progressThe dataset is currently being import processed.
completeThe dataset has been processed and imported for installation.
invalidThe dataset failed import validation.
failedThe dataset import failed due to an internal server error.
Enum:
  • queued
  • in-progress
  • complete
  • invalid
  • failed

Inherits: lib.DatasetImportStatus

[].status.installarray
[].status.install[] Dataset Install Status Entryobject

Entry in a list of install statuses for a dataset.

Inherits: lib.DatasetInstallStatusEntry

[].status.install[].projectId*string

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: lib.ProjectID

[].status.install[].metaStatusstring
Enum:
  • running
  • complete
  • failed-validation
  • failed-installation
  • ready-for-reinstall
  • missing-dependency

Inherits: lib.DatasetInstallStatus

[].status.install[].metaMessagestring
[].status.install[].dataStatusstring
Enum:
  • running
  • complete
  • failed-validation
  • failed-installation
  • ready-for-reinstall
  • missing-dependency

Inherits: lib.DatasetInstallStatus

[].status.install[].dataMessagestring
[].shares* Shared Witharray
[].shares[]object

Inherits: object

[].shares[].userId*integer

Unique user identifier

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

[].shares[].firstName*string
[].shares[].lastName*string
[].shares[].organization*string
[].shares[].accepted*boolean
[].fileCount* File Countinteger

Number of files uploaded for this dataset.

[].fileSizeTotal* File Size Totalinteger

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

Format: int64

[].created* Creation Timestampdatetime

Timestamp of the creation of this dataset.

Response Body

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

400 Bad Request chevron_right expand_more

Bad Request.

One or more request query parameters were not valid.

Bad Request BadRequestError

application/json

Request could not be parsed or was otherwise unusable.

Discriminator: status

Discriminator value: bad-request

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

401 Unauthorized chevron_right expand_more

Unauthorized.

This status is returned when the request contains either no user authorization token or an invalid user authorization token.

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

500 Internal Server Error chevron_right expand_more

Internal Server Error.

This status is returned when an unhandled or unexpected issue arises when attempting to process the request.

Internal Server Error ServerError

application/json

Discriminator: status

Discriminator value: server-error

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • 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"
+}

post /vdi-datasets

Upload Dataset  

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

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

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

The file field may be one of:

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

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

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

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

Request Body chevron_right expand_more

Dataset Post Request DatasetPostRequest

multipart/form-data

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

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

Inherits: object

ParameterTypeDescription
meta* Dataset Metaobject

Metadata about the dataset being submitted.

Inherits: lib.DatasetPostMeta

meta.datasetType* Dataset Typeobject

Type of the dataset that is being uploaded.

Inherits: lib.DatasetPostType

meta.datasetType.name*string
meta.datasetType.version*string
meta.name* Dataset Namestring

User provided name for the dataset.

meta.visibility Dataset Visibilitystring

Default value: "private"

Enum:
  • private
  • protected
  • public

Inherits: lib.DatasetVisibility

meta.summary Dataset Summarystring

User provided summary for the dataset.

meta.description Dataset Descriptionstring

User provided description for the dataset.

meta.origin* Dataset Originstring

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

meta.projects* Project IDsarray

IDs of the projects this dataset is being submitted to.

meta.projects[] Project IDstring

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: lib.ProjectID

meta.dependencies* Dataset Dependenciesarray
meta.dependencies[]object

Inherits: lib.DatasetDependency

meta.dependencies[].resourceIdentifier*string
meta.dependencies[].resourceDisplayName*string
meta.dependencies[].resourceVersion*string
meta.createdOn Creation Datedatetime-only
file Dataset Filefile

Dataset file to upload.

This field is incompatible with the url field.

url Dataset URLstring

URL to a dataset file to upload.

This field is incompatible with the file field.

200 OK chevron_right expand_more

Success

Dataset Upload Response DatasetPostResponse

application/json

Response object returned on successful upload of a dataset.

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

Inherits: object

ParameterTypeDescription
datasetId*string

Unique VDI Dataset identifier string.

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

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

Response Body

{
+  "datasetId": "zaZqAAGLGJhBgg"
+}

400 Bad Request chevron_right expand_more

Bad Request.

Request body did not resemble the expected JSON form.

Bad Request BadRequestError

application/json

Request could not be parsed or was otherwise unusable.

Discriminator: status

Discriminator value: bad-request

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

401 Unauthorized chevron_right expand_more

Unauthorized.

This status is returned when the request contains either no user authorization token or an invalid user authorization token.

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

422 Unprocessable Entity chevron_right expand_more

Unprocessable Entity.

Request body was syntactically valid JSON, however the body failed validation.

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

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • 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."
+      ]
+    }
+  }
+}

500 Internal Server Error chevron_right expand_more

Internal Server Error.

This status is returned when an unhandled or unexpected issue arises when attempting to process the request.

Internal Server Error ServerError

application/json

Discriminator: status

Discriminator value: server-error

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • 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"
+}

post /vdi-datasets/admin/proxy-upload

 

Upload a dataset on behalf of another user.

Headers chevron_right expand_more

ParameterTypeDescription
User-ID* VEuPathDB User IDinteger

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

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: integer

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

Request Body chevron_right expand_more

Dataset Post Request DatasetPostRequest

multipart/form-data

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

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

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

Inherits: object

ParameterTypeDescription
meta* Dataset Metaobject

Metadata about the dataset being submitted.

Inherits: lib.DatasetPostMeta

meta.datasetType* Dataset Typeobject

Type of the dataset that is being uploaded.

Inherits: lib.DatasetPostType

meta.datasetType.name*string
meta.datasetType.version*string
meta.name* Dataset Namestring

User provided name for the dataset.

meta.visibility Dataset Visibilitystring

Default value: "private"

Enum:
  • private
  • protected
  • public

Inherits: lib.DatasetVisibility

meta.summary Dataset Summarystring

User provided summary for the dataset.

meta.description Dataset Descriptionstring

User provided description for the dataset.

meta.origin* Dataset Originstring

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

meta.projects* Project IDsarray

IDs of the projects this dataset is being submitted to.

meta.projects[] Project IDstring

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: lib.ProjectID

meta.dependencies* Dataset Dependenciesarray
meta.dependencies[]object

Inherits: lib.DatasetDependency

meta.dependencies[].resourceIdentifier*string
meta.dependencies[].resourceDisplayName*string
meta.dependencies[].resourceVersion*string
meta.createdOn Creation Datedatetime-only
file Dataset Filefile

Dataset file to upload.

This field is incompatible with the url field.

url Dataset URLstring

URL to a dataset file to upload.

This field is incompatible with the file field.

200 OK chevron_right expand_more

Success

Dataset Upload Response DatasetPostResponse

application/json

Response object returned on successful upload of a dataset.

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

Inherits: object

ParameterTypeDescription
datasetId*string

Unique VDI Dataset identifier string.

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

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

Response Body

{
+  "datasetId": "zaZqAAGLGJhBgg"
+}

400 Bad Request chevron_right expand_more

Bad Request.

Request body did not resemble the expected JSON form.

Bad Request BadRequestError

application/json

Request could not be parsed or was otherwise unusable.

Discriminator: status

Discriminator value: bad-request

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

401 Unauthorized chevron_right expand_more

Unauthorized

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

403 Forbidden chevron_right expand_more

Forbidden

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

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

422 Unprocessable Entity chevron_right expand_more

Unprocessable Entity.

Request body was syntactically valid JSON, however the body failed validation.

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

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • 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."
+      ]
+    }
+  }
+}

500 Internal Server Error chevron_right expand_more

Internal Server Error.

This status is returned when an unhandled or unexpected issue arises when attempting to process the request.

Internal Server Error ServerError

application/json

Discriminator: status

Discriminator value: server-error

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • 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"
+}

get /vdi-datasets/admin/failed-imports

List  

Lists datasets that failed to import.

Parameters chevron_right expand_more

ParameterTypeDescription
Query
user VEuPathDB User IDinteger

Unique user identifier

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: integer

beforestring

Filter results to only those records created before the given date-time value.

Examples:

  • 2023
  • 2023-10
  • 2023-10-02
  • 2023-10-02T17:10
  • 2023-10-02T17:10:00
  • 2023-10-02T17:10:00.000
  • 2023-10-02T17:10:00.000Z

If no timezone is provided, the service will assume its local zone.

afterstring

Filter results to only those records created after the given date-time value.

Examples:

  • 2023
  • 2023-10
  • 2023-10-02
  • 2023-10-02T17:10
  • 2023-10-02T17:10:00
  • 2023-10-02T17:10:00.000
  • 2023-10-02T17:10:00.000Z

If no timezone is provided, the service will assume its local zone.

limitinteger

Max. value: 250

Default value: 100

offsetinteger
sortstring

One of:

  • date

Default value: "date"

orderstring

One of:

  • asc
  • desc

Default value: "desc"

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

200 OK chevron_right expand_more

Broken Import Listing BrokenImportListing

application/json

Inherits: object

ParameterTypeDescription
meta*object

Inherits: lib.BrokenImportListingMeta

meta.count*integer
meta.beforestring
meta.afterstring
meta.userinteger

Unique user identifier

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

meta.limitinteger
meta.offsetinteger
results*array
results[] Broken Import Detailsobject

Inherits: lib.BrokenImportDetails

results[].datasetId*string

Unique VDI Dataset identifier string.

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

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

results[].owner*integer

Unique user identifier

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

results[].datasetType*object

Information about a specific dataset type.

Inherits: lib.DatasetTypeInfo

results[].datasetType.name* Type Namestring
results[].datasetType.displayName Type Display Namestring

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

results[].datasetType.version* Type Versionstring
results[].projectIds*array
results[].projectIds[] Project IDstring

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: lib.ProjectID

results[].messages*array
results[].messages[]string

get /vdi-datasets/admin/list-broken

List Broken Installs  

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

Parameters chevron_right expand_more

ParameterTypeDescription
Query
expanded Expanded Dataset Listboolean

Whether the returned broken dataset install list should be expanded to include additional details about each dataset or should be just a simple list of dataset IDs.

Default value: true

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

200 OK chevron_right expand_more

Success.

Broken dataset install list successfully generated.

Broken Dataset Listing BrokenDatasetListing

application/json

Inherits: object

ParameterTypeDescription
detailsarray
details[] Broken Dataset Detailsobject

Inherits: lib.BrokenDatasetDetails

details[].datasetId*string

Unique VDI Dataset identifier string.

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

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

details[].owner*integer

Unique user identifier

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

details[].datasetType*object

Information about a specific dataset type.

Inherits: lib.DatasetTypeInfo

details[].datasetType.name* Type Namestring
details[].datasetType.displayName Type Display Namestring

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

details[].datasetType.version* Type Versionstring
details[].projectIds*array
details[].projectIds[] Project IDstring

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: lib.ProjectID

details[].status*object

Information about the import and install status of a dataset.

Inherits: lib.DatasetStatusInfo

details[].status.import*string

Import status of the dataset.

ValueDescription
queuedThe dataset has not yet been processed and is waiting in the queue.
in-progressThe dataset is currently being import processed.
completeThe dataset has been processed and imported for installation.
invalidThe dataset failed import validation.
failedThe dataset import failed due to an internal server error.
Enum:
  • queued
  • in-progress
  • complete
  • invalid
  • failed

Inherits: lib.DatasetImportStatus

details[].status.installarray
details[].status.install[] Dataset Install Status Entryobject

Entry in a list of install statuses for a dataset.

Inherits: lib.DatasetInstallStatusEntry

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

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: lib.ProjectID

details[].status.install[].metaStatusstring
Enum:
  • running
  • complete
  • failed-validation
  • failed-installation
  • ready-for-reinstall
  • missing-dependency

Inherits: lib.DatasetInstallStatus

details[].status.install[].metaMessagestring
details[].status.install[].dataStatusstring
Enum:
  • running
  • complete
  • failed-validation
  • failed-installation
  • ready-for-reinstall
  • missing-dependency

Inherits: lib.DatasetInstallStatus

details[].status.install[].dataMessagestring
idsarray
ids[] VDI IDstring

Unique VDI Dataset identifier string.

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

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

401 Unauthorized chevron_right expand_more

Unauthorized

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

500 Internal Server Error chevron_right expand_more

Internal Server Error

Internal Server Error ServerError

application/json

Discriminator: status

Discriminator value: server-error

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • 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"
+}

post /vdi-datasets/admin/install-cleanup

Run Install Cleanup  

Marks all or target datasets that are in a status of installation failure into a ready-for-reinstall 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.

curl -X POST \
+  -H "Content-type: application/json"
+  -d @body.json \
+  undefined/vdi-datasets/admin/install-cleanup

Request Body chevron_right expand_more

Install Cleanup Request InstallCleanupRequest

application/json

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

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

Inherits: object

ParameterTypeDescription
allboolean
targetsarray

Unique items: Yes

targets[] Install Cleanup Targetobject

Inherits: lib.InstallCleanupTarget

targets[].datasetId*string

Unique VDI Dataset identifier string.

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

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

targets[].projectId*string

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: lib.ProjectID

Request Body

All Example

{
+  "all": true
+}

Target Example

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

204 No Content chevron_right expand_more

Success.

Dataset install cleanup process completed successfully.

400 Bad Request chevron_right expand_more

Bad Request.

Request body did not resemble the expected JSON form.

Bad Request BadRequestError

application/json

Request could not be parsed or was otherwise unusable.

Discriminator: status

Discriminator value: bad-request

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

401 Unauthorized chevron_right expand_more

Unauthorized.

This status is returned when the request contains either no user authorization token or an invalid user authorization token.

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

500 Internal Server Error chevron_right expand_more

Internal Server Error.

This status is returned when an unhandled or unexpected issue arises when attempting to process the request.

Internal Server Error ServerError

application/json

Discriminator: status

Discriminator value: server-error

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • 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"
+}

post /vdi-datasets/admin/delete-cleanup

Run Deleted Dataset Cleanup  

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

curl -X POST \
+  undefined/vdi-datasets/admin/delete-cleanup

204 No Content chevron_right expand_more

Action completed successfully.

400 Bad Request chevron_right expand_more

Bad Request.

Request body did not resemble the expected JSON form.

Bad Request BadRequestError

application/json

Request could not be parsed or was otherwise unusable.

Discriminator: status

Discriminator value: bad-request

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

401 Unauthorized chevron_right expand_more

Unauthorized.

This status is returned when the request contains either no user authorization token or an invalid user authorization token.

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

500 Internal Server Error chevron_right expand_more

Internal Server Error.

This status is returned when an unhandled or unexpected issue arises when attempting to process the request.

Internal Server Error ServerError

application/json

Discriminator: status

Discriminator value: server-error

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • 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"
+}

get /vdi-datasets/admin/list-all-datasets

 

Parameters chevron_right expand_more

ParameterTypeDescription
Query
offsetinteger
limitinteger

Min. value: 1

Default value: 100

projectIdstring

Optionally filter the results to only datasets that target the given project ID.

curl -X GET \
+  undefined/vdi-datasets/admin/list-all-datasets?offset=<value>&limit=<value>&projectId=<value>

200 OK chevron_right expand_more

All Datasets Listing Response AllDatasetsListResponse

application/json

Inherits: object

ParameterTypeDescription
meta*object

Inherits: lib.AllDatasetsListMeta

meta.count*integer
meta.offset*integer
meta.limit*integer
meta.total*integer
results*array
results[]object

Inherits: lib.AllDatasetsListEntry

results[].datasetId*string

Unique VDI Dataset identifier string.

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

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

results[].owner*integer

Unique user identifier

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

results[].datasetType*object

Information about a specific dataset type.

Inherits: lib.DatasetTypeInfo

results[].datasetType.name* Type Namestring
results[].datasetType.displayName Type Display Namestring

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

results[].datasetType.version* Type Versionstring
results[].visibility*string
Enum:
  • private
  • protected
  • public

Inherits: lib.DatasetVisibility

results[].name*string
results[].summarystring
results[].descriptionstring
results[].sourceUrlstring
results[].origin*string
results[].projectIds*array
results[].projectIds[] Project IDstring

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: lib.ProjectID

results[].status*object

Information about the import and install status of a dataset.

Inherits: lib.DatasetStatusInfo

results[].status.import*string

Import status of the dataset.

ValueDescription
queuedThe dataset has not yet been processed and is waiting in the queue.
in-progressThe dataset is currently being import processed.
completeThe dataset has been processed and imported for installation.
invalidThe dataset failed import validation.
failedThe dataset import failed due to an internal server error.
Enum:
  • queued
  • in-progress
  • complete
  • invalid
  • failed

Inherits: lib.DatasetImportStatus

results[].status.installarray
results[].status.install[] Dataset Install Status Entryobject

Entry in a list of install statuses for a dataset.

Inherits: lib.DatasetInstallStatusEntry

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

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: lib.ProjectID

results[].status.install[].metaStatusstring
Enum:
  • running
  • complete
  • failed-validation
  • failed-installation
  • ready-for-reinstall
  • missing-dependency

Inherits: lib.DatasetInstallStatus

results[].status.install[].metaMessagestring
results[].status.install[].dataStatusstring
Enum:
  • running
  • complete
  • failed-validation
  • failed-installation
  • ready-for-reinstall
  • missing-dependency

Inherits: lib.DatasetInstallStatus

results[].status.install[].dataMessagestring
results[].created*datetime

get /vdi-datasets/community

List Community Datasets  

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

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

200 OK chevron_right expand_more

Success

application/json

application/json

ParameterTypeDescription
[] Dataset List Itemobject

Short entry with basic details about a dataset.

Inherits: object

[].datasetId* Dataset IDstring

Unique VDI Dataset identifier string.

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

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

[].owner* Owner Detailsobject

Details about the owner of a VDI dataset.

Inherits: lib.DatasetOwner

[].owner.userId* Owner User IDinteger

VEuPathDB user ID of the owner of the dataset.

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

[].owner.firstName Owner First Namestring
[].owner.lastName Owner Last Namestring
[].owner.email Owner Emailstring
[].owner.organization Owner Organizationstring
[].datasetType* Dataset Typeobject

Information about a specific dataset type.

Inherits: lib.DatasetTypeInfo

[].datasetType.name* Type Namestring
[].datasetType.displayName Type Display Namestring

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

[].datasetType.version* Type Versionstring
[].visibility* Dataset Visibilitystring
Enum:
  • private
  • protected
  • public

Inherits: lib.DatasetVisibility

[].name* Dataset Namestring

User provided name for the dataset.

[].summary Dataset Summarystring

User provided summary of the dataset.

[].description Dataset Descriptionstring

User provided description of the dataset.

[].sourceUrl Source URLstring

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

[].origin* Dataset Originstring

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

[].projectIds* Project IDsarray

Project IDs for projects the dataset record was submitted to.

[].projectIds[] Project IDstring

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: lib.ProjectID

[].status* Status Infoobject

Information about the import and install status of a dataset.

Inherits: lib.DatasetStatusInfo

[].status.import*string

Import status of the dataset.

ValueDescription
queuedThe dataset has not yet been processed and is waiting in the queue.
in-progressThe dataset is currently being import processed.
completeThe dataset has been processed and imported for installation.
invalidThe dataset failed import validation.
failedThe dataset import failed due to an internal server error.
Enum:
  • queued
  • in-progress
  • complete
  • invalid
  • failed

Inherits: lib.DatasetImportStatus

[].status.installarray
[].status.install[] Dataset Install Status Entryobject

Entry in a list of install statuses for a dataset.

Inherits: lib.DatasetInstallStatusEntry

[].status.install[].projectId*string

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: lib.ProjectID

[].status.install[].metaStatusstring
Enum:
  • running
  • complete
  • failed-validation
  • failed-installation
  • ready-for-reinstall
  • missing-dependency

Inherits: lib.DatasetInstallStatus

[].status.install[].metaMessagestring
[].status.install[].dataStatusstring
Enum:
  • running
  • complete
  • failed-validation
  • failed-installation
  • ready-for-reinstall
  • missing-dependency

Inherits: lib.DatasetInstallStatus

[].status.install[].dataMessagestring
[].shares* Shared Witharray
[].shares[]object

Inherits: object

[].shares[].userId*integer

Unique user identifier

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

[].shares[].firstName*string
[].shares[].lastName*string
[].shares[].organization*string
[].shares[].accepted*boolean
[].fileCount* File Countinteger

Number of files uploaded for this dataset.

[].fileSizeTotal* File Size Totalinteger

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

Format: int64

[].created* Creation Timestampdatetime

Timestamp of the creation of this dataset.

401 Unauthorized chevron_right expand_more

Unauthorized.

This status is returned when the request contains either no user authorization token or an invalid user authorization token.

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

500 Internal Server Error chevron_right expand_more

Internal Server Error.

This status is returned when an unhandled or unexpected issue arises when attempting to process the request.

Internal Server Error ServerError

application/json

Discriminator: status

Discriminator value: server-error

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • 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"
+}

get /vdi-datasets/{vd-id}

Lookup Dataset  

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 chevron_right expand_more

ParameterTypeDescription
Path
vd-id* VDI IDstring

Unique VDI Dataset identifier string.

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

Min. length: 14

Max. length: 14

Inherits: string

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

200 OK chevron_right expand_more

Target dataset was located and returned.

Dataset Details DatasetDetails

application/json

Details about a specific singular dataset.

Inherits: object

ParameterTypeDescription
datasetId* Dataset IDstring

Unique VDI Dataset identifier string.

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

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

owner* Owner Detailsobject

Details about the owner of a VDI dataset.

Inherits: lib.DatasetOwner

owner.userId* Owner User IDinteger

VEuPathDB user ID of the owner of the dataset.

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

owner.firstName Owner First Namestring
owner.lastName Owner Last Namestring
owner.email Owner Emailstring
owner.organization Owner Organizationstring
datasetType* Dataset Type Infoobject

Information about a specific dataset type.

Inherits: lib.DatasetTypeInfo

datasetType.name* Type Namestring
datasetType.displayName Type Display Namestring

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

datasetType.version* Type Versionstring
name* Dataset Namestring
summary Dataset Summarystring
description Dataset Descriptionstring
sourceUrl Source URLstring

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

origin* Dataset Originstring

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

projectIds* Project IDsarray

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

projectIds[] Project IDstring

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: lib.ProjectID

visibility* Dataset Visibilitystring
Enum:
  • private
  • protected
  • public

Inherits: lib.DatasetVisibility

importMessages Import Messagesarray

Log lines from the import process.

These messages will be warnings and/or validation errors.

Default value: []

importMessages[]string
status* Dataset Status Infoobject

Information about the import and install status of a dataset.

Inherits: lib.DatasetStatusInfo

status.import*string

Import status of the dataset.

ValueDescription
queuedThe dataset has not yet been processed and is waiting in the queue.
in-progressThe dataset is currently being import processed.
completeThe dataset has been processed and imported for installation.
invalidThe dataset failed import validation.
failedThe dataset import failed due to an internal server error.
Enum:
  • queued
  • in-progress
  • complete
  • invalid
  • failed

Inherits: lib.DatasetImportStatus

status.installarray
status.install[] Dataset Install Status Entryobject

Entry in a list of install statuses for a dataset.

Inherits: lib.DatasetInstallStatusEntry

status.install[].projectId*string

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: lib.ProjectID

status.install[].metaStatusstring
Enum:
  • running
  • complete
  • failed-validation
  • failed-installation
  • ready-for-reinstall
  • missing-dependency

Inherits: lib.DatasetInstallStatus

status.install[].metaMessagestring
status.install[].dataStatusstring
Enum:
  • running
  • complete
  • failed-validation
  • failed-installation
  • ready-for-reinstall
  • missing-dependency

Inherits: lib.DatasetInstallStatus

status.install[].dataMessagestring
shares Sharesarray

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

shares[] Share Offerobject

Inherits: lib.ShareOffer

shares[].recipient*object

I AM A UNION!

Inherits: lib.ShareOfferRecipient

shares[].recipient.userId* User IDinteger

Format: int64

shares[].recipient.firstName First Namestring
shares[].recipient.lastName Last Namestring
shares[].recipient.organization Organizationstring
shares[].recipient.email Emailstring
shares[].status*string
Enum:
  • grant
  • revoke

Inherits: lib.ShareOfferAction

created* Creation Timestampdatetime

Timestamp for when this dataset was created.

dependencies* Dataset Dependenciesarray
dependencies[]object

Inherits: lib.DatasetDependency

dependencies[].resourceIdentifier*string
dependencies[].resourceDisplayName*string
dependencies[].resourceVersion*string

Response Body

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

401 Unauthorized chevron_right expand_more

Unauthorized.

This status is returned when the request contains either no user authorization token or an invalid user authorization token.

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

404 Not Found chevron_right expand_more

Target dataset was not located or is not visible to the requesting user.

Not Found NotFoundError

application/json

The requested resource was not found on this server.

Discriminator: status

Discriminator value: not-found

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

500 Internal Server Error chevron_right expand_more

Internal Server Error.

This status is returned when an unhandled or unexpected issue arises when attempting to process the request.

Internal Server Error ServerError

application/json

Discriminator: status

Discriminator value: server-error

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • 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"
+}

patch /vdi-datasets/{vd-id}

Update Dataset  

Updates the metadata for a target dataset.

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

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

Parameters chevron_right expand_more

ParameterTypeDescription
Path
vd-id* VDI IDstring

Unique VDI Dataset identifier string.

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

Min. length: 14

Max. length: 14

Inherits: string

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

Request Body chevron_right expand_more

Dataset Patch Request DatasetPatchRequest

application/json

Request to update the metadata for a dataset.

Inherits: object

ParameterTypeDescription
visibility Dataset Visibilitystring
Enum:
  • private
  • protected
  • public

Inherits: lib.DatasetVisibility

name Dataset Namestring

User provided name for a dataset.

summary Dataset Summarystring

User provided summary for a dataset.

description Dataset Descriptionstring

User provided description for a dataset.

Request Body

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

204 No Content chevron_right expand_more

Target dataset metadata was updated.

400 Bad Request chevron_right expand_more

Bad Request.

Request body did not resemble the expected JSON form.

Bad Request BadRequestError

application/json

Request could not be parsed or was otherwise unusable.

Discriminator: status

Discriminator value: bad-request

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

401 Unauthorized chevron_right expand_more

Unauthorized.

This status is returned when the request contains either no user authorization token or an invalid user authorization token.

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

403 Forbidden chevron_right expand_more

Action Forbidden.

Target dataset is not owned by the requesting user.

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

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

404 Not Found chevron_right expand_more

Target dataset was not found.

Not Found NotFoundError

application/json

The requested resource was not found on this server.

Discriminator: status

Discriminator value: not-found

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

422 Unprocessable Entity chevron_right expand_more

Unprocessable Entity.

Request body was syntactically valid JSON, however the body failed validation.

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

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • 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."
+      ]
+    }
+  }
+}

425 chevron_right expand_more

Too Early.

Patch request was submitted before the dataset data was written to the dataset store.

500 Internal Server Error chevron_right expand_more

Internal Server Error.

This status is returned when an unhandled or unexpected issue arises when attempting to process the request.

Internal Server Error ServerError

application/json

Discriminator: status

Discriminator value: server-error

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • 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"
+}

delete /vdi-datasets/{vd-id}

Delete Dataset  

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 chevron_right expand_more

ParameterTypeDescription
Path
vd-id* VDI IDstring

Unique VDI Dataset identifier string.

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

Min. length: 14

Max. length: 14

Inherits: string

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

204 No Content chevron_right expand_more

Target dataset was marked as deleted.

401 Unauthorized chevron_right expand_more

Unauthorized.

This status is returned when the request contains either no user authorization token or an invalid user authorization token.

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

403 Forbidden chevron_right expand_more

Action Forbidden.

Target dataset is not owned by the requesting user.

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

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

404 Not Found chevron_right expand_more

Target dataset was not located.

Not Found NotFoundError

application/json

The requested resource was not found on this server.

Discriminator: status

Discriminator value: not-found

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

500 Internal Server Error chevron_right expand_more

Internal Server Error.

This status is returned when an unhandled or unexpected issue arises when attempting to process the request.

Internal Server Error ServerError

application/json

Discriminator: status

Discriminator value: server-error

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • 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"
+}

get /vdi-datasets/{vd-id}/files

List Files  

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 chevron_right expand_more

ParameterTypeDescription
Path
vd-id* VDI IDstring

Unique VDI Dataset identifier string.

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

Min. length: 14

Max. length: 14

Inherits: string

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

200 OK chevron_right expand_more

Success

Dataset File Listing DatasetFileListing

application/json

Inherits: object

ParameterTypeDescription
upload*object

Inherits: lib.DatasetZipDetails

upload.zipSize*integer

Format: int64

upload.contents*array
upload.contents[] Dataset File Detailsobject

Inherits: lib.DatasetFileDetails

upload.contents[].fileName* File Namestring
upload.contents[].fileSize* File Sizeinteger

Size of the file in bytes.

Format: int64

installobject

Inherits: lib.DatasetZipDetails

install.zipSize*integer

Format: int64

install.contents*array
install.contents[] Dataset File Detailsobject

Inherits: lib.DatasetFileDetails

install.contents[].fileName* File Namestring
install.contents[].fileSize* File Sizeinteger

Size of the file in bytes.

Format: int64

401 Unauthorized chevron_right expand_more

Unauthorized

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

404 Not Found chevron_right expand_more

Not Found

Not Found NotFoundError

application/json

The requested resource was not found on this server.

Discriminator: status

Discriminator value: not-found

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

500 Internal Server Error chevron_right expand_more

Internal Server Error

Internal Server Error ServerError

application/json

Discriminator: status

Discriminator value: server-error

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • 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 /vdi-datasets/{vd-id}/files/upload

Get Upload Zip File  

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

Parameters chevron_right expand_more

ParameterTypeDescription
Path
vd-id* VDI IDstring

Unique VDI Dataset identifier string.

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

Min. length: 14

Max. length: 14

Inherits: string

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

200 OK chevron_right expand_more

Success

Headers

ParameterTypeDescription
Content-Disposition*string

application/octet-stream

application/octet-stream

401 Unauthorized chevron_right expand_more

Unauthorized

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

404 Not Found chevron_right expand_more

Not Found

Not Found NotFoundError

application/json

The requested resource was not found on this server.

Discriminator: status

Discriminator value: not-found

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

500 Internal Server Error chevron_right expand_more

Internal Server Error

Internal Server Error ServerError

application/json

Discriminator: status

Discriminator value: server-error

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • 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 /vdi-datasets/{vd-id}/files/data

Get Data File  

Parameters chevron_right expand_more

ParameterTypeDescription
Path
vd-id* VDI IDstring

Unique VDI Dataset identifier string.

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

Min. length: 14

Max. length: 14

Inherits: string

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

200 OK chevron_right expand_more

Success

Headers

ParameterTypeDescription
Content-Disposition*string

application/octet-stream

application/octet-stream

401 Unauthorized chevron_right expand_more

Unauthorized

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

404 Not Found chevron_right expand_more

Not Found

Not Found NotFoundError

application/json

The requested resource was not found on this server.

Discriminator: status

Discriminator value: not-found

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

500 Internal Server Error chevron_right expand_more

Internal Server Error

Internal Server Error ServerError

application/json

Discriminator: status

Discriminator value: server-error

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • 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 /vdi-datasets/{vd-id}/shares/{recipient-user-id}/offer

Offer to Share a Dataset  

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 chevron_right expand_more

ParameterTypeDescription
Path
vd-id* VDI IDstring

Unique VDI Dataset identifier string.

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

Min. length: 14

Max. length: 14

Inherits: string

recipient-user-id* VEuPathDB User IDinteger

Unique user identifier

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: integer

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

Request Body chevron_right expand_more

Dataset Share Offer DatasetShareOffer

application/json

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

Inherits: object

ParameterTypeDescription
action* Offer Actionstring

What action to take with the dataset share offer.

Either grant or revoke.

A value of grant means the share should be offered to the user if they do not already have the dataset, or continue to be allowed if they already have access to the dataset.

A value of revoke means the share should not be offered to the target user if they do not already have the dataset, or the sharing should be stopped if the user did already have access to the dataset.

Enum:
  • grant
  • revoke

Inherits: lib.ShareOfferAction

Request Body

Grant Example

{
+  "action": "grant"
+}

Revoke Example

{
+  "action": "revoke"
+}

204 No Content chevron_right expand_more

Share offer record was successfully (re)placed.

400 Bad Request chevron_right expand_more

Bad Request.

Request body did not resemble the expected JSON form.

Bad Request BadRequestError

application/json

Request could not be parsed or was otherwise unusable.

Discriminator: status

Discriminator value: bad-request

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

401 Unauthorized chevron_right expand_more

Unauthorized.

This status is returned when the request contains either no user authorization token or an invalid user authorization token.

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

403 Forbidden chevron_right expand_more

Action Forbidden.

This status is returned when the dataset target of the operation is not owned by the requesting user, thus the requesting user is forbidden from offering shares to the dataset.

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

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

404 Not Found chevron_right expand_more

Not Found.

Either the target dataset or target user was not found.

422 Unprocessable Entity chevron_right expand_more

Unprocessable Entity.

Request body was syntactically valid JSON, however the body failed validation.

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

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • 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."
+      ]
+    }
+  }
+}

500 Internal Server Error chevron_right expand_more

Internal Server Error.

This status is returned when an unhandled or unexpected issue arises when attempting to process the request.

Internal Server Error ServerError

application/json

Discriminator: status

Discriminator value: server-error

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • 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 /vdi-datasets/{vd-id}/shares/{recipient-user-id}/receipt

Receive a dataset Share  

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

Parameters chevron_right expand_more

ParameterTypeDescription
Path
vd-id* VDI IDstring

Unique VDI Dataset identifier string.

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

Min. length: 14

Max. length: 14

Inherits: string

recipient-user-id* VEuPathDB User IDinteger

Unique user identifier

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: integer

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

Request Body chevron_right expand_more

Dataset Share Receipt DatasetShareReceipt

application/json

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

Inherits: object

ParameterTypeDescription
action* Acknowledgement Actionstring

What action to take with acknowledging a dataset share offer.

Either accept or reject.

A value of accept means that the dataset that a share was offered for should become available to the accepting user.

A value of reject means that the dataset that a share was offered for should become unavailable to the rejecting user.

Enum:
  • accept
  • reject

Inherits: lib.ShareReceiptAction

Request Body

Accept Example

{
+  "action": "accept"
+}

Reject Example

{
+  "action": "reject"
+}

204 No Content chevron_right expand_more

Share offer receipt record was successfully created.

400 Bad Request chevron_right expand_more

Bad Request.

Request body did not resemble the expected JSON form.

Bad Request BadRequestError

application/json

Request could not be parsed or was otherwise unusable.

Discriminator: status

Discriminator value: bad-request

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

401 Unauthorized chevron_right expand_more

Unauthorized.

This status is returned when the request contains either no user authorization token or an invalid user authorization token.

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

403 Forbidden chevron_right expand_more

Action Forbidden.

This status is returned when the requesting user is not the target user and/or the target user was not offered a share for the target dataset.

404 Not Found chevron_right expand_more

Not Found.

This status is returned when the target dataset does not exist.

Not Found NotFoundError

application/json

The requested resource was not found on this server.

Discriminator: status

Discriminator value: not-found

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

422 Unprocessable Entity chevron_right expand_more

Unprocessable Entity.

Request body was syntactically valid JSON, however the body failed validation.

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

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • 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."
+      ]
+    }
+  }
+}

500 Internal Server Error chevron_right expand_more

Internal Server Error.

This status is returned when an unhandled or unexpected issue arises when attempting to process the request.

Internal Server Error ServerError

application/json

Discriminator: status

Discriminator value: server-error

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • 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 /vdi-datasets/share-offers

List Share Offers  

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

Parameters chevron_right expand_more

ParameterTypeDescription
Query
status Share Statusstring

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:

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

Default value: "open"

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

200 OK chevron_right expand_more

Success.

A list of zero or more dataset shares were found for the requesting user.

application/json

application/json

ParameterTypeDescription
[] Share Offerobject

Inherits: object

[].datasetId*string

Unique VDI Dataset identifier string.

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

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

[].owner*object

Details about the owner of a VDI dataset.

Inherits: lib.DatasetOwner

[].owner.userId* Owner User IDinteger

VEuPathDB user ID of the owner of the dataset.

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

[].owner.firstName Owner First Namestring
[].owner.lastName Owner Last Namestring
[].owner.email Owner Emailstring
[].owner.organization Owner Organizationstring
[].shareStatus*string
Enum:
  • open
  • accepted
  • rejected

Inherits: lib.ShareOfferStatus

[].datasetType*object

Information about a specific dataset type.

Inherits: lib.DatasetTypeInfo

[].datasetType.name* Type Namestring
[].datasetType.displayName Type Display Namestring

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

[].datasetType.version* Type Versionstring
[].projectIds*array
[].projectIds[] Project IDstring

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: lib.ProjectID

Response Body

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

400 Bad Request chevron_right expand_more

Bad Request.

This response is returned when the status query parameter was provided but was an invalid value.

Bad Request BadRequestError

application/json

Request could not be parsed or was otherwise unusable.

Discriminator: status

Discriminator value: bad-request

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

401 Unauthorized chevron_right expand_more

Unauthorized.

This response is returned when the request either contained an invalid user authorization token, or did not contain a user authorization token at all.

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

500 Internal Server Error chevron_right expand_more

Internal Server Error.

This response is returned when an unhandled or unexpected issue arises when attempting to process the request.

Internal Server Error ServerError

application/json

Discriminator: status

Discriminator value: server-error

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • 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 /vdi-plugins

List  

List the plugins currently registered with the VDI instance.

Parameters chevron_right expand_more

ParameterTypeDescription
Query
project Project Filterstring

Optional parameter that may be used to filter the results of this endpoint to only those that are allowed to be used with the target project.

Valid values (non-case-sensitive):

  • AmoebaDB
  • ClinEpiDB
  • CryptoDB
  • FungiDB
  • GiardiaDB
  • HostDB
  • MicrobiomeDB
  • MicrosporidiaDB
  • PiroplasmaDB
  • PlasmoDB
  • ToxoDB
  • TrichDB
  • TriTrypDB
  • VectorBase
  • VEuPathDB
curl -X GET \
+  undefined/vdi-plugins?project=<value>

200 OK chevron_right expand_more

Success

application/json

application/json

ParameterTypeDescription
[] Plugin Listing Entryobject

Inherits: object

[].displayName* Plugin Display Namestring
[].typeName* Dataset Type Namestring
[].typeVersion* Dataset Type Versionstring
[].projects Relevant Projectsarray

Projects that this plugin is restricted to. An empty or absent list indicates that the plugin has no project restrictions and may be used on any site.

[].projects[]string

Response Body

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

401 Unauthorized chevron_right expand_more

Unauthorized

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

500 Internal Server Error chevron_right expand_more

Internal Server Error

Internal Server Error ServerError

application/json

Discriminator: status

Discriminator value: server-error

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • 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 /vdi-users/self/meta

 

Get user metadata.

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

200 OK chevron_right expand_more

Success

UserMetadata UserMetadata

application/json

Inherits: object

ParameterTypeDescription
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

401 Unauthorized chevron_right expand_more

Unauthorized

Unauthorized UnauthorizedError

application/json

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Response Body

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

500 Internal Server Error chevron_right expand_more

Internal Server Error

Internal Server Error ServerError

application/json

Discriminator: status

Discriminator value: server-error

Inherits: lib.Error

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • 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 /api

 

Renders the API documentation for this service.

curl -X GET \
+  undefined/api

200 OK chevron_right expand_more

text/html

text/html

get /health

 

Prints information about the overall service health.

curl -X GET \
+  undefined/health

200 OK chevron_right expand_more

HealthResponse HealthResponse

application/json

Health details about the service

Inherits: object

ParameterTypeDescription
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

500 Internal Server Error chevron_right expand_more

Internal Server Error ServerError

application/json

Discriminator: status

Discriminator value: server-error

Inherits: error.Error

ParameterTypeDescription
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"
+}

get /metrics

 

Prometheus metrics for the service.

curl -X GET \
+  undefined/metrics

200 OK chevron_right expand_more

text/plain

text/plain

Security Schemes

Types

Type BrokenDatasetListing (object)

Broken Dataset Listing

Inherits: object

Model

ParameterTypeDescription
detailsarray
details[] Broken Dataset Detailsobject

Inherits: lib.BrokenDatasetDetails

details[].datasetId*string

Unique VDI Dataset identifier string.

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

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

details[].owner*integer

Unique user identifier

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

details[].datasetType*object

Information about a specific dataset type.

Inherits: lib.DatasetTypeInfo

details[].datasetType.name* Type Namestring
details[].datasetType.displayName Type Display Namestring

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

details[].datasetType.version* Type Versionstring
details[].projectIds*array
details[].projectIds[] Project IDstring

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: lib.ProjectID

details[].status*object

Information about the import and install status of a dataset.

Inherits: lib.DatasetStatusInfo

details[].status.import*string

Import status of the dataset.

ValueDescription
queuedThe dataset has not yet been processed and is waiting in the queue.
in-progressThe dataset is currently being import processed.
completeThe dataset has been processed and imported for installation.
invalidThe dataset failed import validation.
failedThe dataset import failed due to an internal server error.
Enum:
  • queued
  • in-progress
  • complete
  • invalid
  • failed

Inherits: lib.DatasetImportStatus

details[].status.installarray
details[].status.install[] Dataset Install Status Entryobject

Entry in a list of install statuses for a dataset.

Inherits: lib.DatasetInstallStatusEntry

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

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: lib.ProjectID

details[].status.install[].metaStatusstring
Enum:
  • running
  • complete
  • failed-validation
  • failed-installation
  • ready-for-reinstall
  • missing-dependency

Inherits: lib.DatasetInstallStatus

details[].status.install[].metaMessagestring
details[].status.install[].dataStatusstring
Enum:
  • running
  • complete
  • failed-validation
  • failed-installation
  • ready-for-reinstall
  • missing-dependency

Inherits: lib.DatasetInstallStatus

details[].status.install[].dataMessagestring
idsarray
ids[] VDI IDstring

Unique VDI Dataset identifier string.

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

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

Type BrokenDatasetDetails (object)

Broken Dataset Details

Inherits: object

Model

ParameterTypeDescription
datasetId*string

Unique VDI Dataset identifier string.

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

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

owner*integer

Unique user identifier

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

datasetType*object

Information about a specific dataset type.

Inherits: lib.DatasetTypeInfo

datasetType.name* Type Namestring
datasetType.displayName Type Display Namestring

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

datasetType.version* Type Versionstring
projectIds*array
projectIds[] Project IDstring

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: lib.ProjectID

status*object

Information about the import and install status of a dataset.

Inherits: lib.DatasetStatusInfo

status.import*string

Import status of the dataset.

ValueDescription
queuedThe dataset has not yet been processed and is waiting in the queue.
in-progressThe dataset is currently being import processed.
completeThe dataset has been processed and imported for installation.
invalidThe dataset failed import validation.
failedThe dataset import failed due to an internal server error.
Enum:
  • queued
  • in-progress
  • complete
  • invalid
  • failed

Inherits: lib.DatasetImportStatus

status.installarray
status.install[] Dataset Install Status Entryobject

Entry in a list of install statuses for a dataset.

Inherits: lib.DatasetInstallStatusEntry

status.install[].projectId*string

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: lib.ProjectID

status.install[].metaStatusstring
Enum:
  • running
  • complete
  • failed-validation
  • failed-installation
  • ready-for-reinstall
  • missing-dependency

Inherits: lib.DatasetInstallStatus

status.install[].metaMessagestring
status.install[].dataStatusstring
Enum:
  • running
  • complete
  • failed-validation
  • failed-installation
  • ready-for-reinstall
  • missing-dependency

Inherits: lib.DatasetInstallStatus

status.install[].dataMessagestring

Type BrokenImportListing (object)

Broken Import Listing

Inherits: object

Model

ParameterTypeDescription
meta*object

Inherits: lib.BrokenImportListingMeta

meta.count*integer
meta.beforestring
meta.afterstring
meta.userinteger

Unique user identifier

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

meta.limitinteger
meta.offsetinteger
results*array
results[] Broken Import Detailsobject

Inherits: lib.BrokenImportDetails

results[].datasetId*string

Unique VDI Dataset identifier string.

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

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

results[].owner*integer

Unique user identifier

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

results[].datasetType*object

Information about a specific dataset type.

Inherits: lib.DatasetTypeInfo

results[].datasetType.name* Type Namestring
results[].datasetType.displayName Type Display Namestring

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

results[].datasetType.version* Type Versionstring
results[].projectIds*array
results[].projectIds[] Project IDstring

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: lib.ProjectID

results[].messages*array
results[].messages[]string

Type BrokenImportListingMeta (object)

BrokenImportListingMeta

Inherits: object

Model

ParameterTypeDescription
count*integer
beforestring
afterstring
userinteger

Unique user identifier

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

limitinteger
offsetinteger

Type BrokenImportDetails (object)

Broken Import Details

Inherits: object

Model

ParameterTypeDescription
datasetId*string

Unique VDI Dataset identifier string.

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

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

owner*integer

Unique user identifier

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

datasetType*object

Information about a specific dataset type.

Inherits: lib.DatasetTypeInfo

datasetType.name* Type Namestring
datasetType.displayName Type Display Namestring

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

datasetType.version* Type Versionstring
projectIds*array
projectIds[] Project IDstring

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: lib.ProjectID

messages*array
messages[]string

Type AllDatasetsListResponse (object)

All Datasets Listing Response

Inherits: object

Model

ParameterTypeDescription
meta*object

Inherits: lib.AllDatasetsListMeta

meta.count*integer
meta.offset*integer
meta.limit*integer
meta.total*integer
results*array
results[]object

Inherits: lib.AllDatasetsListEntry

results[].datasetId*string

Unique VDI Dataset identifier string.

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

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

results[].owner*integer

Unique user identifier

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

results[].datasetType*object

Information about a specific dataset type.

Inherits: lib.DatasetTypeInfo

results[].datasetType.name* Type Namestring
results[].datasetType.displayName Type Display Namestring

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

results[].datasetType.version* Type Versionstring
results[].visibility*string
Enum:
  • private
  • protected
  • public

Inherits: lib.DatasetVisibility

results[].name*string
results[].summarystring
results[].descriptionstring
results[].sourceUrlstring
results[].origin*string
results[].projectIds*array
results[].projectIds[] Project IDstring

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: lib.ProjectID

results[].status*object

Information about the import and install status of a dataset.

Inherits: lib.DatasetStatusInfo

results[].status.import*string

Import status of the dataset.

ValueDescription
queuedThe dataset has not yet been processed and is waiting in the queue.
in-progressThe dataset is currently being import processed.
completeThe dataset has been processed and imported for installation.
invalidThe dataset failed import validation.
failedThe dataset import failed due to an internal server error.
Enum:
  • queued
  • in-progress
  • complete
  • invalid
  • failed

Inherits: lib.DatasetImportStatus

results[].status.installarray
results[].status.install[] Dataset Install Status Entryobject

Entry in a list of install statuses for a dataset.

Inherits: lib.DatasetInstallStatusEntry

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

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: lib.ProjectID

results[].status.install[].metaStatusstring
Enum:
  • running
  • complete
  • failed-validation
  • failed-installation
  • ready-for-reinstall
  • missing-dependency

Inherits: lib.DatasetInstallStatus

results[].status.install[].metaMessagestring
results[].status.install[].dataStatusstring
Enum:
  • running
  • complete
  • failed-validation
  • failed-installation
  • ready-for-reinstall
  • missing-dependency

Inherits: lib.DatasetInstallStatus

results[].status.install[].dataMessagestring
results[].created*datetime

Type AllDatasetsListMeta (object)

AllDatasetsListMeta

Inherits: object

Model

ParameterTypeDescription
count*integer
offset*integer
limit*integer
total*integer

Type AllDatasetsListEntry (object)

AllDatasetsListEntry

Inherits: object

Model

ParameterTypeDescription
datasetId*string

Unique VDI Dataset identifier string.

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

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

owner*integer

Unique user identifier

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

datasetType*object

Information about a specific dataset type.

Inherits: lib.DatasetTypeInfo

datasetType.name* Type Namestring
datasetType.displayName Type Display Namestring

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

datasetType.version* Type Versionstring
visibility*string
Enum:
  • private
  • protected
  • public

Inherits: lib.DatasetVisibility

name*string
summarystring
descriptionstring
sourceUrlstring
origin*string
projectIds*array
projectIds[] Project IDstring

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: lib.ProjectID

status*object

Information about the import and install status of a dataset.

Inherits: lib.DatasetStatusInfo

status.import*string

Import status of the dataset.

ValueDescription
queuedThe dataset has not yet been processed and is waiting in the queue.
in-progressThe dataset is currently being import processed.
completeThe dataset has been processed and imported for installation.
invalidThe dataset failed import validation.
failedThe dataset import failed due to an internal server error.
Enum:
  • queued
  • in-progress
  • complete
  • invalid
  • failed

Inherits: lib.DatasetImportStatus

status.installarray
status.install[] Dataset Install Status Entryobject

Entry in a list of install statuses for a dataset.

Inherits: lib.DatasetInstallStatusEntry

status.install[].projectId*string

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: lib.ProjectID

status.install[].metaStatusstring
Enum:
  • running
  • complete
  • failed-validation
  • failed-installation
  • ready-for-reinstall
  • missing-dependency

Inherits: lib.DatasetInstallStatus

status.install[].metaMessagestring
status.install[].dataStatusstring
Enum:
  • running
  • complete
  • failed-validation
  • failed-installation
  • ready-for-reinstall
  • missing-dependency

Inherits: lib.DatasetInstallStatus

status.install[].dataMessagestring
created*datetime

Type InstallCleanupRequest (object)

Install Cleanup Request

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

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

Inherits: object

Model

ParameterTypeDescription
allboolean
targetsarray

Unique items: Yes

targets[] Install Cleanup Targetobject

Inherits: lib.InstallCleanupTarget

targets[].datasetId*string

Unique VDI Dataset identifier string.

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

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

targets[].projectId*string

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: lib.ProjectID

Type InstallCleanupTarget (object)

Install Cleanup Target

Inherits: object

Model

ParameterTypeDescription
datasetId*string

Unique VDI Dataset identifier string.

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

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

projectId*string

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: lib.ProjectID

Type DatasetListShareUser (object)

DatasetListShareUser

Inherits: object

Model

ParameterTypeDescription
userId*integer

Unique user identifier

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

firstName*string
lastName*string
organization*string
accepted*boolean

Type DatasetListEntry (object)

Dataset List Item

Short entry with basic details about a dataset.

Inherits: object

Model

ParameterTypeDescription
datasetId* Dataset IDstring

Unique VDI Dataset identifier string.

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

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

owner* Owner Detailsobject

Details about the owner of a VDI dataset.

Inherits: lib.DatasetOwner

owner.userId* Owner User IDinteger

VEuPathDB user ID of the owner of the dataset.

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

owner.firstName Owner First Namestring
owner.lastName Owner Last Namestring
owner.email Owner Emailstring
owner.organization Owner Organizationstring
datasetType* Dataset Typeobject

Information about a specific dataset type.

Inherits: lib.DatasetTypeInfo

datasetType.name* Type Namestring
datasetType.displayName Type Display Namestring

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

datasetType.version* Type Versionstring
visibility* Dataset Visibilitystring
Enum:
  • private
  • protected
  • public

Inherits: lib.DatasetVisibility

name* Dataset Namestring

User provided name for the dataset.

summary Dataset Summarystring

User provided summary of the dataset.

description Dataset Descriptionstring

User provided description of the dataset.

sourceUrl Source URLstring

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

origin* Dataset Originstring

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

projectIds* Project IDsarray

Project IDs for projects the dataset record was submitted to.

projectIds[] Project IDstring

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: lib.ProjectID

status* Status Infoobject

Information about the import and install status of a dataset.

Inherits: lib.DatasetStatusInfo

status.import*string

Import status of the dataset.

ValueDescription
queuedThe dataset has not yet been processed and is waiting in the queue.
in-progressThe dataset is currently being import processed.
completeThe dataset has been processed and imported for installation.
invalidThe dataset failed import validation.
failedThe dataset import failed due to an internal server error.
Enum:
  • queued
  • in-progress
  • complete
  • invalid
  • failed

Inherits: lib.DatasetImportStatus

status.installarray
status.install[] Dataset Install Status Entryobject

Entry in a list of install statuses for a dataset.

Inherits: lib.DatasetInstallStatusEntry

status.install[].projectId*string

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: lib.ProjectID

status.install[].metaStatusstring
Enum:
  • running
  • complete
  • failed-validation
  • failed-installation
  • ready-for-reinstall
  • missing-dependency

Inherits: lib.DatasetInstallStatus

status.install[].metaMessagestring
status.install[].dataStatusstring
Enum:
  • running
  • complete
  • failed-validation
  • failed-installation
  • ready-for-reinstall
  • missing-dependency

Inherits: lib.DatasetInstallStatus

status.install[].dataMessagestring
shares* Shared Witharray
shares[]object

Inherits: object

shares[].userId*integer

Unique user identifier

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

shares[].firstName*string
shares[].lastName*string
shares[].organization*string
shares[].accepted*boolean
fileCount* File Countinteger

Number of files uploaded for this dataset.

fileSizeTotal* File Size Totalinteger

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

Format: int64

created* Creation Timestampdatetime

Timestamp of the creation of this dataset.

Type DatasetPostRequest (object)

Dataset Post Request

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

Model

ParameterTypeDescription
meta* Dataset Metaobject

Metadata about the dataset being submitted.

Inherits: lib.DatasetPostMeta

meta.datasetType* Dataset Typeobject

Type of the dataset that is being uploaded.

Inherits: lib.DatasetPostType

meta.datasetType.name*string
meta.datasetType.version*string
meta.name* Dataset Namestring

User provided name for the dataset.

meta.visibility Dataset Visibilitystring

Default value: "private"

Enum:
  • private
  • protected
  • public

Inherits: lib.DatasetVisibility

meta.summary Dataset Summarystring

User provided summary for the dataset.

meta.description Dataset Descriptionstring

User provided description for the dataset.

meta.origin* Dataset Originstring

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

meta.projects* Project IDsarray

IDs of the projects this dataset is being submitted to.

meta.projects[] Project IDstring

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: lib.ProjectID

meta.dependencies* Dataset Dependenciesarray
meta.dependencies[]object

Inherits: lib.DatasetDependency

meta.dependencies[].resourceIdentifier*string
meta.dependencies[].resourceDisplayName*string
meta.dependencies[].resourceVersion*string
meta.createdOn Creation Datedatetime-only
file Dataset Filefile

Dataset file to upload.

This field is incompatible with the url field.

url Dataset URLstring

URL to a dataset file to upload.

This field is incompatible with the file field.

Type DatasetPostMeta (object)

DatasetPostMeta

Inherits: object

Model

ParameterTypeDescription
datasetType* Dataset Typeobject

Type of the dataset that is being uploaded.

Inherits: lib.DatasetPostType

datasetType.name*string
datasetType.version*string
name* Dataset Namestring

User provided name for the dataset.

visibility Dataset Visibilitystring

Default value: "private"

Enum:
  • private
  • protected
  • public

Inherits: lib.DatasetVisibility

summary Dataset Summarystring

User provided summary for the dataset.

description Dataset Descriptionstring

User provided description for the dataset.

origin* Dataset Originstring

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

projects* Project IDsarray

IDs of the projects this dataset is being submitted to.

projects[] Project IDstring

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: lib.ProjectID

dependencies* Dataset Dependenciesarray
dependencies[]object

Inherits: lib.DatasetDependency

dependencies[].resourceIdentifier*string
dependencies[].resourceDisplayName*string
dependencies[].resourceVersion*string
createdOn Creation Datedatetime-only

Type DatasetPostType (object)

DatasetPostType

Inherits: object

Model

ParameterTypeDescription
name*string
version*string

Type DatasetPostResponse (object)

Dataset Upload Response

Response object returned on successful upload of a dataset.

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

Inherits: object

Model

ParameterTypeDescription
datasetId*string

Unique VDI Dataset identifier string.

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

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

Type ShareOfferEntry (object)

Share Offer

Inherits: object

Model

ParameterTypeDescription
datasetId*string

Unique VDI Dataset identifier string.

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

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

owner*object

Details about the owner of a VDI dataset.

Inherits: lib.DatasetOwner

owner.userId* Owner User IDinteger

VEuPathDB user ID of the owner of the dataset.

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

owner.firstName Owner First Namestring
owner.lastName Owner Last Namestring
owner.email Owner Emailstring
owner.organization Owner Organizationstring
shareStatus*string
Enum:
  • open
  • accepted
  • rejected

Inherits: lib.ShareOfferStatus

datasetType*object

Information about a specific dataset type.

Inherits: lib.DatasetTypeInfo

datasetType.name* Type Namestring
datasetType.displayName Type Display Namestring

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

datasetType.version* Type Versionstring
projectIds*array
projectIds[] Project IDstring

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: lib.ProjectID

Type ShareOfferStatus (string)

Share Offer Status
Enum:
  • open
  • accepted
  • rejected

Inherits: string

Type DatasetFileListing (object)

Dataset File Listing

Inherits: object

Model

ParameterTypeDescription
upload*object

Inherits: lib.DatasetZipDetails

upload.zipSize*integer

Format: int64

upload.contents*array
upload.contents[] Dataset File Detailsobject

Inherits: lib.DatasetFileDetails

upload.contents[].fileName* File Namestring
upload.contents[].fileSize* File Sizeinteger

Size of the file in bytes.

Format: int64

installobject

Inherits: lib.DatasetZipDetails

install.zipSize*integer

Format: int64

install.contents*array
install.contents[] Dataset File Detailsobject

Inherits: lib.DatasetFileDetails

install.contents[].fileName* File Namestring
install.contents[].fileSize* File Sizeinteger

Size of the file in bytes.

Format: int64

Type DatasetZipDetails (object)

Dataset Zip Details

Inherits: object

Model

ParameterTypeDescription
zipSize*integer

Format: int64

contents*array
contents[] Dataset File Detailsobject

Inherits: lib.DatasetFileDetails

contents[].fileName* File Namestring
contents[].fileSize* File Sizeinteger

Size of the file in bytes.

Format: int64

Type DatasetFileDetails (object)

Dataset File Details

Inherits: object

Model

ParameterTypeDescription
fileName* File Namestring
fileSize* File Sizeinteger

Size of the file in bytes.

Format: int64

Type DatasetDetails (object)

Dataset Details

Details about a specific singular dataset.

Inherits: object

Model

ParameterTypeDescription
datasetId* Dataset IDstring

Unique VDI Dataset identifier string.

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

Min. length: 14

Max. length: 14

Inherits: lib.VDI-ID

owner* Owner Detailsobject

Details about the owner of a VDI dataset.

Inherits: lib.DatasetOwner

owner.userId* Owner User IDinteger

VEuPathDB user ID of the owner of the dataset.

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: lib.User-ID

owner.firstName Owner First Namestring
owner.lastName Owner Last Namestring
owner.email Owner Emailstring
owner.organization Owner Organizationstring
datasetType* Dataset Type Infoobject

Information about a specific dataset type.

Inherits: lib.DatasetTypeInfo

datasetType.name* Type Namestring
datasetType.displayName Type Display Namestring

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

datasetType.version* Type Versionstring
name* Dataset Namestring
summary Dataset Summarystring
description Dataset Descriptionstring
sourceUrl Source URLstring

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

origin* Dataset Originstring

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

projectIds* Project IDsarray

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

projectIds[] Project IDstring

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: lib.ProjectID

visibility* Dataset Visibilitystring
Enum:
  • private
  • protected
  • public

Inherits: lib.DatasetVisibility

importMessages Import Messagesarray

Log lines from the import process.

These messages will be warnings and/or validation errors.

Default value: []

importMessages[]string
status* Dataset Status Infoobject

Information about the import and install status of a dataset.

Inherits: lib.DatasetStatusInfo

status.import*string

Import status of the dataset.

ValueDescription
queuedThe dataset has not yet been processed and is waiting in the queue.
in-progressThe dataset is currently being import processed.
completeThe dataset has been processed and imported for installation.
invalidThe dataset failed import validation.
failedThe dataset import failed due to an internal server error.
Enum:
  • queued
  • in-progress
  • complete
  • invalid
  • failed

Inherits: lib.DatasetImportStatus

status.installarray
status.install[] Dataset Install Status Entryobject

Entry in a list of install statuses for a dataset.

Inherits: lib.DatasetInstallStatusEntry

status.install[].projectId*string

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: lib.ProjectID

status.install[].metaStatusstring
Enum:
  • running
  • complete
  • failed-validation
  • failed-installation
  • ready-for-reinstall
  • missing-dependency

Inherits: lib.DatasetInstallStatus

status.install[].metaMessagestring
status.install[].dataStatusstring
Enum:
  • running
  • complete
  • failed-validation
  • failed-installation
  • ready-for-reinstall
  • missing-dependency

Inherits: lib.DatasetInstallStatus

status.install[].dataMessagestring
shares Sharesarray

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

shares[] Share Offerobject

Inherits: lib.ShareOffer

shares[].recipient*object

I AM A UNION!

Inherits: lib.ShareOfferRecipient

shares[].recipient.userId* User IDinteger

Format: int64

shares[].recipient.firstName First Namestring
shares[].recipient.lastName Last Namestring
shares[].recipient.organization Organizationstring
shares[].recipient.email Emailstring
shares[].status*string
Enum:
  • grant
  • revoke

Inherits: lib.ShareOfferAction

created* Creation Timestampdatetime

Timestamp for when this dataset was created.

dependencies* Dataset Dependenciesarray
dependencies[]object

Inherits: lib.DatasetDependency

dependencies[].resourceIdentifier*string
dependencies[].resourceDisplayName*string
dependencies[].resourceVersion*string

Type ShareOffer (object)

Share Offer

Inherits: object

Model

ParameterTypeDescription
recipient*object

I AM A UNION!

Inherits: lib.ShareOfferRecipient

recipient.userId* User IDinteger

Format: int64

recipient.firstName First Namestring
recipient.lastName Last Namestring
recipient.organization Organizationstring
recipient.email Emailstring
status*string
Enum:
  • grant
  • revoke

Inherits: lib.ShareOfferAction

Examples

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

Type ShareOfferRecipient (object)

Share Offer Recipient

I AM A UNION!

Inherits: object

Model

ParameterTypeDescription
userId* User IDinteger

Format: int64

firstName First Namestring
lastName Last Namestring
organization Organizationstring
email Emailstring

Examples

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

Type DatasetPatchRequest (object)

Dataset Patch Request

Request to update the metadata for a dataset.

Inherits: object

Model

ParameterTypeDescription
visibility Dataset Visibilitystring
Enum:
  • private
  • protected
  • public

Inherits: lib.DatasetVisibility

name Dataset Namestring

User provided name for a dataset.

summary Dataset Summarystring

User provided summary for a dataset.

description Dataset Descriptionstring

User provided description for a dataset.

Type DatasetShareOffer (object)

Dataset Share Offer

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

Inherits: object

Model

ParameterTypeDescription
action* Offer Actionstring

What action to take with the dataset share offer.

Either grant or revoke.

A value of grant means the share should be offered to the user if they do not already have the dataset, or continue to be allowed if they already have access to the dataset.

A value of revoke means the share should not be offered to the target user if they do not already have the dataset, or the sharing should be stopped if the user did already have access to the dataset.

Enum:
  • grant
  • revoke

Inherits: lib.ShareOfferAction

Type DatasetShareReceipt (object)

Dataset Share Receipt

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

Inherits: object

Model

ParameterTypeDescription
action* Acknowledgement Actionstring

What action to take with acknowledging a dataset share offer.

Either accept or reject.

A value of accept means that the dataset that a share was offered for should become available to the accepting user.

A value of reject means that the dataset that a share was offered for should become unavailable to the rejecting user.

Enum:
  • accept
  • reject

Inherits: lib.ShareReceiptAction

Type PluginListItem (object)

Plugin Listing Entry

Inherits: object

Model

ParameterTypeDescription
displayName* Plugin Display Namestring
typeName* Dataset Type Namestring
typeVersion* Dataset Type Versionstring
projects Relevant Projectsarray

Projects that this plugin is restricted to. An empty or absent list indicates that the plugin has no project restrictions and may be used on any site.

projects[]string

Type UserMetadata (object)

UserMetadata

Inherits: object

Model

ParameterTypeDescription
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

Type UserQuotaDetails (object)

UserQuotaDetails

Inherits: object

Model

ParameterTypeDescription
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

Type VDI-ID (string)

VDI ID

Unique VDI Dataset identifier string.

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

Min. length: 14

Max. length: 14

Inherits: string

Type User-ID (integer)

VEuPathDB User ID

Unique user identifier

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: integer

Type ProjectID (string)

Project ID

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: string

Type DatasetOwner (object)

Dataset Owner

Details about the owner of a VDI dataset.

Inherits: object

Model

ParameterTypeDescription
userId* Owner User IDinteger

VEuPathDB user ID of the owner of the dataset.

Min. value: 1

Max. value: 9223372036854776000

Format: int64

Inherits: integer

firstName Owner First Namestring
lastName Owner Last Namestring
email Owner Emailstring
organization Owner Organizationstring

Type DatasetTypeInfo (object)

Dataset Type Info

Information about a specific dataset type.

Inherits: object

Model

ParameterTypeDescription
name* Type Namestring
displayName Type Display Namestring

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

version* Type Versionstring

Type ShareOfferAction (string)

ShareOfferAction
Enum:
  • grant
  • revoke

Inherits: string

Type ShareReceiptAction (string)

ShareReceiptAction
Enum:
  • accept
  • reject

Inherits: string

Type DatasetVisibility (string)

DatasetVisibility
Enum:
  • private
  • protected
  • public

Inherits: string

Type DatasetStatusInfo (object)

Dataset Status Info

Information about the import and install status of a dataset.

Inherits: object

Model

ParameterTypeDescription
import*string

Import status of the dataset.

ValueDescription
queuedThe dataset has not yet been processed and is waiting in the queue.
in-progressThe dataset is currently being import processed.
completeThe dataset has been processed and imported for installation.
invalidThe dataset failed import validation.
failedThe dataset import failed due to an internal server error.
Enum:
  • queued
  • in-progress
  • complete
  • invalid
  • failed

Inherits: lib.DatasetImportStatus

installarray
install[] Dataset Install Status Entryobject

Entry in a list of install statuses for a dataset.

Inherits: lib.DatasetInstallStatusEntry

install[].projectId*string

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: string

install[].metaStatusstring
Enum:
  • running
  • complete
  • failed-validation
  • failed-installation
  • ready-for-reinstall
  • missing-dependency

Inherits: lib.DatasetInstallStatus

install[].metaMessagestring
install[].dataStatusstring
Enum:
  • running
  • complete
  • failed-validation
  • failed-installation
  • ready-for-reinstall
  • missing-dependency

Inherits: lib.DatasetInstallStatus

install[].dataMessagestring

Type DatasetImportStatus (string)

Dataset Import Status

Import status of the dataset.

ValueDescription
queuedThe dataset has not yet been processed and is waiting in the queue.
in-progressThe dataset is currently being import processed.
completeThe dataset has been processed and imported for installation.
invalidThe dataset failed import validation.
failedThe dataset import failed due to an internal server error.
Enum:
  • queued
  • in-progress
  • complete
  • invalid
  • failed

Inherits: string

Type DatasetInstallStatus (string)

Dataset Install Status
Enum:
  • running
  • complete
  • failed-validation
  • failed-installation
  • ready-for-reinstall
  • missing-dependency

Inherits: string

Type DatasetInstallStatusEntry (object)

Dataset Install Status Entry

Entry in a list of install statuses for a dataset.

Inherits: object

Model

ParameterTypeDescription
projectId*string

Name or ID of a target VEuPathDB project.

Valid project IDs are:

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

Inherits: string

metaStatusstring
Enum:
  • running
  • complete
  • failed-validation
  • failed-installation
  • ready-for-reinstall
  • missing-dependency

Inherits: string

metaMessagestring
dataStatusstring
Enum:
  • running
  • complete
  • failed-validation
  • failed-installation
  • ready-for-reinstall
  • missing-dependency

Inherits: string

dataMessagestring

Type DatasetDependency (object)

DatasetDependency

Inherits: object

Model

ParameterTypeDescription
resourceIdentifier*string
resourceDisplayName*string
resourceVersion*string

Type Error (object)

Error

Discriminator: status

Inherits: object

Model

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Type ErrorType (string)

ErrorType
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: string

Type BadRequestError (object)

Bad Request

Request could not be parsed or was otherwise unusable.

Discriminator: status

Discriminator value: bad-request

Inherits: lib.Error

Model

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Examples

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

Type UnauthorizedError (object)

Unauthorized

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: lib.Error

Model

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Examples

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

Type ForbiddenError (object)

Forbidden

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

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Examples

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

Type NotFoundError (object)

Not Found

The requested resource was not found on this server.

Discriminator: status

Discriminator value: not-found

Inherits: lib.Error

Model

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Examples

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

Type MethodNotAllowedError (object)

Method Not Allowed

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

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Examples

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

Type ConflictError (object)

Conflict

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

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Examples

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

Type GoneError (object)

Gone

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

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string

Examples

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

Type UnprocessableEntityError (object)

Unprocessable Entity

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

Discriminator: status

Discriminator value: invalid-input

Inherits: lib.Error

Model

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • 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."
+      ]
+    }
+  }
+}

Type ServerError (object)

Internal Server Error

Discriminator: status

Discriminator value: server-error

Inherits: lib.Error

Model

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • conflict
  • gone
  • invalid-input
  • server-error

Inherits: lib.ErrorType

message*string
requestId*string

Examples

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

Type Error (object)

Error

Discriminator: status

Inherits: object

Model

ParameterTypeDescription
status*string
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • invalid-input
  • server-error

Inherits: error.ErrorType

message*string

Type ErrorType (string)

ErrorType
Enum:
  • bad-request
  • unauthorized
  • forbidden
  • not-found
  • bad-method
  • invalid-input
  • server-error

Inherits: string

Type BadRequestError (object)

Bad Request

Request could not be parsed or was otherwise unusable.

Discriminator: status

Discriminator value: bad-request

Inherits: error.Error

Model

ParameterTypeDescription
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"
+}

Type UnauthorizedError (object)

Unauthorized

Unauthenticated client requested a resource that requires authentication.

Discriminator: status

Discriminator value: unauthorized

Inherits: error.Error

Model

ParameterTypeDescription
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"
+}

Type ForbiddenError (object)

Forbidden

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

ParameterTypeDescription
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"
+}

Type NotFoundError (object)

Not Found

The requested resource was not found on this server.

Discriminator: status

Discriminator value: not-found

Inherits: error.Error

Model

ParameterTypeDescription
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"
+}

Type MethodNotAllowedError (object)

Method Not Allowed

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

ParameterTypeDescription
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"
+}

Type UnprocessableEntityError (object)

Unprocessable Entity

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

Discriminator: status

Discriminator value: invalid-input

Inherits: error.Error

Model

ParameterTypeDescription
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."
+      ]
+    }
+  }
+}

Type ServerError (object)

Internal Server Error

Discriminator: status

Discriminator value: server-error

Inherits: error.Error

Model

ParameterTypeDescription
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"
+}

Type HealthResponse (object)

HealthResponse

Health details about the service

Inherits: object

Model

ParameterTypeDescription
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

Type DependencyStatus (object)

DependencyStatus

Inherits: object

Model

ParameterTypeDescription
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