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openapi.yaml
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openapi.yaml
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swagger: '2.0'
basePath: /
consumes:
- application/json
definitions:
container-image:
properties:
name:
description: The container image url
type: string
type: object
container-resources:
properties:
cpu:
description: Cpu units to as a limit for the container (e.g. 0.1, 1)
example: '1'
type: string
memory:
description: Memory defined as either bytes, mebibytes (e.g. 100Mi which is
104857600 bytes), or gibibytes (100Gi)
example: 500Mi
type: string
type: object
data-filename:
properties:
name:
description: The name of the data file
type: string
type: object
dataset-s3-configuration:
properties:
accessKeyID:
default: ''
description: Access key id
type: string
bucket:
default: ''
description: Name of bucket
type: string
endpoint:
default: ''
description: Endpoint URL (e.g. https://s3.eu-gb.cloud-object-storage.appdomain.cloud)
type: string
region:
default: ''
description: Region (optional)
type: string
secretAccessKey:
default: ''
description: Secret access key
type: string
required:
- accessKeyID
- bucket
- endpoint
- secretAccessKey
type: object
executionoptiondefaults:
properties:
variables:
default: []
description: The default values of the variables in the virtual experiment
DSL
items:
$ref: '#/definitions/variablewithdefaultvalues'
type: array
type: object
experiment-instance:
properties:
experiment:
$ref: '#/definitions/ve'
id:
type: string
k8s-labels:
example:
rest-uid: ionisation-energy-z3u2c
type: object
outputs:
example:
AnionResults:
creationtime: '2019-12-04 19:00:54.993316'
description: Anion homo/lumo results
filename: energies.csv
filepath: /tmp/workdir/ionisation-energy-2019-12-04T181218.613966.instance/output/energies.csv
final: 'no'
production: 'yes'
type: csv
version: '14'
type: object
status:
$ref: '#/definitions/experiment-status'
required:
- id
type: object
experiment-lambda-start:
properties:
additionalOptions:
items:
description: Additional options to elaunch.py
example: --registerWorkflow=True
type: string
type: array
data:
items:
$ref: '#/definitions/file-content'
type: array
datasetStoreURI:
description: Dataset URI to store outputs (uses github.com/datashim-io/datashim)
i.e. dataset://<dataset-name>/path/in/dataset/to/upload/outputs/to. Mutually
exclusive with s3Store.
type: string
environmentVariables:
example:
RUNTIME_SECRET_TOKEN: <token>
type: object
lambdaFlowIR:
description: JSON representation of FlowIR
example:
flowir key: flowir value
type: object
metadata:
example:
exp-label: no-spaces-allowed
type: object
orchestrator_resources:
allOf:
- $ref: '#/definitions/container-resources'
description: Hardware resource limits for the container that is hosting the
workflow orchestrator
s3:
allOf:
- $ref: '#/definitions/s3'
description: S3 configuration (read the description of the Filename-Content
pair model too)
s3Store:
allOf:
- $ref: '#/definitions/s3-output'
description: Configuration to store outputs of workflow instance to a S3 bucket.
Mutually exclusive with datasetStoreURI
scripts:
description: Scripts to placed under the `bin` directory of the experiment
items:
$ref: '#/definitions/file-content'
type: array
variables:
example:
functional: B3LYPV3
numberMolecules: 2
startIndex: 10
type: object
volumes:
items:
$ref: '#/definitions/mount-volume'
type: array
type: object
experiment-start:
properties:
additionalOptions:
description: Additional options to orchestrator that executes this experiment
items:
example: --registerWorkflow=True
type: string
type: array
data:
default: []
description: The data files to the experiment, following the parameterisation
settings (if any)
items:
$ref: '#/definitions/file-content'
type: array
datasetStoreURI:
description: Dataset URI to store outputs (uses github.com/datashim-io/datashim)
i.e. dataset://<dataset-name>/path/in/dataset/to/upload/outputs/to. Mutually
exclusive with s3Store.
type: string
environmentVariables:
default: {}
description: 'key: value environment variables to inject in the pod which
hosts the orchestrator of the experiment'
type: object
inputs:
default: []
description: The required inputs to the experiment (if any)
items:
$ref: '#/definitions/file-content'
type: array
metadata:
default: {}
description: 'key: value metadata values to associate with the experiment.
The orchestrator will use these values to populate the userMetadata document
in the ST4SD Datastore, should the experiment be registered with the datastore'
type: object
orchestrator_resources:
allOf:
- $ref: '#/definitions/container-resources'
description: Hardware resource limits for the container that is hosting the
workflow orchestrator
platform:
description: The platform to use for the execution of the virtual experiment.
It should match the parameterisation options of the parameterised virtual
experiment package you are starting.
type: string
runtimePolicy:
$ref: '#/definitions/experiment-start-policy'
s3:
allOf:
- $ref: '#/definitions/s3'
description: S3 configuration (read the description of the Filename-Content
pair model too)
s3Store:
allOf:
- $ref: '#/definitions/s3-output'
default: {}
description: Configuration to store outputs of workflow instance to a S3 bucket.
Mutually exclusive with datasetStoreURI
variables:
default: {}
description: 'key: value variable pairs (must follow the parameterisation
settings)'
type: object
volumes:
default: []
description: Optional volumes to mount in the pods
items:
$ref: '#/definitions/mount-volume'
type: array
type: object
experiment-start-policy:
properties:
config:
description: Configuration options for runtime policy
example: {}
type: object
name:
description: Nane of runtime policy
type: string
type: object
experiment-status:
properties:
current-stage:
type: string
error-description:
type: string
exit-status:
type: string
experiment-state:
example: running
type: string
meta:
type: object
stage-progress:
type: number
stage-state:
example: running
type: string
stages:
items:
type: string
type: array
total-progress:
type: number
required:
- experiment-state
- stage-progress
- stage-state
- total-progress
type: object
file-content:
properties:
content:
description: Content of file. Mutually exclusive with sourceFilename and targetFilename
example: 'mole:capb,slampd,smlta
conc:4.2,1.4,0.5
salt:2.8'
type: string
filename:
description: Filename. Mutually exclusive with sourceFilename and targetFilename
example: field.conf
type: string
sourceFilename:
description: path to the filename. Mutually exclusive with filename and content.
If set, must also provide sourceFilename
type: string
targetFilename:
description: How to rename sourceFilename. Mutually exclusive with filename
and content. If set, must also provide targetFilename
type: string
type: object
imagepullsecret:
properties:
password:
type: string
server:
description: docker registry, e.g. res-drl-hpc-docker-local.artifactory.swg-devops.com
example: url-docker-registry
type: string
username:
description: username to use when authenticating to docker registry
type: string
required:
- password
- server
- username
type: object
input-filename:
properties:
name:
description: The name of the input file
type: string
type: object
internal-experiment:
properties:
pvep:
allOf:
- $ref: '#/definitions/ve'
description: The Parameterised Virtual Experiment Package that parameterizes
the execution of the workflow
workflow:
allOf:
- $ref: '#/definitions/internal-experiment-workflow'
description: The definition of the workflow
type: object
internal-experiment-workflow:
properties:
dsl:
description: The dictionary representing an experiment in DSL format
type: object
type: object
library-graph:
properties:
components:
items:
description: The DSL 2.0 definition of a component template, there must
be at least one.
type: object
type: array
entrypoint:
description: The DSL 2.0 definition of the entrypoint - optional if there
is exactly 1 workflow template. If set, it must point to a workflow template
type: object
workflows:
items:
description: The DSL 2.0 definition of a workflow template, there must be
at least one.
type: object
type: array
type: object
mount-volume:
properties:
applicationDependency:
description: Application dependency for which flow will create a link that
points to the mount-path of this volume (optional). This is expected to
be an entry under the list of strings defined by the application-dependencies.<platform-name>
field within the FlowIR of the workflow.
type: string
subPath:
description: Path within the volume from which the container's volume should
be mounted. Defaults to "" (volume's root).
type: string
type:
allOf:
- $ref: '#/definitions/volume-type'
default: {}
description: Volume type definition
type: object
option-valuefrom-secretkeyref:
properties:
key:
description: Name of the key inside the Kubernetes Secret object
type: string
name:
description: Name of the Kubernetes Secret object
type: string
required:
- name
type: object
orchestratorresources:
properties:
cpu:
description: How many cores to request for the orchestrator executing the
workflow
type: string
memory:
description: How much memory to request for the orchestrator executing the
workflow
type: string
type: object
package-history:
properties:
tags:
items:
$ref: '#/definitions/package-history-tag'
type: array
untagged:
items:
$ref: '#/definitions/package-history-untagged'
type: array
type: object
package-history-tag:
properties:
head:
description: The digest that the tag points to
example: sha256x67357eeed694e4f954fda270d6adba7b2399823c1b30dd1513d9e8c08d919399
type: string
tag:
description: The tag e.g. latest
example: latest
type: string
type: object
package-history-untagged:
properties:
digest:
description: A digest which is no longer the head of any of the tags
example: sha256xd5067fc65aa4b569348caf347ca76983f6ecd2e45cc708410ba806f3835905ef
type: string
type: object
query-experiment-common:
properties:
matchPackageVersion:
default: false
description: Whether to match the version of packages
type: boolean
mustHaveOnePackage:
default: true
description: Match only parameterised virtual experiment packages with just
one base package
type: boolean
type: object
query-experiments:
properties:
common:
$ref: '#/definitions/query-experiment-common'
package:
$ref: '#/definitions/query-experiments-package'
relationship:
$ref: '#/definitions/query-experiments-relationship'
type: object
query-experiments-package:
properties:
definition:
$ref: '#/definitions/ve-base-package'
type: object
query-experiments-relationship:
properties:
identifier:
description: The identifier of the relationship
type: string
transform:
$ref: '#/definitions/query-experiments-relationship-transform'
type: object
query-experiments-relationship-transform:
properties:
matchInputGraph:
default: false
description: Whether to query using the package of the inputGraph
type: boolean
matchOutputGraph:
default: false
description: Whether to query using the package of the inputGraph
type: boolean
type: object
query-relationships:
properties:
identifier:
description: Regular expression to match names of relationships
type: string
transform:
$ref: '#/definitions/query-relationships-transform'
type: object
query-relationships-transform:
properties:
inputGraph:
$ref: '#/definitions/query-relationships-transform-inputgraph'
outputGraph:
$ref: '#/definitions/query-relationships-transform-outputgraph'
type: object
query-relationships-transform-inputgraph:
properties:
identifier:
description: The parameterised virtual experiment package containing the inputGraph
type: string
required:
- identifier
type: object
query-relationships-transform-outputgraph:
properties:
identifier:
description: Regular expression to match the identifiers of outputGraphs in
transform relationships
type: string
type: object
relationship:
properties:
description:
description: Human readable description of transformation relationship
type: string
identifier:
example: pm3-to-dft
type: string
transform:
$ref: '#/definitions/relationship-transform'
required:
- identifier
type: object
relationship-synthesize:
properties:
options:
$ref: '#/definitions/relationship-synthesize-options'
parameterisation:
$ref: '#/definitions/ve-parameterisation'
type: object
relationship-synthesize-options:
properties:
generateParameterisation:
default: true
description: Whether to auto-generate parameterisation options. When False
the method will not auto-generate any parameterisation configuration for
the synthesized parameterised virtual experiment package. When True the
method generates 1 preset for each variable in the final experiment which
has a unique value. It overrides this information using the presets/executionOptions
of the parent(outputGraph). It overrides this merged information using the
"parameterisation" settings that are part of this payload. The default is
`True`
type: boolean
type: object
relationship-transform:
properties:
inputGraph:
$ref: '#/definitions/query-relationships-transform-inputgraph'
outputGraph:
$ref: '#/definitions/query-relationships-transform-outputgraph'
relationship:
$ref: '#/definitions/relationship-transform-relationship'
type: object
relationship-transform-relationship:
properties:
graphParameters:
items:
$ref: '#/definitions/relationship-transform-relationship-graphparameters'
type: array
graphResults:
items:
$ref: '#/definitions/relationship-transform-relationship-graphresults'
type: array
inferParameters:
default: true
description: Whether to auto-update relationship with information about mappings
bettween parameters of the 2 graph fragments
type: boolean
inferResults:
default: true
description: Whether to auto-update relationship with information about mappings
bettween results of the 2 graph fragments
type: boolean
type: object
relationship-transform-relationship-graphparameters:
properties:
inputGraphParameter:
$ref: '#/definitions/relationship-transform-relationship-graphpvalue'
outputGraphParameter:
$ref: '#/definitions/relationship-transform-relationship-graphpvalue'
type: object
relationship-transform-relationship-graphpvalue:
properties:
default:
description: An optional default value that the symbolic name may contain
type: string
name:
description: Symbolic name
type: string
type: object
relationship-transform-relationship-graphresults:
properties:
inputGraphResult:
$ref: '#/definitions/relationship-transform-relationship-graphpvalue'
outputGraphResult:
$ref: '#/definitions/relationship-transform-relationship-graphpvalue'
type: object
s3:
properties:
accessKeyID:
default: ''
description: Access key id
type: string
bucket:
default: ''
description: Name of bucket
type: string
dataset:
description: Identifier of Dataset to use (uses https://github.com/datashim-io/datashim).
If set, remaining S3 information will not be used
type: string
endpoint:
default: ''
description: Endpoint URL (e.g. https://s3.eu-gb.cloud-object-storage.appdomain.cloud)
type: string
region:
default: ''
description: Region (optional)
type: string
secretAccessKey:
default: ''
description: Secret access key
type: string
type: object
s3-credentials:
properties:
accessKeyID:
description: Access key id
type: string
bucket:
description: Name of bucket
type: string
endpoint:
description: Endpoint URL (e.g. https://s3.eu-gb.cloud-object-storage.appdomain.cloud)
type: string
region:
description: Region (optional)
type: string
secretAccessKey:
description: Secret access key
type: string
type: object
s3-output:
properties:
bucketPath:
description: The ST4SD runtime core will upload the workflow outputs under
this path
type: string
credentials:
allOf:
- $ref: '#/definitions/s3-credentials'
description: S3 Configuration
required:
- bucketPath
- credentials
type: object
utilities-dsl:
properties:
components:
description: An array of component blueprints
items:
description: One component blueprint
type: object
type: array
entrypoint:
description: The entrypoint definition
type: object
workflows:
description: An array of workflow definition
items:
description: One workflow blueprint
type: object
type: array
type: object
utilities-pvep:
properties:
dsl:
description: The DSL 2.0 definition of a workflow
type: object
pvep:
description: An optional template to use when constructing the Parameterised
Virtual Experiment Pakckage (PVEP)
type: object
type: object
valueinplatform:
properties:
platform:
type: string
value:
type: string
type: object
variablewithdefaultvalues:
properties:
name:
type: string
valueFrom:
default: []
items:
$ref: '#/definitions/valueinplatform'
type: array
type: object
ve:
properties:
base:
allOf:
- $ref: '#/definitions/ve-base'
description: The configuration of the base packages
metadata:
allOf:
- $ref: '#/definitions/ve-metadata'
description: Metadata of the parameterised virtual experiment package
parameterisation:
allOf:
- $ref: '#/definitions/ve-parameterisation'
description: The parameterisation options
required:
- base
- metadata
type: object
ve-base:
properties:
packages:
default: []
description: The packages that make up this parameterised virtual experiment
package
items:
$ref: '#/definitions/ve-base-package'
type: array
required:
- packages
type: object
ve-base-package:
properties:
config:
allOf:
- $ref: '#/definitions/ve-base-package-config'
description: Configuration options for the package
name:
default: main
description: Unique name of base package in this virtual experiment entry.
Defaults to "main"
type: string
source:
allOf:
- $ref: '#/definitions/ve-base-package-source'
description: Information on the location of the package
required:
- source
type: object
ve-base-package-config:
properties:
manifestPath:
description: The path to the manifest file in the package
type: string
path:
description: The path to the workflow definition in the package
type: string
type: object
ve-base-package-source:
properties:
dataset:
allOf:
- $ref: '#/definitions/ve-base-package-source-dataset'
description: The configuration for a package that exists on a Dataset. Mutually
exclusive with @git
git:
allOf:
- $ref: '#/definitions/ve-base-package-source-git'
description: The configuration for a package that exists on a git server.
Mutually exclusive with @dataset
type: object
ve-base-package-source-dataset:
properties:
location:
allOf:
- $ref: '#/definitions/ve-base-package-source-dataset-info'
description: The Dataset which holds the package
security:
allOf:
- $ref: '#/definitions/ve-base-package-source-dataset-info'
description: The information required to get the package from the dataset
version:
description: The version of the package
type: string
required:
- location
type: object
ve-base-package-source-dataset-info:
properties:
dataset:
description: The name of the dataset
type: string
required:
- dataset
type: object
ve-base-package-source-git:
properties:
location:
allOf:
- $ref: '#/definitions/ve-base-package-source-git-location'
description: The location of the package on git
security:
allOf:
- $ref: '#/definitions/ve-base-package-source-git-security'
description: The information required to get the package from git
version:
description: The commit id of the package on git
type: string
required:
- location
type: object
ve-base-package-source-git-location:
properties:
branch:
description: Git branch name, mutually exclusive with @tag and @commit
type: string
commit:
description: Git commit digest, mutually exclusive with @branch and @tag
type: string
tag:
description: Git tag name, mutually exclusive with @branch and @commit
type: string
url:
description: Git url, must provide this if package is hosted on a Git server
type: string
required:
- url
type: object
ve-base-package-source-git-security:
properties:
oauth:
allOf:
- $ref: '#/definitions/ve-base-package-source-git-security-oauth'
description: The oauth-token to use when retrieving the package from git
type: object
ve-base-package-source-git-security-oauth:
properties:
value:
description: The value of the oauth-token, when using this field the runtime
service will store the token in a new Kubernetes Secret and update the Parameterised
Virtual Experiment Package to reference the Secret instead of the oauth-token
directly. Mutually exclusive with @valueFrom
type: string
valueFrom:
allOf:
- $ref: '#/definitions/ve-base-package-source-git-security-oauth-valuefrom'
description: A pointer to the oauth-token. Mutually exclusive with @value
type: object
ve-base-package-source-git-security-oauth-valuefrom:
properties:
secretKeyRef:
allOf:
- $ref: '#/definitions/option-valuefrom-secretkeyref'
description: Description of the Kubernetes Secret key that contains the value
of the oauth-token
type: object
ve-metadata:
properties:
package:
allOf:
- $ref: '#/definitions/ve-metadata-package'
description: Metadata aboud the parameterised virtual experiment package
registry:
allOf:
- $ref: '#/definitions/ve-metadata-registry'
description: Metadata that the registry generates
required:
- package
type: object
ve-metadata-package:
properties:
description:
description: The description of the parameterised virtual experiment package
type: string
keywords:
default: []
description: Keywords associated with the parameterised virtual experiment
package
items:
type: string
type: array
license:
description: The license of the parameterised virtual experiment package
type: string
maintainer:
description: The maintainer of the parameterised virtual experiment package
type: string
name:
description: The name of the parameterised virtual experiment package
type: string
tags:
default: []
description: The tags associated with the parameterised virtual experiment
package
items:
type: string
type: array
required:
- name
type: object
ve-metadata-registry:
properties:
containerImages:
default: []
items:
$ref: '#/definitions/container-image'
type: array
createdOn:
type: string
data:
items:
$ref: '#/definitions/data-filename'
type: array
digest:
type: string
executionOptionsDefaults:
$ref: '#/definitions/executionoptiondefaults'
inputs:
default: []
items:
$ref: '#/definitions/input-filename'
type: array
interface:
default: {}
type: object
tags:
default: []
items:
type: string
type: array
timesExecuted:
default: 0
type: integer
type: object
ve-parameterisation:
properties:
executionOptions:
allOf:
- $ref: '#/definitions/ve-parameterisation-executionoptions'
description: Parameterisation options for settings that users can override
at execution time (within constraints)
presets:
allOf:
- $ref: '#/definitions/ve-parameterisation-presets'
description: Parameterisation options for settings that users cannot override
at execution time
type: object
ve-parameterisation-executionoptions:
properties:
data:
default: []
description: Parameterisation options for data files which the users can override
at execution time
items:
$ref: '#/definitions/data-filename'
type: array
platform:
default: []
description: Parameterisation options for the platform to specialize the workflow
at execution time.The users can override this option at execution time (within
constraints)
items:
type: string
type: array
variables:
default: []
description: Parameterisation options for variables which the users can override
at execution time (within constraints)
items:
$ref: '#/definitions/ve-parameterisation-executionoptions-variable'
type: array
type: object
ve-parameterisation-executionoptions-variable:
properties:
name:
type: string
value:
description: This is the default value of the variable, providing this field
means that the variable can recieve *any* value
type: string
valueFrom:
description: An array of choices that this variable must be set to. If at
execution time the variable does not receive a value, then the default value
is the first value in this array
items:
$ref: '#/definitions/ve-parameterisation-executionoptions-variable-choice'
type: array
type: object
ve-parameterisation-executionoptions-variable-choice:
properties:
value:
description: The value of the variable, must be compatible with the parameterisation
options of the parameterised virtual experiment package
type: string
type: object
ve-parameterisation-presets:
properties:
data:
default: []
description: The configuration for data-files
items:
$ref: '#/definitions/data-filename'
type: array
environmentVariables:
default: []
description: Environment variables to inject into the processes that orchestrate
the execution of the workflow
items:
$ref: '#/definitions/ve-parameterisation-presets-environment-variables'
type: array
platform:
description: The platform to specialize the workflow for
type: string
runtime:
allOf:
- $ref: '#/definitions/ve-parameterisation-runtime'
description: The runtime configuration of the orchestrator executing the workflow