Helper class for Google Pipelines.
| Modifiers | Name | Description |
|---|---|---|
enum |
GooglePipelinesHelper.ActionFlags |
As defined by Google pipeline API https://cloud.google.com/genomics/reference/rest/Shared.Types/Flag |
| Type | Name and description |
|---|---|
static java.util.List<java.lang.String> |
ENV_VAR_TO_INCLUDE |
static java.lang.String |
SCOPE_CLOUD_PLATFORM |
java.lang.String |
applicationName |
com.google.api.client.googleapis.auth.oauth2.GoogleCredential |
credential |
com.google.api.services.genomics.v2alpha1.Genomics |
genomicsClient |
| Constructor and description |
|---|
GooglePipelinesHelper
(com.google.api.client.googleapis.auth.oauth2.GoogleCredential credential = null, java.lang.String name = "Nextflow GooglePipelinesExecutor") |
| Type Params | Return Type | Name and description |
|---|---|---|
|
void |
cancelOperation(com.google.api.services.compute.model.Operation operation) |
|
com.google.api.services.compute.model.Operation |
checkOperationStatus(com.google.api.services.compute.model.Operation operation) |
|
com.google.api.services.lifesciences.v2beta.model.Mount |
configureMount(java.lang.String diskName, java.lang.String mountPath, boolean readOnly = false) |
|
com.google.api.services.lifesciences.v2beta.model.Resources |
configureResources(java.lang.String machineType, java.lang.String projectId, java.util.List<java.lang.String> zone, java.util.List<java.lang.String> region, java.lang.String diskName, java.lang.Integer diskSizeGb, java.util.List<java.lang.String> scopes, boolean preemptible, nextflow.executor.res.AcceleratorResource accelerator) |
|
com.google.api.services.lifesciences.v2beta.model.Action |
createAction(java.lang.String name, java.lang.String imageUri, java.util.List<java.lang.String> commands, java.util.List<com.google.api.services.genomics.v2alpha1.model.Mount> mounts, java.util.List<ActionFlags> flags = [], java.lang.String entrypoint = null) |
|
protected com.google.api.services.lifesciences.v2beta.model.Action |
createMainAction(GooglePipelinesSubmitRequest req) |
|
com.google.api.services.lifesciences.v2beta.model.Pipeline |
createPipeline(java.util.List<com.google.api.services.genomics.v2alpha1.model.Action> actions, com.google.api.services.lifesciences.v2beta.model.Resources resources) |
|
protected com.google.api.services.lifesciences.v2beta.model.Resources |
createResources(GooglePipelinesSubmitRequest req) |
|
protected com.google.api.services.lifesciences.v2beta.model.Action |
createStagingAction(GooglePipelinesSubmitRequest req) |
|
protected com.google.api.services.lifesciences.v2beta.model.Action |
createUnstagingAction(GooglePipelinesSubmitRequest req) |
|
java.util.Map<java.lang.String, java.lang.String> |
getEnvironment() |
|
void |
init() |
|
com.google.api.services.compute.model.Operation |
runPipeline(com.google.api.services.lifesciences.v2beta.model.Pipeline pipeline, java.util.Map<java.lang.String, java.lang.String> labels = [:]) |
|
static java.lang.String |
sanitizeName(java.lang.String name) |
|
com.google.api.services.compute.model.Operation |
submitPipeline(GooglePipelinesSubmitRequest req) |
| Methods inherited from class | Name |
|---|---|
class java.lang.Object |
java.lang.Object#wait(long, int), java.lang.Object#wait(long), java.lang.Object#wait(), java.lang.Object#equals(java.lang.Object), java.lang.Object#toString(), java.lang.Object#hashCode(), java.lang.Object#getClass(), java.lang.Object#notify(), java.lang.Object#notifyAll() |
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