Helper class for Google Pipelines.
| Modifiers | Name | Description |
|---|---|---|
static enum |
GoogleLifeSciencesHelper.ActionFlags |
As defined by Google pipeline API https://cloud.google.com/genomics/reference/rest/Shared.Types/Flag |
| Modifiers | Name | Description |
|---|---|---|
static java.lang.String |
DEFAULT_APP_NAME |
|
static java.util.List<java.lang.String> |
DEFAULT_LOCATIONS |
|
static java.lang.String |
SCOPE_CLOUD_PLATFORM |
|
static java.lang.String |
SSH_DAEMON_NAME |
| Type | Name and description |
|---|---|
java.lang.String |
applicationName |
com.google.api.services.lifesciences.v2beta.CloudLifeSciences |
client |
GoogleLifeSciencesConfig |
config |
com.google.auth.oauth2.GoogleCredentials |
credentials |
| Constructor and description |
|---|
protected GoogleLifeSciencesHelper
(com.google.auth.oauth2.GoogleCredentials credential = null, java.lang.String name = DEFAULT_APP_NAME) |
GoogleLifeSciencesHelper
(GoogleLifeSciencesConfig config) |
| 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) |
|
void |
checkValidLocation() |
|
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.lifesciences.v2beta.model.Mount> mounts, java.util.List<ActionFlags> flags = [], java.lang.String entrypoint = null) |
|
protected com.google.api.services.lifesciences.v2beta.model.Action |
createMainAction(GoogleLifeSciencesSubmitRequest req) |
|
com.google.api.services.lifesciences.v2beta.model.Pipeline |
createPipeline(java.util.List<com.google.api.services.lifesciences.v2beta.model.Action> actions, com.google.api.services.lifesciences.v2beta.model.Resources resources) |
|
protected com.google.api.services.lifesciences.v2beta.model.Resources |
createResources(GoogleLifeSciencesSubmitRequest req) |
|
protected com.google.api.services.lifesciences.v2beta.model.Action |
createSshDaemonAction(GoogleLifeSciencesSubmitRequest req) |
|
protected com.google.api.services.lifesciences.v2beta.model.Action |
createStagingAction(GoogleLifeSciencesSubmitRequest req) |
|
protected com.google.api.services.lifesciences.v2beta.model.Action |
createUnstagingAction(GoogleLifeSciencesSubmitRequest req) |
|
java.util.Map<java.lang.String, java.lang.String> |
getEnvironment() |
|
static java.lang.String |
getLocalTaskDir(java.nio.file.Path workDir) |
|
java.lang.String |
getMainScript(java.nio.file.Path workDir) |
|
static java.lang.String |
getRemoteTaskDir(java.nio.file.Path workDir) |
|
java.lang.String |
getStagingScript(java.nio.file.Path workDir) |
|
java.lang.String |
getUnstagingScript(java.nio.file.Path workDir) |
|
GoogleLifeSciencesHelper |
init() |
|
com.google.api.services.compute.model.Operation |
runPipeline(java.lang.String project, java.lang.String location, 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) |
|
protected com.google.api.services.lifesciences.v2beta.model.Action |
setFlags(com.google.api.services.lifesciences.v2beta.model.Action action, java.util.List<ActionFlags> flags) |
|
com.google.api.services.compute.model.Operation |
submitPipeline(GoogleLifeSciencesSubmitRequest 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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