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@JaeAeich
JaeAeich committed May 4, 2024
1 parent 50fc8c0 commit bf2ae8b
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Showing 2 changed files with 67 additions and 54 deletions.
94 changes: 48 additions & 46 deletions pro_tes/ga4gh/tes/models.py
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@ class TesCreateTaskResponse(CustomBaseModel):

class TesExecutor(CustomBaseModel):
image: str = Field(
[""],
default=[""],
description=(
"Name of the container image. The string will be passed as "
" the image\nargument to the containerization run command. "
Expand All @@ -49,7 +49,7 @@ class TesExecutor(CustomBaseModel):
examples=["ubuntu:20.04"],
)
command: list[str] = Field(
[""],
default=[""],
description=(
"A sequence of program arguments to execute, where the "
" first argument\nis the program to execute (i.e. argv). "
Expand All @@ -59,7 +59,7 @@ class TesExecutor(CustomBaseModel):
examples=["/bin/md5", "/data/file1"],
)
workdir: Optional[str] = Field(
None,
default=None,
description=(
"The working directory that the command will be executed "
" in.\nIf not defined, the system will default to the directory"
Expand All @@ -68,7 +68,7 @@ class TesExecutor(CustomBaseModel):
examples=["/data/"],
)
stdin: Optional[str] = Field(
None,
default=None,
description=(
"Path inside the container to a file which will be "
" piped\nto the executor's stdin. This must be an absolute path. "
Expand All @@ -82,7 +82,7 @@ class TesExecutor(CustomBaseModel):
examples=["/data/file1"],
)
stdout: Optional[str] = Field(
None,
default=None,
description=(
"Path inside the container to a file where the "
" executor's\nstdout will be written to. Must be an absolute"
Expand All @@ -92,7 +92,7 @@ class TesExecutor(CustomBaseModel):
examples=["/tmp/stdout.log"],
)
stderr: Optional[str] = Field(
None,
default=None,
description=(
"Path inside the container to a file where the "
" executor's\nstderr will be written to. Must be an absolute"
Expand All @@ -102,7 +102,7 @@ class TesExecutor(CustomBaseModel):
examples=["/tmp/stderr.log"],
)
env: Optional[dict[str, str]] = Field(
None,
default=None,
description=(
"Enviromental variables to set within the container. "
' Example:\n```\n{\n "env" : {\n "ENV_CONFIG_PATH"'
Expand All @@ -115,17 +115,17 @@ class TesExecutor(CustomBaseModel):

class TesExecutorLog(CustomBaseModel):
start_time: Optional[str] = Field(
None,
default=None,
description="Time the executor started, in RFC 3339 format.",
examples=["2020-10-02T10:00:00-05:00"],
)
end_time: Optional[str] = Field(
None,
default=None,
description="Time the executor ended, in RFC 3339 format.",
examples=["2020-10-02T11:00:00-05:00"],
)
stdout: Optional[str] = Field(
None,
default=None,
description=(
"Stdout content.\n\nThis is meant for convenience. No "
" guarantees are made about the content.\nImplementations may"
Expand All @@ -137,7 +137,7 @@ class TesExecutorLog(CustomBaseModel):
),
)
stderr: Optional[str] = Field(
None,
default=None,
description=(
"Stderr content.\n\nThis is meant for convenience. No "
" guarantees are made about the content.\nImplementations may"
Expand All @@ -150,7 +150,7 @@ class TesExecutorLog(CustomBaseModel):
)
# exit code not optional according to specs, but Funnel may return 'null'
exit_code: Optional[int] = Field(
None,
default=None,
description="Exit code.",
)

Expand All @@ -164,7 +164,7 @@ class TesInput(CustomBaseModel):
name: Optional[str] = None
description: Optional[str] = None
url: Optional[str] = Field(
None,
default=None,
description=(
'REQUIRED, unless "content" is set.\n\nURL in long term '
" storage, for example:\n - s3://my-object-store/file1\n - "
Expand All @@ -183,7 +183,7 @@ class TesInput(CustomBaseModel):
)
type: TesFileType
content: Optional[str] = Field(
None,
default=None,
description=(
"File content literal.\n\nImplementations should support a "
" minimum of 128 KiB in this field\nand may define their own "
Expand All @@ -195,10 +195,10 @@ class TesInput(CustomBaseModel):

class TesOutput(CustomBaseModel):
name: Optional[str] = Field(
None, description="User-provided name of output file"
default=None, description="User-provided name of output file"
)
description: Optional[str] = Field(
None,
default=None,
description=(
"Optional users provided description field, can be used "
" for documentation."
Expand Down Expand Up @@ -250,10 +250,10 @@ class TesOutputFileLog(CustomBaseModel):

class TesResources(CustomBaseModel):
cpu_cores: Optional[int] = Field(
None, description="Requested number of CPUs", examples=[4]
default=None, description="Requested number of CPUs", examples=[4]
)
preemptible: Optional[bool] = Field(
None,
default=None,
description=(
"Define if the task is allowed to run on preemptible "
" compute instances,\nfor example, AWS Spot. This option may have"
Expand All @@ -263,17 +263,17 @@ class TesResources(CustomBaseModel):
examples=[False],
)
ram_gb: Optional[float] = Field(
None,
default=None,
description="Requested RAM required in gigabytes (GB)",
examples=[8]
)
disk_gb: Optional[float] = Field(
None,
default=None,
description="Requested disk size in gigabytes (GB)",
examples=[40]
)
zones: Optional[list[str]] = Field(
None,
default=None,
description=(
"Request that the task be run in these compute zones. How "
" this string\nis utilized will be dependent on the backend"
Expand Down Expand Up @@ -355,7 +355,7 @@ class Service(CustomBaseModel):
)
type: Optional[ServiceType]
description: Optional[str] = Field(
None,
default=None,
description=(
"Description of the service. Should be human readable and "
" provide information about the service."
Expand All @@ -366,7 +366,7 @@ class Service(CustomBaseModel):
..., description="Organization providing the service"
)
contactUrl: Optional[AnyUrl] = Field(
None,
default=None,
description=(
"URL of the contact for the provider of this service, e.g. "
" a link to a contact form (RFC 3986 format), or an email "
Expand All @@ -375,7 +375,7 @@ class Service(CustomBaseModel):
examples=["mailto:[email protected]"],
)
documentationUrl: Optional[AnyUrl] = Field(
None,
default=None,
description=(
"URL of the documentation of this service (RFC 3986"
" format).This should help someone learn how to use"
Expand All @@ -385,23 +385,23 @@ class Service(CustomBaseModel):
examples=["https://docs.myservice.example.com"],
)
createdAt: Optional[datetime] = Field(
None,
default=None,
description=(
"Timestamp describing when the service was first deployed "
" and available (RFC 3339 format)"
),
examples=["2019-06-04T12:58:19Z"],
)
updatedAt: Optional[datetime] = Field(
None,
default=None,
description=(
"Timestamp describing when the service was last updated "
" (RFC 3339 format)"
),
examples=["2019-06-04T12:58:19Z"],
)
environment: Optional[str] = Field(
None,
default=None,
description=(
"Environment the service is running in. Use this to "
" distinguish between production, development and testing/staging "
Expand Down Expand Up @@ -459,7 +459,7 @@ class Metadata(CustomBaseModel):
"""Create model instance for metadata."""

forwarded_to: Optional[TesNextTes] = Field(
None,
default=None,
description="TaskLog describes logging information related to a Task",
)

Expand All @@ -469,19 +469,19 @@ class TesTaskLog(CustomBaseModel):
..., description="Logs for each executor"
)
metadata: Optional[Metadata] = Field(
None,
default=None,
description=(
"Arbitrary logging metadata included by the implementation."
),
examples=[{"host": "worker-001", "slurmm_id": 123456}],
)
start_time: Optional[str] = Field(
None,
default=None,
description="When the task started, in RFC 3339 format.",
examples=["2020-10-02T10:00:00-05:00"],
)
end_time: Optional[str] = Field(
None,
default=None,
description="When the task ended, in RFC 3339 format.",
examples=["2020-10-02T11:00:00-05:00"],
)
Expand All @@ -493,7 +493,7 @@ class TesTaskLog(CustomBaseModel):
),
)
system_logs: Optional[list[str]] = Field(
None,
default=None,
description=(
"System logs are any logs the system decides are relevant, "
" \nwhich are not tied directly to an Executor"
Expand All @@ -514,7 +514,7 @@ class TesServiceType(ServiceType):

class TesServiceInfo(Service):
storage: Optional[list[str]] = Field(
None,
default=None,
description=(
"Lists some, but not necessarily all, storage locations "
" supported\nby the service."
Expand All @@ -529,21 +529,24 @@ class TesServiceInfo(Service):

class TesTask(CustomBaseModel):
id: Optional[str] = Field(
None,
default=None,
description="Task identifier assigned by the server.",
examples=["job-0012345"],
)
state: Optional[TesState] = None
name: Optional[str] = Field(None, description="User-provided task name.")
name: Optional[str] = Field(
default=None,
description="User-provided task name."
)
description: Optional[str] = Field(
None,
default=None,
description=(
"Optional user-provided description of task for "
" documentation purposes."
),
)
inputs: Optional[list[TesInput]] = Field(
None,
default=None,
description=(
"Input files that will be used by the task. Inputs will be "
" downloaded\nand mounted into the executor container as"
Expand All @@ -555,7 +558,7 @@ class TesTask(CustomBaseModel):
}]]
)
outputs: Optional[list[TesOutput]] = Field(
None,
default=None,
description=(
"Output files.\nOutputs will be uploaded from the executor "
" container to long-term storage."
Expand All @@ -570,7 +573,7 @@ class TesTask(CustomBaseModel):
)
resources: Optional[TesResources] = None
executors: list[TesExecutor] = Field(
[TesExecutor],
default=[TesExecutor],
description=(
"An array of executors to be run. Each of the executors "
" will run one\nat a time sequentially. Each executor is a"
Expand All @@ -582,7 +585,7 @@ class TesTask(CustomBaseModel):
),
)
volumes: Optional[list[str]] = Field(
None,
default=None,
description=(
"Volumes are directories which may be used to share data "
" between\nExecutors. Volumes are initialized as empty"
Expand All @@ -598,7 +601,7 @@ class TesTask(CustomBaseModel):
examples=[["/vol/A/"]],
)
tags: Optional[dict[str, str]] = Field(
None,
default=None,
description=(
"A key-value map of arbitrary tags. These can be used to "
" store meta-data\nand annotations about a task."
Expand All @@ -608,17 +611,16 @@ class TesTask(CustomBaseModel):
),
examples=[{"WORKFLOW_ID": "cwl-01234", "PROJECT_GROUP": "alice-lab"}],
)

logs: Optional[list[TesTaskLog]] = Field(
None,
default=None,
description=(
"Task logging information.\nNormally, this will contain "
" only one entry, but in the case where\na task fails and is "
" retried, an entry will be appended to this list."
),
)
creation_time: Optional[str] = Field(
None,
default=None,
description=(
"Date + time the task was created, in RFC 3339 format.\n "
" This is set by the system, not the client."
Expand All @@ -643,7 +645,7 @@ class TesListTasksResponse(CustomBaseModel):
),
)
next_page_token: Optional[str] = Field(
None,
default=None,
description=(
"Token used to return the next page of results. This value "
" can be used\nin the `page_token` field of the next ListTasks "
Expand Down Expand Up @@ -716,7 +718,7 @@ class DbDocument(CustomBaseModel):
tes_endpoint: External TES endpoint.
"""

task: TesTask = TesTask() # type: ignore
task: TesTask = TesTask()
task_original: TesTask = TesTask(executors=[]) # type: ignore
user_id: Optional[str] = None
worker_id: str = ""
Expand Down
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