From 1331fea82bb6d6a1d57baa366ad7057176fbc2b9 Mon Sep 17 00:00:00 2001
From: athith-g <66563785+athith-g@users.noreply.github.com>
Date: Mon, 22 Jul 2024 14:38:33 -0400
Subject: [PATCH] feat: update TES models to v1.1 (#179)

* feat: add ignore_error to TesExecutor

* feat: add backend_parameters and backend_parameters_strict to TesResources

* feat: add new tesStates

* refactor: make TesFileType optional

* feat: add streamable to TesInput

* refactor: avoid string literal

* fix: shorten doc line lengths

* fix: change example to examples

---------

Co-authored-by: Alex Kanitz <alexander.kanitz@unibas.ch>
---
 pro_tes/ga4gh/tes/models.py | 57 +++++++++++++++++++++++++++++++++++--
 1 file changed, 55 insertions(+), 2 deletions(-)

diff --git a/pro_tes/ga4gh/tes/models.py b/pro_tes/ga4gh/tes/models.py
index 2f0b039..a9bdb2c 100644
--- a/pro_tes/ga4gh/tes/models.py
+++ b/pro_tes/ga4gh/tes/models.py
@@ -111,6 +111,15 @@ class TesExecutor(CustomBaseModel):
         ),
         examples=[{"BLASTDB": "/data/GRC38", "HMMERDB": "/data/hmmer"}],
     )
+    ignore_error: Optional[bool] = Field(
+        default=None,
+        description=(
+            "Default behavior of running an array of executors is that "
+            "execution stopson the first error. If `ignore_error` is `True`, "
+            "then the runner will record error exit codes, but will continue "
+            "on to the next tesExecutor."
+        ),
+    )
 
 
 class TesExecutorLog(CustomBaseModel):
@@ -181,7 +190,7 @@ class TesInput(CustomBaseModel):
         ),
         examples=["/data/file1"],
     )
-    type: TesFileType
+    type: Optional[TesFileType] = TesFileType.FILE
     content: Optional[str] = Field(
         default=None,
         description=(
@@ -191,6 +200,20 @@ class TesInput(CustomBaseModel):
             ' "url"             must be ignored.'
         ),
     )
+    streamable: Optional[bool] = Field(
+        default=None,
+        description=(
+            "Indicate that a file resource could be accessed using a"
+            " streaming interface, ie a FUSE mounted s3 object. This flag"
+            " indicates that using a streaming mount, as opposed to "
+            "downloading the whole file to the local scratch space, may be "
+            "faster despite the latency and overhead. This does not mean that"
+            " the backend will use a streaming interface, as it may not be "
+            "provided by the vendor, but if the capacity is avalible it can "
+            " be used without degrading the performance of the underlying"
+            " program."
+        ),
+    )
 
 
 class TesOutput(CustomBaseModel):
@@ -220,7 +243,7 @@ class TesOutput(CustomBaseModel):
             " absolute path."
         ),
     )
-    type: TesFileType
+    type: Optional[TesFileType] = TesFileType.FILE
 
 
 class TesOutputFileLog(CustomBaseModel):
@@ -284,6 +307,34 @@ class TesResources(CustomBaseModel):
         ),
         examples=["us-west-1"],
     )
+    backend_parameters: Optional[dict[str, str]] = Field(
+        default=None,
+        description=(
+            "Key/value pairs for backend configuration.ServiceInfo shall "
+            "return a list of keys that a backend supports. Keys are case "
+            "insensitive. It is expected that clients pass all runtime or "
+            "hardware requirement key/values that are not mapped to existing"
+            " tesResources properties to backend_parameters. Backends shall"
+            " log system warnings if a key is passed that is unsupported. "
+            "Backends shall not store or return unsupported keys if included "
+            "in a task. If backend_parameters_strict equals true, backends "
+            "should fail the task if any key/values are unsupported, "
+            " otherwise, backends should attempt to run the task Intended "
+            "uses include VM size selection, coprocessor configuration,"
+            ' etc. \nExample: ```\n{\n  "backend_parameters" : {\n    '
+            '"VmSize" :"Standard_D64_v3"\n  }\n}\n```'
+        ),
+        examples=[{"VmSize": "Standard_D64_v3"}],
+    )
+    backend_parameters_strict: Optional[bool] = Field(
+        default=False,
+        description=(
+            "If set to true, backends should fail the task if any"
+            " backend_parameters key/values are unsupported, otherwise, "
+            "backends should attempt to run the task"
+        ),
+        examples=[False],
+    )
 
 
 class Artifact(Enum):
@@ -434,6 +485,8 @@ class TesState(Enum):
     EXECUTOR_ERROR = "EXECUTOR_ERROR"
     SYSTEM_ERROR = "SYSTEM_ERROR"
     CANCELED = "CANCELED"
+    PREEMPTED = "PREEMPTED"
+    CANCELING = "CANCELING"
 
 
 class TesNextTes(CustomBaseModel):