From d4fa86bdcca630dce0902a11389492dc1a763161 Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Mon, 11 Jul 2022 16:10:15 -0500 Subject: [PATCH 01/13] Add in support for workflow enginer and version when submitting a request. --- openapi/components/schemas/RunRequest.yaml | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/openapi/components/schemas/RunRequest.yaml b/openapi/components/schemas/RunRequest.yaml index 55326ccd..1fb523cf 100644 --- a/openapi/components/schemas/RunRequest.yaml +++ b/openapi/components/schemas/RunRequest.yaml @@ -27,6 +27,14 @@ properties: type: object additionalProperties: type: string + workflow_engine: + type: string + description: >- + The workflow engine, must be one supported by this WES instance + workflow_engine_version: + type: string + description: >- + The workflow engine version, must be one supported by this WES instance workflow_url: type: string description: >- @@ -36,4 +44,4 @@ properties: description: >- To execute a workflow, send a run request including all the details needed to begin downloading - and executing a given workflow. \ No newline at end of file + and executing a given workflow. From c6d321258c00b5ac6c0e92b4b1c933ecb6da8c93 Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Tue, 12 Jul 2022 11:14:38 -0500 Subject: [PATCH 02/13] Expand out Workflow Engine version to by array of strings. --- openapi/components/schemas/ServiceInfo.yaml | 4 ++-- openapi/components/schemas/WorkflowEngineVersion.yaml | 9 +++++++++ 2 files changed, 11 insertions(+), 2 deletions(-) create mode 100644 openapi/components/schemas/WorkflowEngineVersion.yaml diff --git a/openapi/components/schemas/ServiceInfo.yaml b/openapi/components/schemas/ServiceInfo.yaml index 1ae78454..bcf0ded2 100644 --- a/openapi/components/schemas/ServiceInfo.yaml +++ b/openapi/components/schemas/ServiceInfo.yaml @@ -20,7 +20,7 @@ allOf: workflow_engine_versions: type: object additionalProperties: - type: string + $ref: './WorkflowEngineVersion.yaml' default_workflow_engine_parameters: type: array items: @@ -47,4 +47,4 @@ allOf: - default_workflow_engine_parameters - system_state_counts - auth_instructions_url - - tags \ No newline at end of file + - tags diff --git a/openapi/components/schemas/WorkflowEngineVersion.yaml b/openapi/components/schemas/WorkflowEngineVersion.yaml new file mode 100644 index 00000000..e06bfcad --- /dev/null +++ b/openapi/components/schemas/WorkflowEngineVersion.yaml @@ -0,0 +1,9 @@ +title: WorkflowEngineVersion +type: object +properties: + workflow_engine_version: + type: array + items: + type: string + description: an array of one or more acceptable engines for the `workflow_engine` +description: Available workflow engines supported by a given instance of the service. From 84913d25793e9cfb2bec2e7bf9360eb31ad5b40c Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Tue, 9 Aug 2022 09:02:41 -0500 Subject: [PATCH 03/13] Update RunRequest.yaml --- openapi/components/schemas/RunRequest.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/openapi/components/schemas/RunRequest.yaml b/openapi/components/schemas/RunRequest.yaml index 1fb523cf..7f44acac 100644 --- a/openapi/components/schemas/RunRequest.yaml +++ b/openapi/components/schemas/RunRequest.yaml @@ -30,11 +30,13 @@ properties: workflow_engine: type: string description: >- - The workflow engine, must be one supported by this WES instance + The workflow engine, must be one supported by this WES instance. Required if workflow_engine_version is provided. workflow_engine_version: type: string description: >- - The workflow engine version, must be one supported by this WES instance + The workflow engine version, must be one supported by this WES instance. + If workflow_engine is provided, but workflow_engine_version is not, clients can make no assumptions with regard to the engine version the WES instance uses to process the request if + that WES instance supports multiple versions of the requested engine. workflow_url: type: string description: >- From 27cd763a881ecd9656821db668754358ddc2484d Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Tue, 9 Aug 2022 09:44:14 -0500 Subject: [PATCH 04/13] Add in workflow_engine and version to the run spec. --- openapi/paths/runs.yaml | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/openapi/paths/runs.yaml b/openapi/paths/runs.yaml index 4080d1ba..d00bb800 100644 --- a/openapi/paths/runs.yaml +++ b/openapi/paths/runs.yaml @@ -69,6 +69,10 @@ The `workflow_type` is the type of workflow language and must be "CWL" or "WDL" currently (or another alternative supported by this WES instance). The `workflow_type_version` is the version of the workflow language submitted and must be one supported by this WES instance. + + The `workflow_engine` is the engine that supports the workflow_type and must be supported by this WES instance. + + The `workflow_engine_version` is the version of workflow engine and must besupported by this WES instance. See the `RunRequest` documentation for details about other fields. operationId: RunWorkflow @@ -88,6 +92,10 @@ type: string tags: type: string + workflow_engine: + type: string + workflow_engine_version: + type: string workflow_engine_parameters: type: string workflow_url: From a8190f6b14410a05c3a2cd7798eece6de6cbf9ae Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Tue, 9 Aug 2022 10:16:36 -0500 Subject: [PATCH 05/13] Fix typo --- openapi/paths/runs.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/openapi/paths/runs.yaml b/openapi/paths/runs.yaml index d00bb800..dbf74c43 100644 --- a/openapi/paths/runs.yaml +++ b/openapi/paths/runs.yaml @@ -72,7 +72,7 @@ The `workflow_engine` is the engine that supports the workflow_type and must be supported by this WES instance. - The `workflow_engine_version` is the version of workflow engine and must besupported by this WES instance. + The `workflow_engine_version` is the version of workflow engine and must be supported by this WES instance. See the `RunRequest` documentation for details about other fields. operationId: RunWorkflow From e46a97da7c3b8a17e8486e530293ed1484b5d3ce Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Tue, 9 Aug 2022 10:20:09 -0500 Subject: [PATCH 06/13] Fix for consitency --- openapi/components/schemas/WorkflowEngineVersion.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/openapi/components/schemas/WorkflowEngineVersion.yaml b/openapi/components/schemas/WorkflowEngineVersion.yaml index e06bfcad..df740eae 100644 --- a/openapi/components/schemas/WorkflowEngineVersion.yaml +++ b/openapi/components/schemas/WorkflowEngineVersion.yaml @@ -5,5 +5,5 @@ properties: type: array items: type: string - description: an array of one or more acceptable engines for the `workflow_engine` + description: An array of one or more acceptable engines for the `workflow_engine` description: Available workflow engines supported by a given instance of the service. From 60129649748dff6114510ccac541abd3c05d8912 Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Fri, 26 Aug 2022 15:59:17 -0500 Subject: [PATCH 07/13] Add more clarity about engine and version --- openapi/components/schemas/RunRequest.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/openapi/components/schemas/RunRequest.yaml b/openapi/components/schemas/RunRequest.yaml index 7f44acac..6ae88ef8 100644 --- a/openapi/components/schemas/RunRequest.yaml +++ b/openapi/components/schemas/RunRequest.yaml @@ -47,3 +47,6 @@ description: >- To execute a workflow, send a run request including all the details needed to begin downloading and executing a given workflow. + + If workflow_engine and workflow_engine_version is not provided, clients can use the most recent workflow_engine_version of workflow_enginer that WES instance uses to process the request if + supports for the requested workflow_type. From 809fb190eca056f8a56b152e112797ae5241cf8e Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Fri, 26 Aug 2022 16:05:06 -0500 Subject: [PATCH 08/13] Update description --- openapi/components/schemas/WorkflowEngineVersion.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/openapi/components/schemas/WorkflowEngineVersion.yaml b/openapi/components/schemas/WorkflowEngineVersion.yaml index df740eae..70061463 100644 --- a/openapi/components/schemas/WorkflowEngineVersion.yaml +++ b/openapi/components/schemas/WorkflowEngineVersion.yaml @@ -5,5 +5,5 @@ properties: type: array items: type: string - description: An array of one or more acceptable engines for the `workflow_engine` -description: Available workflow engines supported by a given instance of the service. + description: An array of one or more acceptable engines versions for the `workflow_engine` +description: Available workflow engine versions supported by a given instance of the service. From c1e81b88cd79f51e95351015a7c7808d7e5db061 Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Mon, 29 Aug 2022 16:23:22 -0500 Subject: [PATCH 09/13] Address changes requested. --- openapi/components/schemas/RunRequest.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/openapi/components/schemas/RunRequest.yaml b/openapi/components/schemas/RunRequest.yaml index 6ae88ef8..308b82d8 100644 --- a/openapi/components/schemas/RunRequest.yaml +++ b/openapi/components/schemas/RunRequest.yaml @@ -35,7 +35,7 @@ properties: type: string description: >- The workflow engine version, must be one supported by this WES instance. - If workflow_engine is provided, but workflow_engine_version is not, clients can make no assumptions with regard to the engine version the WES instance uses to process the request if + If workflow_engine is provided, but workflow_engine_version is not, servers can make no assumptions with regard to the engine version the WES instance uses to process the request if that WES instance supports multiple versions of the requested engine. workflow_url: type: string @@ -48,5 +48,5 @@ description: >- and executing a given workflow. - If workflow_engine and workflow_engine_version is not provided, clients can use the most recent workflow_engine_version of workflow_enginer that WES instance uses to process the request if + If workflow_engine and workflow_engine_version are not provided, servers can use the most recent workflow_engine_version of workflow_engine that WES instance uses to process the request if supports for the requested workflow_type. From 88612d5edf8702e72c634718144a8112a272393e Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Tue, 15 Nov 2022 12:36:31 -0600 Subject: [PATCH 10/13] Fix indentation. --- openapi/workflow_execution_service.openapi.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/openapi/workflow_execution_service.openapi.yaml b/openapi/workflow_execution_service.openapi.yaml index a703f847..be25a00c 100644 --- a/openapi/workflow_execution_service.openapi.yaml +++ b/openapi/workflow_execution_service.openapi.yaml @@ -693,7 +693,7 @@ components: items: type: string description: An array of one or more acceptable engines versions for the `workflow_engine` -description: Available workflow engine versions supported by a given instance of the service. + description: Available workflow engine versions supported by a given instance of the service. RunListResponse: title: RunListResponse type: object From aa1cbaa651611e06d677ef34795b04fb0a27aca6 Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Tue, 10 Jan 2023 09:24:36 -0600 Subject: [PATCH 11/13] Resolve reorganization of yaml's into 1 single yaml. --- openapi/workflow_execution_service.openapi.yaml | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/openapi/workflow_execution_service.openapi.yaml b/openapi/workflow_execution_service.openapi.yaml index 6d7ebec7..33212088 100644 --- a/openapi/workflow_execution_service.openapi.yaml +++ b/openapi/workflow_execution_service.openapi.yaml @@ -506,6 +506,7 @@ components: - SYSTEM_ERROR - CANCELED - CANCELING + - PREEMPTED type: string description: > State can take any of the following values: @@ -532,6 +533,10 @@ components: + CANCELED: The task was canceled by the user. + CANCELING: The task was canceled by the user, and is in the process of stopping. + + + PREEMPTED: The task is stopped (preempted) by the system. The reasons for this would be tied to + the specific system running the job. Generally, this means that the system reclaimed the compute + capacity for reallocation. RunStatus: title: RunStatus required: From 2b63c4eb20ea7bf5481ffdaf77810ef9328b7bb1 Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Tue, 10 Jan 2023 11:36:18 -0600 Subject: [PATCH 12/13] Remove preempted with accidental merge. --- openapi/workflow_execution_service.openapi.yaml | 5 ----- 1 file changed, 5 deletions(-) diff --git a/openapi/workflow_execution_service.openapi.yaml b/openapi/workflow_execution_service.openapi.yaml index 4b55530c..be25a00c 100644 --- a/openapi/workflow_execution_service.openapi.yaml +++ b/openapi/workflow_execution_service.openapi.yaml @@ -519,7 +519,6 @@ components: - SYSTEM_ERROR - CANCELED - CANCELING - - PREEMPTED type: string description: > State can take any of the following values: @@ -546,10 +545,6 @@ components: + CANCELED: The task was canceled by the user. + CANCELING: The task was canceled by the user, and is in the process of stopping. - - + PREEMPTED: The task is stopped (preempted) by the system. The reasons for this would be tied to - the specific system running the job. Generally, this means that the system reclaimed the compute - capacity for reallocation. RunStatus: title: RunStatus required: From 8b0993fc09364fbd21f618718f837df39a1daefe Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Tue, 10 Jan 2023 11:37:16 -0600 Subject: [PATCH 13/13] Add required parameter for: - workflow_type - workflow_type_version - workflow_url --- openapi/workflow_execution_service.openapi.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/openapi/workflow_execution_service.openapi.yaml b/openapi/workflow_execution_service.openapi.yaml index be25a00c..9d1abd70 100644 --- a/openapi/workflow_execution_service.openapi.yaml +++ b/openapi/workflow_execution_service.openapi.yaml @@ -559,6 +559,10 @@ components: RunRequest: title: RunRequest type: object + required: + - workflow_type + - workflow_type_version + - workflow_url properties: workflow_params: type: object