From d28a30f6fedd6146a2702b1f4c4dc1dedadb0ec6 Mon Sep 17 00:00:00 2001 From: Brad Macdonald Date: Tue, 24 Oct 2023 14:08:20 -0600 Subject: [PATCH 01/20] adds mock responses --- tests/services/nextflowtower/responses.py | 248 ++++++++++++++++++++++ 1 file changed, 248 insertions(+) diff --git a/tests/services/nextflowtower/responses.py b/tests/services/nextflowtower/responses.py index e4151d3..6a74e93 100644 --- a/tests/services/nextflowtower/responses.py +++ b/tests/services/nextflowtower/responses.py @@ -527,3 +527,251 @@ ], "totalSize": 3, } + +list_workflow_tasks = { + "tasks": [ + { + "task": { + "id": 4638140, + "taskId": 1, + "status": "COMPLETED", + "dateCreated": "2023-10-16T21:04:14Z", + "lastUpdated": "2023-10-16T21:07:27Z", + "name": "sayHello (1)", + "module": [], + "queue": "TowerForge-5im9knMLfGTl9qrPNcDk0t-work", + "memory": None, + "script": "\necho 'Bonjour world!'\n", + "tag": None, + "time": None, + "executor": "awsbatch", + "duration": 178310, + "start": "2023-10-16T21:07:03Z", + "container": "wave.seqera.io/wt/35bcf310401b/nextflow/bash:latest", + "process": "sayHello", + "attempt": 1, + "scratch": None, + "workdir": "s3://example-project-tower-scratch/work/53/d1a4bedd867b9b005c1e86291334cf", + "disk": None, + "cloudZone": "us-east-1d", + "priceModel": "spot", + "cost": 0.0000576389, + "errorAction": None, + "realtime": 2, + "nativeId": "1ffe9499-1566-4140-b652-cb930413cf77", + "pcpu": 66.7, + "pmem": 0.0, + "rss": 0, + "vmem": 0, + "peakRss": 0, + "peakVmem": 0, + "rchar": 54098, + "wchar": 199, + "syscr": 147, + "syscw": 13, + "readBytes": 352256, + "writeBytes": 0, + "volCtxt": 0, + "invCtxt": 0, + "env": None, + "submit": "2023-10-16T21:04:15Z", + "exitStatus": 0, + "complete": "2023-10-16T21:07:13Z", + "cpus": 1, + "machineType": "c6i.2xlarge", + "hash": "53/d1a4be", + "exit": "0", + } + }, + { + "task": { + "id": 4638141, + "taskId": 2, + "status": "COMPLETED", + "dateCreated": "2023-10-16T21:04:14Z", + "lastUpdated": "2023-10-16T21:07:27Z", + "name": "sayHello (2)", + "module": [], + "queue": "TowerForge-5im9knMLfGTl9qrPNcDk0t-work", + "memory": None, + "script": "\necho 'Ciao world!'\n", + "tag": None, + "time": None, + "executor": "awsbatch", + "duration": 178068, + "start": "2023-10-16T21:07:03Z", + "container": "wave.seqera.io/wt/35bcf310401b/nextflow/bash:latest", + "process": "sayHello", + "attempt": 1, + "scratch": None, + "workdir": "s3://example-project-tower-scratch/work/8b/96b02f951f46594c6d6f310e77abc7", + "disk": None, + "cloudZone": "us-east-1d", + "priceModel": "spot", + "cost": 0.0000634028, + "errorAction": None, + "realtime": 3, + "nativeId": "aa5d92fe-c2f1-4879-a768-dbc6b1c6a277", + "pcpu": 53.3, + "pmem": 0.0, + "rss": 0, + "vmem": 0, + "peakRss": 0, + "peakVmem": 0, + "rchar": 54092, + "wchar": 196, + "syscr": 147, + "syscw": 13, + "readBytes": 352256, + "writeBytes": 0, + "volCtxt": 0, + "invCtxt": 0, + "env": None, + "submit": "2023-10-16T21:04:15Z", + "exitStatus": 0, + "complete": "2023-10-16T21:07:13Z", + "cpus": 1, + "machineType": "c6i.2xlarge", + "hash": "8b/96b02f", + "exit": "0", + } + }, + { + "task": { + "id": 4638142, + "taskId": 3, + "status": "COMPLETED", + "dateCreated": "2023-10-16T21:04:14Z", + "lastUpdated": "2023-10-16T21:07:27Z", + "name": "sayHello (3)", + "module": [], + "queue": "TowerForge-5im9knMLfGTl9qrPNcDk0t-work", + "memory": None, + "script": "\necho 'Hello world!'\n", + "tag": None, + "time": None, + "executor": "awsbatch", + "duration": 177940, + "start": "2023-10-16T21:07:13Z", + "container": "wave.seqera.io/wt/35bcf310401b/nextflow/bash:latest", + "process": "sayHello", + "attempt": 1, + "scratch": None, + "workdir": "s3://example-project-tower-scratch/work/0f/929495d8a0f66c9e85a4c4f0820a54", + "disk": None, + "cloudZone": "us-east-1d", + "priceModel": "spot", + "cost": 0.0000057639, + "errorAction": None, + "realtime": 3, + "nativeId": "7696237a-8cc1-42cb-847a-a352fdbdfcff", + "pcpu": 53.3, + "pmem": 0.0, + "rss": 0, + "vmem": 0, + "peakRss": 0, + "peakVmem": 0, + "rchar": 54094, + "wchar": 197, + "syscr": 147, + "syscw": 13, + "readBytes": 352256, + "writeBytes": 0, + "volCtxt": 0, + "invCtxt": 0, + "env": None, + "submit": "2023-10-16T21:04:15Z", + "exitStatus": 0, + "complete": "2023-10-16T21:07:13Z", + "cpus": 1, + "machineType": "c6i.2xlarge", + "hash": "0f/929495", + "exit": "0", + } + }, + { + "task": { + "id": 4638143, + "taskId": 4, + "status": "COMPLETED", + "dateCreated": "2023-10-16T21:04:14Z", + "lastUpdated": "2023-10-16T21:07:27Z", + "name": "sayHello (4)", + "module": [], + "queue": "TowerForge-5im9knMLfGTl9qrPNcDk0t-work", + "memory": None, + "script": "\necho 'Hola world!'\n", + "tag": None, + "time": None, + "executor": "awsbatch", + "duration": 178217, + "start": "2023-10-16T21:07:03Z", + "container": "wave.seqera.io/wt/35bcf310401b/nextflow/bash:latest", + "process": "sayHello", + "attempt": 1, + "scratch": None, + "workdir": "s3://example-project-tower-scratch/work/de/3458310872e3784b889a5b7abe823e", + "disk": None, + "cloudZone": "us-east-1d", + "priceModel": "spot", + "cost": 0.0000576389, + "errorAction": None, + "realtime": 3, + "nativeId": "fecc5768-5d45-479e-8f37-89e17a32d216", + "pcpu": 72.7, + "pmem": 0.0, + "rss": 0, + "vmem": 0, + "peakRss": 0, + "peakVmem": 0, + "rchar": 54093, + "wchar": 196, + "syscr": 147, + "syscw": 13, + "readBytes": 352256, + "writeBytes": 0, + "volCtxt": 0, + "invCtxt": 0, + "env": None, + "submit": "2023-10-16T21:04:15Z", + "exitStatus": 0, + "complete": "2023-10-16T21:07:13Z", + "cpus": 1, + "machineType": "c6i.2xlarge", + "hash": "de/345831", + "exit": "0", + } + }, + ], + "total": 4, +} + +get_task_log = { + "log": { + "entries": [ + "Ciao world!" + ], + "rewindToken": None, + "forwardToken": None, + "pending": False, + "message": None, + "downloads": [ + { + "fileName": ".command.out", + "displayText": "Task stdout", + "saveName": "task-2.command.out.txt" + }, + { + "fileName": ".command.err", + "displayText": "Task stderr", + "saveName": "task-2.command.err.txt" + }, + { + "fileName": ".command.log", + "displayText": "Task log file", + "saveName": "task-2.command.log.txt" + } + ], + "truncated": False + } +} From adea7e163c934c6001de4e4ac2cfbe832ec44fb9 Mon Sep 17 00:00:00 2001 From: Brad Macdonald Date: Tue, 24 Oct 2023 14:08:36 -0600 Subject: [PATCH 02/20] adds workflow task model class --- src/orca/services/nextflowtower/models.py | 70 +++++++++++++++++++++++ 1 file changed, 70 insertions(+) diff --git a/src/orca/services/nextflowtower/models.py b/src/orca/services/nextflowtower/models.py index b48c25e..ecd98ff 100644 --- a/src/orca/services/nextflowtower/models.py +++ b/src/orca/services/nextflowtower/models.py @@ -336,3 +336,73 @@ def __repr__(self) -> str: def status(self) -> WorkflowStatus: """Workflow run status.""" return WorkflowStatus(self.state) + + +@dataclass(kw_only=False) +class WorkflowTask(BaseTowerModel): + """Nextflow Tower workflow task details.""" + + { + "id": 4638140, + "taskId": 1, + "status": "COMPLETED", + "name": "sayHello (1)", + "module": [], + "queue": "TowerForge-5im9knMLfGTl9qrPNcDk0t-work", + "memory": None, + "script": "\necho 'Bonjour world!'\n", + "tag": None, + "executor": "awsbatch", + "duration": 178310, + "container": "wave.seqera.io/wt/35bcf310401b/nextflow/bash:latest", + "process": "sayHello", + "attempt": 1, + "scratch": None, + "workdir": "s3://example-project-tower-scratch/work/53/d1a4bedd867b9b005c1e86291334cf", + "disk": None, + "priceModel": "spot", + "cost": 5.76389e-05, + "errorAction": None, + "nativeId": "1ffe9499-1566-4140-b652-cb930413cf77", + "env": None, + "exitStatus": 0, + "cpus": 1, + "machineType": "c6i.2xlarge", + "hash": "53/d1a4be", + } + id: int + task_id: int + status: str + name: str + module: list[str] + queue: str + memory: Optional[int] + script: str + tag: Optional[str] + executor: str + duration: int + container: str + process: str + attempt: int + scratch: Optional[str] + work_dir: str + disk: Optional[int] + price_model: str + cost: float + error_action: Optional[str] + native_id: str + env: Optional[str] + exit_status: int + cpus: Optional[int] + machine_type: str + hash: str + + _key_mapping = { + "task_id": "taskId", + "work_dir": "workdir", + "price_model": "priceModel", + "error_action": "errorAction", + "native_id": "nativeId", + "exit_status": "exitStatus", + "machine_type": "machineType", + } From 94056e29290a55201941e0c3fb0cc2b1477eee08 Mon Sep 17 00:00:00 2001 From: Brad Macdonald Date: Tue, 24 Oct 2023 14:15:15 -0600 Subject: [PATCH 03/20] updates mock name --- tests/services/nextflowtower/responses.py | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) diff --git a/tests/services/nextflowtower/responses.py b/tests/services/nextflowtower/responses.py index 6a74e93..ff4f0fe 100644 --- a/tests/services/nextflowtower/responses.py +++ b/tests/services/nextflowtower/responses.py @@ -528,7 +528,7 @@ "totalSize": 3, } -list_workflow_tasks = { +get_workflow_tasks = { "tasks": [ { "task": { @@ -748,9 +748,7 @@ get_task_log = { "log": { - "entries": [ - "Ciao world!" - ], + "entries": ["Ciao world!"], "rewindToken": None, "forwardToken": None, "pending": False, @@ -759,19 +757,19 @@ { "fileName": ".command.out", "displayText": "Task stdout", - "saveName": "task-2.command.out.txt" + "saveName": "task-2.command.out.txt", }, { "fileName": ".command.err", "displayText": "Task stderr", - "saveName": "task-2.command.err.txt" + "saveName": "task-2.command.err.txt", }, { "fileName": ".command.log", "displayText": "Task log file", - "saveName": "task-2.command.log.txt" - } + "saveName": "task-2.command.log.txt", + }, ], - "truncated": False + "truncated": False, } } From 462aaa1796e0434989e5ead102bd2976b9528cde Mon Sep 17 00:00:00 2001 From: Brad Macdonald Date: Tue, 24 Oct 2023 15:25:42 -0600 Subject: [PATCH 04/20] adds client methods --- src/orca/services/nextflowtower/client.py | 44 +++++++++++++++++++++++ 1 file changed, 44 insertions(+) diff --git a/src/orca/services/nextflowtower/client.py b/src/orca/services/nextflowtower/client.py index 5d14c1f..da0c668 100644 --- a/src/orca/services/nextflowtower/client.py +++ b/src/orca/services/nextflowtower/client.py @@ -369,3 +369,47 @@ def list_workflows( json = self.get(path=path, params=params) items = self.unwrap(json, "workflows") return [models.Workflow.from_json(item["workflow"]) for item in items] + + def get_workflow_tasks( + self, + workflow_id: str, + workspace_id: Optional[int] = None, + ) -> list[models.WorkflowTask]: + """Retrieve the details of a workflow run's tasks. + + Args: + workflow_id: The ID number for a workflow run to + get tasks from. + workspace_id: The ID number of the workspace the workflow + exists within. Defaults to None. + + Returns: + List of WorkflowTask objects. + """ + path = f"/workflow/{workflow_id}/tasks" + params = self.generate_params(workspace_id) + json = self.get(path=path, params=params) + items = self.unwrap(json, "tasks") + return [models.WorkflowTask.from_json(item["task"]) for item in items] + + def get_task_logs( + self, workflow_id: str, task_id: str, workspace_id: Optional[int] + ) -> str: + """Retrieve the logs for a given workflow task. + + Args: + workflow_id: The ID number for a workflow run the + tasks belongs to. + task_id: The task_id for the task to get logs from. + workspace_id: The ID number of the workspace the workflow + exists within. Defaults to None. + + Returns: + WorkflowTask Execution logs. + """ + path = f"/workflow/{workflow_id}/log/{task_id}" + params = self.generate_params(workspace_id) + json = self.get(path=path, params=params) + items = self.unwrap(json, "log") + log_list = items["entries"] + return "\n".join(log_list) From 475ab74b574997fe1b04b8cf5502f38feac31c6a Mon Sep 17 00:00:00 2001 From: Brad Macdonald Date: Tue, 24 Oct 2023 15:26:58 -0600 Subject: [PATCH 05/20] adds ops methods --- src/orca/services/nextflowtower/ops.py | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/src/orca/services/nextflowtower/ops.py b/src/orca/services/nextflowtower/ops.py index 92c1d47..807f541 100644 --- a/src/orca/services/nextflowtower/ops.py +++ b/src/orca/services/nextflowtower/ops.py @@ -272,3 +272,26 @@ async def monitor_workflow( logger.info(f"{workflow} is now done!") return workflow.status + + def get_workflow_tasks(self, workflow_id: str) -> list[dict]: + """Retrieve the details of a workflow run's tasks. + + Args: + workflow_id: Workflow run ID. + + Returns: + List of task details. + """ + return self.client.get_workflow_tasks(workflow_id, self.workspace_id) + + def get_task_logs(self, workflow_id: str, task_id: str) -> str: + """Retrieve the execution logs for a given workflow task. + + Args: + workflow_id: Workflow run ID. + task_id: Task ID. + + Returns: + Task logs. + """ + return self.client.get_task_logs(workflow_id, task_id, self.workspace_id) From cd27aa39fdee5b239e3a0bf87ea54c3857a38420 Mon Sep 17 00:00:00 2001 From: Brad Macdonald Date: Tue, 24 Oct 2023 15:27:09 -0600 Subject: [PATCH 06/20] updates mock responses --- tests/services/nextflowtower/responses.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/services/nextflowtower/responses.py b/tests/services/nextflowtower/responses.py index ff4f0fe..89ed395 100644 --- a/tests/services/nextflowtower/responses.py +++ b/tests/services/nextflowtower/responses.py @@ -746,7 +746,7 @@ "total": 4, } -get_task_log = { +get_task_logs = { "log": { "entries": ["Ciao world!"], "rewindToken": None, From 9d1391596a0d0e6ae17cafd0fc1c7981b6860f5a Mon Sep 17 00:00:00 2001 From: Brad Macdonald Date: Tue, 24 Oct 2023 15:27:17 -0600 Subject: [PATCH 07/20] adds client tests --- tests/services/nextflowtower/test_client.py | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/tests/services/nextflowtower/test_client.py b/tests/services/nextflowtower/test_client.py index fd26c6e..cf487d3 100644 --- a/tests/services/nextflowtower/test_client.py +++ b/tests/services/nextflowtower/test_client.py @@ -148,3 +148,22 @@ def test_that_list_workflows_works(client, mocker, get_response): result = client.list_workflows() mock.assert_called() assert len(result) == 3 + + +def test_that_get_workflow_tasks_works(client, mocker, get_response): + mock = mocker.patch.object(client, "request_json") + mock.return_value = get_response("get_workflow_tasks") + result = client.get_workflow_tasks(workspace_id=98765, workflow_id="123456789") + mock.assert_called() + print(result) + assert len(result) == 4 + + +def test_that_get_task_logs_works(client, mocker, get_response): + mock = mocker.patch.object(client, "request_json") + mock.return_value = get_response("get_task_logs") + result = client.get_task_logs( + workspace_id=98765, task_id=1, workflow_id="123456789" + ) + mock.assert_called() + assert result == "Ciao world!" From 0a9ca503dbda8bef207a5c0c140d8f10678073a5 Mon Sep 17 00:00:00 2001 From: Brad Macdonald Date: Tue, 24 Oct 2023 15:30:04 -0600 Subject: [PATCH 08/20] removes dictionary from models --- src/orca/services/nextflowtower/models.py | 28 ----------------------- 1 file changed, 28 deletions(-) diff --git a/src/orca/services/nextflowtower/models.py b/src/orca/services/nextflowtower/models.py index ecd98ff..51216bb 100644 --- a/src/orca/services/nextflowtower/models.py +++ b/src/orca/services/nextflowtower/models.py @@ -342,34 +342,6 @@ def status(self) -> WorkflowStatus: class WorkflowTask(BaseTowerModel): """Nextflow Tower workflow task details.""" - { - "id": 4638140, - "taskId": 1, - "status": "COMPLETED", - "name": "sayHello (1)", - "module": [], - "queue": "TowerForge-5im9knMLfGTl9qrPNcDk0t-work", - "memory": None, - "script": "\necho 'Bonjour world!'\n", - "tag": None, - "executor": "awsbatch", - "duration": 178310, - "container": "wave.seqera.io/wt/35bcf310401b/nextflow/bash:latest", - "process": "sayHello", - "attempt": 1, - "scratch": None, - "workdir": "s3://example-project-tower-scratch/work/53/d1a4bedd867b9b005c1e86291334cf", - "disk": None, - "priceModel": "spot", - "cost": 5.76389e-05, - "errorAction": None, - "nativeId": "1ffe9499-1566-4140-b652-cb930413cf77", - "env": None, - "exitStatus": 0, - "cpus": 1, - "machineType": "c6i.2xlarge", - "hash": "53/d1a4be", - } id: int task_id: int status: str From 62fce82e9b1e64ca9042a183089dc25c1fce2364 Mon Sep 17 00:00:00 2001 From: Brad Macdonald Date: Tue, 24 Oct 2023 15:34:39 -0600 Subject: [PATCH 09/20] fix pre-commit issues --- src/orca/services/nextflowtower/ops.py | 9 +++++++-- tests/services/nextflowtower/responses.py | 8 ++++---- 2 files changed, 11 insertions(+), 6 deletions(-) diff --git a/src/orca/services/nextflowtower/ops.py b/src/orca/services/nextflowtower/ops.py index 807f541..1fe2aae 100644 --- a/src/orca/services/nextflowtower/ops.py +++ b/src/orca/services/nextflowtower/ops.py @@ -11,7 +11,12 @@ from orca.services.nextflowtower.client import NextflowTowerClient from orca.services.nextflowtower.client_factory import NextflowTowerClientFactory from orca.services.nextflowtower.config import NextflowTowerConfig -from orca.services.nextflowtower.models import LaunchInfo, Workflow, WorkflowStatus +from orca.services.nextflowtower.models import ( + LaunchInfo, + Workflow, + WorkflowStatus, + WorkflowTask, +) from orca.services.nextflowtower.utils import increment_suffix logger = logging.getLogger(__name__) @@ -273,7 +278,7 @@ async def monitor_workflow( logger.info(f"{workflow} is now done!") return workflow.status - def get_workflow_tasks(self, workflow_id: str) -> list[dict]: + def get_workflow_tasks(self, workflow_id: str) -> list[WorkflowTask]: """Retrieve the details of a workflow run's tasks. Args: diff --git a/tests/services/nextflowtower/responses.py b/tests/services/nextflowtower/responses.py index 89ed395..f17944a 100644 --- a/tests/services/nextflowtower/responses.py +++ b/tests/services/nextflowtower/responses.py @@ -551,7 +551,7 @@ "process": "sayHello", "attempt": 1, "scratch": None, - "workdir": "s3://example-project-tower-scratch/work/53/d1a4bedd867b9b005c1e86291334cf", + "workdir": "s3://example-bucket/work/53/d1a4bedd867b9b005c1e86291334cf", "disk": None, "cloudZone": "us-east-1d", "priceModel": "spot", @@ -604,7 +604,7 @@ "process": "sayHello", "attempt": 1, "scratch": None, - "workdir": "s3://example-project-tower-scratch/work/8b/96b02f951f46594c6d6f310e77abc7", + "workdir": "s3://example-bucket/work/8b/96b02f951f46594c6d6f310e77abc7", "disk": None, "cloudZone": "us-east-1d", "priceModel": "spot", @@ -657,7 +657,7 @@ "process": "sayHello", "attempt": 1, "scratch": None, - "workdir": "s3://example-project-tower-scratch/work/0f/929495d8a0f66c9e85a4c4f0820a54", + "workdir": "s3://example-bucket/work/0f/929495d8a0f66c9e85a4c4f0820a54", "disk": None, "cloudZone": "us-east-1d", "priceModel": "spot", @@ -710,7 +710,7 @@ "process": "sayHello", "attempt": 1, "scratch": None, - "workdir": "s3://example-project-tower-scratch/work/de/3458310872e3784b889a5b7abe823e", + "workdir": "s3://example-bucket/work/de/3458310872e3784b889a5b7abe823e", "disk": None, "cloudZone": "us-east-1d", "priceModel": "spot", From 5740d7904ef0ada58867b1d48282fd326bb9e10b Mon Sep 17 00:00:00 2001 From: Brad Macdonald Date: Wed, 25 Oct 2023 12:21:27 -0600 Subject: [PATCH 10/20] updates pagination --- src/orca/services/nextflowtower/client.py | 6 ++++-- tests/services/nextflowtower/test_client.py | 1 - 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/src/orca/services/nextflowtower/client.py b/src/orca/services/nextflowtower/client.py index da0c668..5ac4f92 100644 --- a/src/orca/services/nextflowtower/client.py +++ b/src/orca/services/nextflowtower/client.py @@ -113,7 +113,9 @@ def request_paged(self, method: str, path: str, **kwargs) -> dict[str, Any]: while num_items < total_size: kwargs["params"]["offset"] = num_items json = self.request_json(method, path, **kwargs) - total_size = json.pop("totalSize") + total_size = ( + json.pop("totalSize") if json.get("totalSize") else json.pop("total") + ) key_name, items = json.popitem() num_items += len(items) all_items.extend(items) @@ -134,7 +136,7 @@ def get(self, path: str, **kwargs) -> dict[str, Any]: A dictionary from deserializing the JSON response. """ json = self.request_json("GET", path, **kwargs) - if "totalSize" in json: + if "totalSize" in json or "total" in json: json = self.request_paged("GET", path, **kwargs) return json diff --git a/tests/services/nextflowtower/test_client.py b/tests/services/nextflowtower/test_client.py index cf487d3..df16981 100644 --- a/tests/services/nextflowtower/test_client.py +++ b/tests/services/nextflowtower/test_client.py @@ -155,7 +155,6 @@ def test_that_get_workflow_tasks_works(client, mocker, get_response): mock.return_value = get_response("get_workflow_tasks") result = client.get_workflow_tasks(workspace_id=98765, workflow_id="123456789") mock.assert_called() - print(result) assert len(result) == 4 From 99f7c50b8655bb6243b5820ab13b8c9195cc4433 Mon Sep 17 00:00:00 2001 From: Brad Macdonald Date: Wed, 25 Oct 2023 13:11:19 -0600 Subject: [PATCH 11/20] adds ops unit tests --- tests/services/nextflowtower/test_ops.py | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/tests/services/nextflowtower/test_ops.py b/tests/services/nextflowtower/test_ops.py index c06a9a3..150e3bd 100644 --- a/tests/services/nextflowtower/test_ops.py +++ b/tests/services/nextflowtower/test_ops.py @@ -302,3 +302,25 @@ async def test_that_monitor_workflow_works_for_an_incomplete_workflow( assert mock.call_count > 1 assert result == models.WorkflowStatus("SUCCEEDED") + + +def test_that_get_workflow_tasks_works(mocked_ops, mocker, get_response, client): + response = get_response("get_workflow_tasks") + expected = [ + models.WorkflowTask.from_json(task["task"]) for task in response["tasks"] + ] + mock = mocker.patch.object(mocked_ops.client, "get_workflow_tasks") + mock.return_value = expected + result = mocked_ops.get_workflow_tasks(workflow_id="123456789") + mock.assert_called() + assert expected == result + + +def test_that_get_task_logs_works(mocked_ops, mocker, get_response): + response = get_response("get_task_logs") + expected = "Ciao world!" + mock = mocker.patch.object(mocked_ops.client, "get_task_logs") + mock.return_value = expected + result = mocked_ops.get_task_logs(task_id=1, workflow_id="123456789") + mock.assert_called() + assert result == "Ciao world!" From ae50aeecb945e958ebdb268079e7a0568660883b Mon Sep 17 00:00:00 2001 From: Brad Macdonald Date: Wed, 25 Oct 2023 13:12:38 -0600 Subject: [PATCH 12/20] removes unused line --- tests/services/nextflowtower/test_ops.py | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/services/nextflowtower/test_ops.py b/tests/services/nextflowtower/test_ops.py index 150e3bd..b83e623 100644 --- a/tests/services/nextflowtower/test_ops.py +++ b/tests/services/nextflowtower/test_ops.py @@ -317,7 +317,6 @@ def test_that_get_workflow_tasks_works(mocked_ops, mocker, get_response, client) def test_that_get_task_logs_works(mocked_ops, mocker, get_response): - response = get_response("get_task_logs") expected = "Ciao world!" mock = mocker.patch.object(mocked_ops.client, "get_task_logs") mock.return_value = expected From fbfbb77047a17f3e61acac135c9dc5459c17378c Mon Sep 17 00:00:00 2001 From: Brad Macdonald Date: Wed, 25 Oct 2023 13:28:25 -0600 Subject: [PATCH 13/20] adds pandas to dev packages --- 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s3fs~=2023.5 + pandas~=2.1.1 [options.entry_points] # Add here console scripts like: From 3851426b5c58bbdba8a3a73385e172fba36684c1 Mon Sep 17 00:00:00 2001 From: Brad Macdonald Date: Wed, 25 Oct 2023 13:55:42 -0600 Subject: [PATCH 14/20] adds log demo --- demo_nf_logs.py | 86 +++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 86 insertions(+) create mode 100644 demo_nf_logs.py diff --git a/demo_nf_logs.py b/demo_nf_logs.py new file mode 100644 index 0000000..34484b5 --- /dev/null +++ b/demo_nf_logs.py @@ -0,0 +1,86 @@ +import asyncio + +from metaflow import FlowSpec, Parameter, step +import pandas as pd +from orca.services.nextflowtower import NextflowTowerOps + + +class LogsFlow(FlowSpec): + tower = NextflowTowerOps() + + workflow_id = Parameter( + "workflow_id", + type=str, + help="Nextflow workflow ID", + ) + + # Example error reasons for the nf-histoqc workflow + log_reasons = [ + "NO tissue remains detectable!", + "NO tissue remains detectable in mask!", + "Inappropriate argument value (of correct type)", + ] + + async def get_logs(self, task): + """Retrieve execution logs for an individual task.""" + print(f"Getting logs for task: {task.task_id}") + return { + "task_id": task.task_id, + "tag": task.tag, + "execution_log": self.tower.get_task_logs( + workflow_id=self.workflow_id, task_id=task.task_id + ), + } + + async def retrieve_workflow_task_logs(self): + """Asynchronously retrieve execution logs for all tasks in a workflow.""" + print("Getting workflow tasks") + tasks = self.tower.get_workflow_tasks(workflow_id=self.workflow_id) + print("Getting logs for each task") + task_log_list = await asyncio.gather(*[self.get_logs(task) for task in tasks]) + return task_log_list + + def determine_failure_reasons(self, task_log_list): + """Check for failure reasons in execution logs. Attribute failure reasons to each task.""" + for task in task_log_list: + failure_reasons = [] + for reason in self.log_reasons: + if reason in task["execution_log"]: + failure_reasons.append(reason) + task["failure_reasons"] = ", ".join(failure_reasons) + if not task["failure_reasons"]: + task["failure_reasons"] = "Failure Reason Undetermined" + task.pop("execution_log") + + @step + def start(self): + """Entry point.""" + self.next(self.get_task_logs) + + @step + def get_task_logs(self): + """Collect all task logs for a workflow.""" + self.task_log_list = asyncio.run(self.retrieve_workflow_task_logs()) + self.next(self.compile_failure_reasons) + + @step + def compile_failure_reasons(self): + """Compile failure reasons for each task.""" + self.determine_failure_reasons(self.task_log_list) + self.next(self.export_results) + + @step + def export_results(self): + """Export results to CSV.""" + logs_df = pd.DataFrame(self.task_log_list) + logs_df.to_csv("task_logs.csv", index=False) + self.next(self.end) + + @step + def end(self): + """End point.""" + print("Done") + + +if __name__ == "__main__": + LogsFlow() From e4a2fb13e40f6258595dc24645f490ce45bc1e4d Mon Sep 17 00:00:00 2001 From: Brad Macdonald Date: Wed, 25 Oct 2023 14:08:13 -0600 Subject: [PATCH 15/20] address pre-commit --- demo_nf_logs.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/demo_nf_logs.py b/demo_nf_logs.py index 34484b5..af36108 100644 --- a/demo_nf_logs.py +++ b/demo_nf_logs.py @@ -1,7 +1,8 @@ import asyncio -from metaflow import FlowSpec, Parameter, step import pandas as pd +from metaflow import FlowSpec, Parameter, step + from orca.services.nextflowtower import NextflowTowerOps @@ -41,7 +42,8 @@ async def retrieve_workflow_task_logs(self): return task_log_list def determine_failure_reasons(self, task_log_list): - """Check for failure reasons in execution logs. Attribute failure reasons to each task.""" + """Check for failure reasons in execution logs. + Attribute failure reasons to each task.""" for task in task_log_list: failure_reasons = [] for reason in self.log_reasons: From 6dd58875d4132fe437f23d7ac7fcb5010206fcd8 Mon Sep 17 00:00:00 2001 From: Brad Macdonald Date: Wed, 25 Oct 2023 14:17:02 -0600 Subject: [PATCH 16/20] updates for failed workflow runs --- demo_nf_logs.py | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) diff --git a/demo_nf_logs.py b/demo_nf_logs.py index af36108..079e9da 100644 --- a/demo_nf_logs.py +++ b/demo_nf_logs.py @@ -7,6 +7,9 @@ class LogsFlow(FlowSpec): + """Retrieve execution logs and failure reasons for all + failed tasks in a workflow.""" + tower = NextflowTowerOps() workflow_id = Parameter( @@ -15,7 +18,7 @@ class LogsFlow(FlowSpec): help="Nextflow workflow ID", ) - # Example error reasons for the nf-histoqc workflow + # Example error reasons for nf-histoqc log_reasons = [ "NO tissue remains detectable!", "NO tissue remains detectable in mask!", @@ -34,11 +37,14 @@ async def get_logs(self, task): } async def retrieve_workflow_task_logs(self): - """Asynchronously retrieve execution logs for all tasks in a workflow.""" + """Asynchronously retrieve execution logs for all failed tasks in a workflow.""" print("Getting workflow tasks") tasks = self.tower.get_workflow_tasks(workflow_id=self.workflow_id) - print("Getting logs for each task") - task_log_list = await asyncio.gather(*[self.get_logs(task) for task in tasks]) + failed_tasks = [task for task in tasks if task.status == "FAILED"] + print("Getting logs for each failed task") + task_log_list = await asyncio.gather( + *[self.get_logs(task) for task in failed_tasks] + ) return task_log_list def determine_failure_reasons(self, task_log_list): @@ -61,7 +67,7 @@ def start(self): @step def get_task_logs(self): - """Collect all task logs for a workflow.""" + """Collect task logs for a workflow.""" self.task_log_list = asyncio.run(self.retrieve_workflow_task_logs()) self.next(self.compile_failure_reasons) From a5e8ef7549e956205e57bd4d85c46f124090d89e Mon Sep 17 00:00:00 2001 From: Brad Macdonald Date: Wed, 25 Oct 2023 14:44:53 -0600 Subject: [PATCH 17/20] adds missing type hints --- demo_nf_logs.py | 6 ++++-- src/orca/services/nextflowtower/client.py | 2 +- src/orca/services/nextflowtower/ops.py | 2 +- 3 files changed, 6 insertions(+), 4 deletions(-) diff --git a/demo_nf_logs.py b/demo_nf_logs.py index 079e9da..a3a2902 100644 --- a/demo_nf_logs.py +++ b/demo_nf_logs.py @@ -1,9 +1,11 @@ import asyncio +from typing import List import pandas as pd from metaflow import FlowSpec, Parameter, step from orca.services.nextflowtower import NextflowTowerOps +from orca.services.nextflowtower.models import WorkflowTask class LogsFlow(FlowSpec): @@ -25,7 +27,7 @@ class LogsFlow(FlowSpec): "Inappropriate argument value (of correct type)", ] - async def get_logs(self, task): + async def get_logs(self, task: WorkflowTask): """Retrieve execution logs for an individual task.""" print(f"Getting logs for task: {task.task_id}") return { @@ -47,7 +49,7 @@ async def retrieve_workflow_task_logs(self): ) return task_log_list - def determine_failure_reasons(self, task_log_list): + def determine_failure_reasons(self, task_log_list: List[dict]): """Check for failure reasons in execution logs. Attribute failure reasons to each task.""" for task in task_log_list: diff --git a/src/orca/services/nextflowtower/client.py b/src/orca/services/nextflowtower/client.py index 5ac4f92..613e1c6 100644 --- a/src/orca/services/nextflowtower/client.py +++ b/src/orca/services/nextflowtower/client.py @@ -395,7 +395,7 @@ def get_workflow_tasks( return [models.WorkflowTask.from_json(item["task"]) for item in items] def get_task_logs( - self, workflow_id: str, task_id: str, workspace_id: Optional[int] + self, workflow_id: str, task_id: int, workspace_id: Optional[int] ) -> str: """Retrieve the logs for a given workflow task. diff --git a/src/orca/services/nextflowtower/ops.py b/src/orca/services/nextflowtower/ops.py index 1fe2aae..7dc2669 100644 --- a/src/orca/services/nextflowtower/ops.py +++ b/src/orca/services/nextflowtower/ops.py @@ -289,7 +289,7 @@ def get_workflow_tasks(self, workflow_id: str) -> list[WorkflowTask]: """ return self.client.get_workflow_tasks(workflow_id, self.workspace_id) - def get_task_logs(self, workflow_id: str, task_id: str) -> str: + def get_task_logs(self, workflow_id: str, task_id: int) -> str: """Retrieve the execution logs for a given workflow task. Args: From d39006dd7e99d03a3e768d3077ea55f8797adffb Mon Sep 17 00:00:00 2001 From: Brad Macdonald Date: Wed, 25 Oct 2023 15:36:03 -0600 Subject: [PATCH 18/20] allow for totalSize to be 0 and default to 0 --- src/orca/services/nextflowtower/client.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/src/orca/services/nextflowtower/client.py b/src/orca/services/nextflowtower/client.py index 613e1c6..1d71e3f 100644 --- a/src/orca/services/nextflowtower/client.py +++ b/src/orca/services/nextflowtower/client.py @@ -114,7 +114,11 @@ def request_paged(self, method: str, path: str, **kwargs) -> dict[str, Any]: kwargs["params"]["offset"] = num_items json = self.request_json(method, path, **kwargs) total_size = ( - json.pop("totalSize") if json.get("totalSize") else json.pop("total") + json.pop("totalSize") + if json.get("totalSize") is not None + else json.pop("total") + if json.get("total") is not None + else 0 ) key_name, items = json.popitem() num_items += len(items) From cdfdad2fb74db14743bc230f78da35ba3e81c239 Mon Sep 17 00:00:00 2001 From: Brad Macdonald Date: Wed, 25 Oct 2023 16:08:43 -0600 Subject: [PATCH 19/20] updates pop logic --- src/orca/services/nextflowtower/client.py | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/src/orca/services/nextflowtower/client.py b/src/orca/services/nextflowtower/client.py index 1d71e3f..75b980a 100644 --- a/src/orca/services/nextflowtower/client.py +++ b/src/orca/services/nextflowtower/client.py @@ -113,13 +113,7 @@ def request_paged(self, method: str, path: str, **kwargs) -> dict[str, Any]: while num_items < total_size: kwargs["params"]["offset"] = num_items json = self.request_json(method, path, **kwargs) - total_size = ( - json.pop("totalSize") - if json.get("totalSize") is not None - else json.pop("total") - if json.get("total") is not None - else 0 - ) + total_size = json.pop("totalSize", None) or json.pop("total", 0) key_name, items = json.popitem() num_items += len(items) all_items.extend(items) From 552e08c26000cf9979f3ea18c3a02f9a6609d76c Mon Sep 17 00:00:00 2001 From: Brad Macdonald Date: Thu, 26 Oct 2023 09:08:43 -0600 Subject: [PATCH 20/20] removes demo file and pandas --- Pipfile.lock | 86 +++----------------------------------------- demo_nf_logs.py | 96 ------------------------------------------------- setup.cfg | 1 - 3 files changed, 5 insertions(+), 178 deletions(-) delete mode 100644 demo_nf_logs.py diff --git a/Pipfile.lock b/Pipfile.lock index 35fa605..46d138a 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1459,7 +1459,7 @@ "extras": [ "all" ], - "version": "==1.3.2.post1.dev12+gae50aee.d20231025" + "version": "==1.3.2.post1.dev19+gcdfdad2.d20231026" }, "pycparser": { "hashes": [ @@ -2524,10 +2524,10 @@ }, "asttokens": { "hashes": [ - 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"version": "==1.3.2.post1.dev12+gae50aee.d20231025" + "version": "==1.3.2.post1.dev19+gcdfdad2.d20231026" }, "pycodestyle": { "hashes": [ @@ -5396,14 +5328,6 @@ "markers": "python_version >= '3.8'", "version": "==4.8.0" }, - "tzdata": { - "hashes": [ - "sha256:11ef1e08e54acb0d4f95bdb1be05da659673de4acbd21bf9c69e94cc5e907a3a", - "sha256:7e65763eef3120314099b6939b5546db7adce1e7d6f2e179e3df563c70511eda" - ], - "markers": "python_version >= '2'", - "version": "==2023.3" - }, "uc-micro-py": { "hashes": [ "sha256:30ae2ac9c49f39ac6dce743bd187fcd2b574b16ca095fa74cd9396795c954c54", diff --git a/demo_nf_logs.py b/demo_nf_logs.py deleted file mode 100644 index a3a2902..0000000 --- a/demo_nf_logs.py +++ /dev/null @@ -1,96 +0,0 @@ -import asyncio -from typing import List - -import pandas as pd -from metaflow import FlowSpec, Parameter, step - -from orca.services.nextflowtower import NextflowTowerOps -from orca.services.nextflowtower.models import WorkflowTask - - -class LogsFlow(FlowSpec): - """Retrieve execution logs and failure reasons for all - failed tasks in a workflow.""" - - tower = NextflowTowerOps() - - workflow_id = Parameter( - "workflow_id", - type=str, - help="Nextflow workflow ID", - ) - - # Example error reasons for nf-histoqc - log_reasons = [ - "NO tissue remains detectable!", - "NO tissue remains detectable in mask!", - "Inappropriate argument value (of correct type)", - ] - - async def get_logs(self, task: WorkflowTask): - """Retrieve execution logs for an individual task.""" - print(f"Getting logs for task: {task.task_id}") - return { - "task_id": task.task_id, - "tag": task.tag, - "execution_log": self.tower.get_task_logs( - workflow_id=self.workflow_id, task_id=task.task_id - ), - } - - async def retrieve_workflow_task_logs(self): - """Asynchronously retrieve execution logs for all failed tasks in a workflow.""" - print("Getting workflow tasks") - tasks = self.tower.get_workflow_tasks(workflow_id=self.workflow_id) - failed_tasks = [task for task in tasks if task.status == "FAILED"] - print("Getting logs for each failed task") - task_log_list = await asyncio.gather( - *[self.get_logs(task) for task in failed_tasks] - ) - return task_log_list - - def determine_failure_reasons(self, task_log_list: List[dict]): - """Check for failure reasons in execution logs. - Attribute failure reasons to each task.""" - for task in task_log_list: - failure_reasons = [] - for reason in self.log_reasons: - if reason in task["execution_log"]: - failure_reasons.append(reason) - task["failure_reasons"] = ", ".join(failure_reasons) - if not task["failure_reasons"]: - task["failure_reasons"] = "Failure Reason Undetermined" - task.pop("execution_log") - - @step - def start(self): - """Entry point.""" - self.next(self.get_task_logs) - - @step - def get_task_logs(self): - """Collect task logs for a workflow.""" - self.task_log_list = asyncio.run(self.retrieve_workflow_task_logs()) - self.next(self.compile_failure_reasons) - - @step - def compile_failure_reasons(self): - """Compile failure reasons for each task.""" - self.determine_failure_reasons(self.task_log_list) - self.next(self.export_results) - - @step - def export_results(self): - """Export results to CSV.""" - logs_df = pd.DataFrame(self.task_log_list) - logs_df.to_csv("task_logs.csv", index=False) - self.next(self.end) - - @step - def end(self): - """End point.""" - print("Done") - - -if __name__ == "__main__": - LogsFlow() diff --git a/setup.cfg b/setup.cfg index 8790d81..42bcda2 100644 --- a/setup.cfg +++ b/setup.cfg @@ -101,7 +101,6 @@ dev = typing-extensions~=4.5 metaflow~=2.9 s3fs~=2023.5 - pandas~=2.1.1 [options.entry_points] # Add here console scripts like: