diff --git a/app/api/dependencies.py b/app/api/dependencies.py
index b94a488584440c31c92ec48878745fcd0aa2bd48..eb8d75a1062526e917c610540e75bf78cbb061f5 100644
--- a/app/api/dependencies.py
+++ b/app/api/dependencies.py
@@ -255,7 +255,7 @@ async def get_current_workflow_version(
git_commit_hash: str = Path(
...,
description="Git commit git_commit_hash of specific version.",
- regex=r"^([0-9a-f]{40}|latest)$",
+ pattern=r"^([0-9a-f]{40}|latest)$",
examples=["ba8bcd9294c2c96aedefa1763a84a18077c50c0f"],
),
) -> WorkflowVersion:
diff --git a/app/api/endpoints/workflow.py b/app/api/endpoints/workflow.py
index 8735fa2066d2fa7fea55e39f84200d2c9795ce3f..ddad1ec42533feb9a3168c622958055551a61bdf 100644
--- a/app/api/endpoints/workflow.py
+++ b/app/api/endpoints/workflow.py
@@ -1,7 +1,7 @@
from typing import Annotated, Any, Awaitable, Callable, List, Optional, Set
from uuid import UUID
-from clowmdb.models import Workflow, WorkflowVersion
+from clowmdb.models import Workflow, WorkflowMode, WorkflowVersion
from fastapi import APIRouter, BackgroundTasks, Depends, HTTPException, Query, Response, status
from app.api.dependencies import AuthorizationDependency, CurrentUser, CurrentWorkflow, DBSession, HTTPClient, S3Service
@@ -361,12 +361,10 @@ async def update_workflow(
detail=f"Workflow Version with git_commit_hash'{version_update.git_commit_hash}' already exists",
)
# Get previous version
- previous_version = await CRUDWorkflowVersion.get_latest(db, workflow.workflow_id, published=False)
+ previous_version: WorkflowVersion = await CRUDWorkflowVersion.get_latest(db, workflow.workflow_id, published=False)
# Get modes of previous version
- previous_version_modes = await CRUDWorkflowMode.list_modes(
- db, previous_version.workflow_modes # type: ignore[union-attr]
- )
+ previous_version_modes = await CRUDWorkflowMode.list_modes(db, previous_version.git_commit_hash)
if version_update.delete_modes is not None:
# Check if mode to delete actually exist
@@ -375,7 +373,7 @@ async def update_workflow(
if delete_mode not in mode_ids:
raise HTTPException(
status_code=status.HTTP_400_BAD_REQUEST,
- detail=f"Workflow mode {delete_mode} does not exist for the latest version of workflow {workflow.workflow_id}", # noqa: E501
+ detail=f"Workflow mode {delete_mode} does not exist for the latest version {previous_version.git_commit_hash} of workflow {workflow.workflow_id}", # noqa: E501
)
# Filter out modes that should be deleted in new workflow version
previous_version_modes = [
@@ -385,13 +383,13 @@ async def update_workflow(
# Build a git repository object based on the repository url
repo = build_repository(workflow.repository_url, version_update.git_commit_hash)
- check_repo_modes = previous_version_modes
+ check_repo_modes = previous_version_modes.copy()
# If there are new modes, add them to the list for file checking
if version_update.append_modes is not None:
check_repo_modes += version_update.append_modes
await check_repo(repo=repo, client=client, modes=check_repo_modes)
- append_modes_db = []
+ append_modes_db: List[WorkflowMode] = []
# Create new modes in database
if version_update.append_modes is not None:
append_modes_db = await CRUDWorkflowMode.create(db, version_update.append_modes)
diff --git a/app/api/endpoints/workflow_execution.py b/app/api/endpoints/workflow_execution.py
index ca3c30bcfa7d398003f29b8a3386d1cc40dcd323..9052e0c89310097efc3b7fa0f36178b7302a613e 100644
--- a/app/api/endpoints/workflow_execution.py
+++ b/app/api/endpoints/workflow_execution.py
@@ -295,7 +295,7 @@ async def list_workflow_executions(
None,
description="Filter for workflow version",
examples=["ba8bcd9294c2c96aedefa1763a84a18077c50c0f"],
- regex=r"^[0-9a-f]{40}$",
+ pattern=r"^[0-9a-f]{40}$",
),
) -> List[WorkflowExecutionOut]:
"""
diff --git a/app/api/endpoints/workflow_version.py b/app/api/endpoints/workflow_version.py
index e910f9431582b43e50d03286fd6a803d46b9a492..6d75cab22f22b4799e765619df071fa4bb166c90 100644
--- a/app/api/endpoints/workflow_version.py
+++ b/app/api/endpoints/workflow_version.py
@@ -108,7 +108,7 @@ async def get_workflow_version(
git_commit_hash: str = Path(
...,
description="Git commit git_commit_hash of specific version or 'latest'.",
- regex=r"^([0-9a-f]{40}|latest)$",
+ pattern=r"^([0-9a-f]{40}|latest)$",
examples=["latest", "ba8bcd9294c2c96aedefa1763a84a18077c50c0f"],
),
) -> WorkflowVersionSchema:
diff --git a/app/schemas/workflow.py b/app/schemas/workflow.py
index 17f2e0aa274d6c9680fe978b75fd4464aa3cbff1..9359b7129eaa601cf1ccea443084412b6f2a5be6 100644
--- a/app/schemas/workflow.py
+++ b/app/schemas/workflow.py
@@ -138,7 +138,7 @@ class WorkflowUpdate(BaseModel):
...,
description="Version of the Workflow. Should follow semantic versioning",
examples=["v1.1.0"],
- minlength=5,
+ min_length=5,
max_length=10,
)
git_commit_hash: str = Field(
diff --git a/app/schemas/workflow_version.py b/app/schemas/workflow_version.py
index cad1201d5c9efcd8970dfee75eae3412d2cec9df..0d5615a6d11f8f91dc601d2635027f8be81d79a3 100644
--- a/app/schemas/workflow_version.py
+++ b/app/schemas/workflow_version.py
@@ -20,7 +20,7 @@ class WorkflowVersion(WorkflowVersionStatus):
...,
description="Version of the Workflow. Should follow semantic versioning",
examples=["v1.0.0"],
- minlength=5,
+ min_length=5,
max_length=10,
)
git_commit_hash: str = Field(
diff --git a/app/tests/api/test_workflow.py b/app/tests/api/test_workflow.py
index cc5b51c5350cc8ab4073590cb0b4bb084d3e9060..47058d463e86ba40dd046fce54a47dcf549de140 100644
--- a/app/tests/api/test_workflow.py
+++ b/app/tests/api/test_workflow.py
@@ -415,7 +415,7 @@ class TestWorkflowRoutesCreate(_TestWorkflowRoutes):
mock_s3_service: MockS3ServiceResource,
) -> None:
"""
- Exhaustive Test for successfully creating a workflow.
+ Exhaustive Test for successfully creating a workflow with a workflow mode.
Parameters
----------
@@ -660,6 +660,83 @@ class TestWorkflowRoutesDelete(_TestWorkflowRoutes):
schema_file = random_workflow.versions[0].git_commit_hash + ".json"
assert schema_file not in mock_s3_service.Bucket(settings.WORKFLOW_BUCKET).objects.all_keys()
+ @pytest.mark.asyncio
+ async def test_delete_private_workflow(
+ self,
+ client: AsyncClient,
+ random_user: UserWithAuthHeader,
+ random_private_workflow: WorkflowOut,
+ mock_s3_service: MockS3ServiceResource,
+ ) -> None:
+ """
+ Test for deleting a workflow by its id.
+
+ Parameters
+ ----------
+ client : httpx.AsyncClient
+ HTTP Client to perform the request on.
+ random_user : app.tests.utils.user.UserWithAuthHeader
+ Random user for testing.
+ random_private_workflow : app.schemas.workflow.WorkflowOut
+ Random workflow for testing.
+ mock_s3_service : app.tests.mocks.mock_s3_resource.MockS3ServiceResource
+ Mock S3 Service to manipulate objects.
+ """
+ response = await client.delete(
+ "/".join([self.base_path, str(random_private_workflow.workflow_id)]),
+ headers=random_user.auth_headers,
+ )
+ assert response.status_code == status.HTTP_204_NO_CONTENT
+ icon_slug = str(random_private_workflow.versions[0].icon_url).split("/")[-1]
+ assert icon_slug not in mock_s3_service.Bucket(settings.ICON_BUCKET).objects.all_keys()
+ schema_file = random_private_workflow.versions[0].git_commit_hash + ".json"
+ assert schema_file not in mock_s3_service.Bucket(settings.WORKFLOW_BUCKET).objects.all_keys()
+ scm_file = f"{random_private_workflow.workflow_id.hex}.scm"
+ assert scm_file not in mock_s3_service.Bucket(settings.PARAMS_BUCKET).objects.all_keys()
+
+ @pytest.mark.asyncio
+ async def test_delete_workflow_with_mode(
+ self,
+ client: AsyncClient,
+ db: AsyncSession,
+ random_user: UserWithAuthHeader,
+ random_workflow: WorkflowOut,
+ random_workflow_mode: WorkflowMode,
+ mock_s3_service: MockS3ServiceResource,
+ ) -> None:
+ """
+ Test for deleting a workflow by its id.
+
+ Parameters
+ ----------
+ client : httpx.AsyncClient
+ HTTP Client to perform the request on.
+ random_user : app.tests.utils.user.UserWithAuthHeader
+ Random user for testing.
+ random_workflow : app.schemas.workflow.WorkflowOut
+ Random workflow for testing.
+ mock_s3_service : app.tests.mocks.mock_s3_resource.MockS3ServiceResource
+ Mock S3 Service to manipulate objects.
+ random_workflow_mode : clowmdb.model.WorkflowMode
+ Random workflow mode for testing
+ db : sqlalchemy.ext.asyncio.AsyncSession.
+ Async database session to perform query on.
+ """
+ response = await client.delete(
+ "/".join([self.base_path, str(random_workflow.workflow_id)]),
+ headers=random_user.auth_headers,
+ )
+ assert response.status_code == status.HTTP_204_NO_CONTENT
+ icon_slug = str(random_workflow.versions[0].icon_url).split("/")[-1]
+ assert icon_slug not in mock_s3_service.Bucket(settings.ICON_BUCKET).objects.all_keys()
+ schema_file = f"{random_workflow.versions[0].git_commit_hash}-{random_workflow_mode.mode_id.hex}.json"
+ assert schema_file not in mock_s3_service.Bucket(settings.WORKFLOW_BUCKET).objects.all_keys()
+
+ mode_db = await db.scalar(
+ select(WorkflowMode).where(WorkflowMode._mode_id == random_workflow_mode.mode_id.bytes)
+ )
+ assert mode_db is None
+
class TestWorkflowRoutesUpdate(_TestWorkflowRoutes):
@pytest.mark.asyncio
@@ -677,6 +754,8 @@ class TestWorkflowRoutesUpdate(_TestWorkflowRoutes):
HTTP Client to perform the request on.
random_user : app.tests.utils.user.UserWithAuthHeader
Random user for testing.
+ random_workflow : app.schemas.workflow.WorkflowOut
+ Random workflow for testing.
"""
git_commit_hash = random_hex_string()
version_update = WorkflowUpdate(
@@ -699,6 +778,241 @@ class TestWorkflowRoutesUpdate(_TestWorkflowRoutes):
assert db_version is not None
assert db_version.status == WorkflowVersion.Status.CREATED
+ @pytest.mark.asyncio
+ async def test_update_workflow_with_append_modes(
+ self,
+ db: AsyncSession,
+ client: AsyncClient,
+ random_user: UserWithAuthHeader,
+ random_workflow: WorkflowOut,
+ random_workflow_mode: WorkflowMode,
+ mock_s3_service: MockS3ServiceResource,
+ ) -> None:
+ """
+ Test for successfully updating a workflow and adding new modes.
+
+ Parameters
+ ----------
+ db : sqlalchemy.ext.asyncio.AsyncSession.
+ Async database session to perform query on.
+ client : httpx.AsyncClient
+ HTTP Client to perform the request on.
+ random_user : app.tests.utils.user.UserWithAuthHeader
+ Random user for testing.
+ random_workflow : app.schemas.workflow.WorkflowOut
+ Random workflow for testing.
+ random_workflow_mode : clowmdb.model.WorkflowMode
+ Random workflow mode for testing
+ mock_s3_service : app.tests.mocks.mock_s3_resource.MockS3ServiceResource
+ Mock S3 Service to manipulate objects.
+ """
+ git_commit_hash = random_hex_string()
+ version_update = WorkflowUpdate(
+ git_commit_hash=git_commit_hash,
+ version=random_lower_string(8),
+ append_modes=[
+ WorkflowModeIn(
+ name=random_lower_string(10), entrypoint=random_lower_string(16), schema_path=random_lower_string()
+ )
+ ],
+ ).model_dump()
+ response = await client.post(
+ "/".join([self.base_path, str(random_workflow.workflow_id), "update"]),
+ json=version_update,
+ headers=random_user.auth_headers,
+ )
+ assert response.status_code == status.HTTP_201_CREATED
+ created_version = response.json()
+ assert created_version["git_commit_hash"] == git_commit_hash
+ assert created_version["status"] == WorkflowVersion.Status.CREATED
+ assert created_version["icon_url"] == str(random_workflow.versions[0].icon_url)
+ assert created_version["modes"] is not None
+ assert len(created_version["modes"]) == 2
+
+ stmt = select(WorkflowVersion).where(WorkflowVersion.git_commit_hash == git_commit_hash)
+ db_version = await db.scalar(stmt)
+ assert db_version is not None
+ assert db_version.status == WorkflowVersion.Status.CREATED
+
+ new_mode_id = next((UUID(m) for m in created_version["modes"] if m != str(random_workflow_mode.mode_id)), None)
+ assert new_mode_id is not None
+ assert (
+ f"{git_commit_hash}-{new_mode_id.hex}.json"
+ in mock_s3_service.Bucket(settings.WORKFLOW_BUCKET).objects.all_keys()
+ )
+ assert (
+ f"{git_commit_hash}-{random_workflow_mode.mode_id.hex}.json"
+ in mock_s3_service.Bucket(settings.WORKFLOW_BUCKET).objects.all_keys()
+ )
+
+ # Clean up after test
+ await db.execute(delete(WorkflowMode).where(WorkflowMode._mode_id == new_mode_id.bytes))
+ await db.commit()
+ mock_s3_service.Bucket(settings.WORKFLOW_BUCKET).Object(f"{git_commit_hash}-{new_mode_id.hex}.json").delete()
+
+ @pytest.mark.asyncio
+ async def test_update_workflow_with_delete_non_existing_modes(
+ self,
+ db: AsyncSession,
+ client: AsyncClient,
+ random_user: UserWithAuthHeader,
+ random_workflow: WorkflowOut,
+ ) -> None:
+ """
+ Test for updating a workflow and delete an non-existing mode.
+
+ Parameters
+ ----------
+ db : sqlalchemy.ext.asyncio.AsyncSession.
+ Async database session to perform query on.
+ client : httpx.AsyncClient
+ HTTP Client to perform the request on.
+ random_user : app.tests.utils.user.UserWithAuthHeader
+ Random user for testing.
+ random_workflow : app.schemas.workflow.WorkflowOut
+ Random workflow for testing.
+ """
+ git_commit_hash = random_hex_string()
+ version_update = WorkflowUpdate(
+ git_commit_hash=git_commit_hash, version=random_lower_string(8), delete_modes=[str(uuid4())]
+ ).model_dump_json()
+ response = await client.post(
+ "/".join([self.base_path, str(random_workflow.workflow_id), "update"]),
+ data=version_update, # type: ignore[arg-type]
+ headers=random_user.auth_headers,
+ )
+ assert response.status_code == status.HTTP_400_BAD_REQUEST
+
+ @pytest.mark.asyncio
+ async def test_update_workflow_with_delete_modes(
+ self,
+ db: AsyncSession,
+ client: AsyncClient,
+ random_user: UserWithAuthHeader,
+ random_workflow: WorkflowOut,
+ random_workflow_mode: WorkflowMode,
+ mock_s3_service: MockS3ServiceResource,
+ ) -> None:
+ """
+ Test for successfully updating a workflow and delete an old mode.
+
+ Parameters
+ ----------
+ db : sqlalchemy.ext.asyncio.AsyncSession.
+ Async database session to perform query on.
+ client : httpx.AsyncClient
+ HTTP Client to perform the request on.
+ random_user : app.tests.utils.user.UserWithAuthHeader
+ Random user for testing.
+ random_workflow : app.schemas.workflow.WorkflowOut
+ Random workflow for testing.
+ random_workflow_mode : clowmdb.model.WorkflowMode
+ Random workflow mode for testing
+ mock_s3_service : app.tests.mocks.mock_s3_resource.MockS3ServiceResource
+ Mock S3 Service to manipulate objects.
+ """
+ git_commit_hash = random_hex_string()
+ version_update = WorkflowUpdate(
+ git_commit_hash=git_commit_hash,
+ version=random_lower_string(8),
+ delete_modes=[str(random_workflow_mode.mode_id)],
+ ).model_dump_json()
+ response = await client.post(
+ "/".join([self.base_path, str(random_workflow.workflow_id), "update"]),
+ data=version_update, # type: ignore[arg-type]
+ headers=random_user.auth_headers,
+ )
+ assert response.status_code == status.HTTP_201_CREATED
+ created_version = response.json()
+ assert created_version["git_commit_hash"] == git_commit_hash
+ assert created_version["status"] == WorkflowVersion.Status.CREATED
+ assert created_version["icon_url"] == str(random_workflow.versions[0].icon_url)
+ assert created_version["modes"] is not None
+ assert created_version["modes"] is None or len(created_version["modes"]) == 0
+
+ stmt = select(WorkflowVersion).where(WorkflowVersion.git_commit_hash == git_commit_hash)
+ db_version = await db.scalar(stmt)
+ assert db_version is not None
+ assert db_version.status == WorkflowVersion.Status.CREATED
+
+ assert (
+ f"{git_commit_hash}-{random_workflow_mode.mode_id.hex}.json"
+ not in mock_s3_service.Bucket(settings.WORKFLOW_BUCKET).objects.all_keys()
+ )
+
+ @pytest.mark.asyncio
+ async def test_update_workflow_with_append_and_delete_modes(
+ self,
+ db: AsyncSession,
+ client: AsyncClient,
+ random_user: UserWithAuthHeader,
+ random_workflow: WorkflowOut,
+ random_workflow_mode: WorkflowMode,
+ mock_s3_service: MockS3ServiceResource,
+ ) -> None:
+ """
+ Test for successfully updating a workflow with adding a new mode and delete an old mode.
+
+ Parameters
+ ----------
+ db : sqlalchemy.ext.asyncio.AsyncSession.
+ Async database session to perform query on.
+ client : httpx.AsyncClient
+ HTTP Client to perform the request on.
+ random_user : app.tests.utils.user.UserWithAuthHeader
+ Random user for testing.
+ random_workflow : app.schemas.workflow.WorkflowOut
+ Random workflow for testing.
+ random_workflow_mode : clowmdb.model.WorkflowMode
+ Random workflow mode for testing
+ mock_s3_service : app.tests.mocks.mock_s3_resource.MockS3ServiceResource
+ Mock S3 Service to manipulate objects.
+ """
+ git_commit_hash = random_hex_string()
+ version_update = WorkflowUpdate(
+ git_commit_hash=git_commit_hash,
+ version=random_lower_string(8),
+ delete_modes=[str(random_workflow_mode.mode_id)],
+ append_modes=[
+ WorkflowModeIn(
+ name=random_lower_string(10), entrypoint=random_lower_string(16), schema_path=random_lower_string()
+ )
+ ],
+ ).model_dump_json()
+ response = await client.post(
+ "/".join([self.base_path, str(random_workflow.workflow_id), "update"]),
+ data=version_update, # type: ignore[arg-type]
+ headers=random_user.auth_headers,
+ )
+ assert response.status_code == status.HTTP_201_CREATED
+ created_version = response.json()
+ assert created_version["git_commit_hash"] == git_commit_hash
+ assert created_version["status"] == WorkflowVersion.Status.CREATED
+ assert created_version["icon_url"] == str(random_workflow.versions[0].icon_url)
+ assert created_version["modes"] is not None
+ assert len(created_version["modes"]) == 1
+ assert created_version["modes"][0] != str(random_workflow_mode.mode_id)
+
+ stmt = select(WorkflowVersion).where(WorkflowVersion.git_commit_hash == git_commit_hash)
+ db_version = await db.scalar(stmt)
+ assert db_version is not None
+ assert db_version.status == WorkflowVersion.Status.CREATED
+
+ mode_id = UUID(created_version["modes"][0])
+ assert (
+ f"{git_commit_hash}-{mode_id.hex}.json"
+ in mock_s3_service.Bucket(settings.WORKFLOW_BUCKET).objects.all_keys()
+ )
+ assert (
+ f"{git_commit_hash}-{random_workflow_mode.mode_id.hex}.json"
+ not in mock_s3_service.Bucket(settings.WORKFLOW_BUCKET).objects.all_keys()
+ )
+
+ # Clean up after test
+ await db.execute(delete(WorkflowMode).where(WorkflowMode._mode_id == mode_id.bytes))
+ await db.commit()
+ mock_s3_service.Bucket(settings.WORKFLOW_BUCKET).Object(f"{git_commit_hash}-{mode_id.hex}.json").delete()
+
@pytest.mark.asyncio
async def test_update_workflow_with_error(
self, db: AsyncSession, client: AsyncClient, random_user: UserWithAuthHeader, random_workflow: WorkflowOut
@@ -714,6 +1028,8 @@ class TestWorkflowRoutesUpdate(_TestWorkflowRoutes):
HTTP Client to perform the request on.
random_user : app.tests.utils.user.UserWithAuthHeader
Random user for testing.
+ random_workflow : app.schemas.workflow.WorkflowOut
+ Random workflow for testing.
"""
version_update = WorkflowUpdate(
git_commit_hash=random_hex_string(),
@@ -774,6 +1090,8 @@ class TestWorkflowRoutesUpdate(_TestWorkflowRoutes):
HTTP Client to perform the request on.
random_second_user : app.tests.utils.user.UserWithAuthHeader
Random second user for testing.
+ random_workflow : app.schemas.workflow.WorkflowOut
+ Random workflow for testing.
"""
version_update = WorkflowUpdate(
git_commit_hash=random_hex_string(),
diff --git a/app/tests/api/test_workflow_execution.py b/app/tests/api/test_workflow_execution.py
index c66ebc7ac089ac24e3871b2b670b2b0fd089542b..b310215c8bbb5a7c6e6387971acff87934936ad6 100644
--- a/app/tests/api/test_workflow_execution.py
+++ b/app/tests/api/test_workflow_execution.py
@@ -11,6 +11,7 @@ from sqlalchemy.ext.asyncio import AsyncSession
from app.core.config import settings
from app.schemas.workflow import WorkflowOut
from app.schemas.workflow_execution import DevWorkflowExecutionIn, WorkflowExecutionIn
+from app.schemas.workflow_mode import WorkflowModeIn
from app.scm import SCM
from app.tests.mocks import MockS3ServiceResource, MockSlurmCluster
from app.tests.utils.bucket import add_permission_for_bucket
@@ -34,7 +35,7 @@ class TestWorkflowExecutionRoutesCreate(_TestWorkflowExecutionRoutes):
mock_slurm_cluster: MockSlurmCluster,
) -> None:
"""
- Test for starting a workflow execution.
+ Test for starting a workflow execution from a public GitHub repository.
Parameters
----------
@@ -148,11 +149,12 @@ class TestWorkflowExecutionRoutesCreate(_TestWorkflowExecutionRoutes):
mock_slurm_cluster: MockSlurmCluster,
) -> None:
"""
- Test for starting a workflow execution.
+ Test for starting a workflow execution from a public GitLab repository.
Parameters
----------
- db :
+ db : sqlalchemy.ext.asyncio.AsyncSession.
+ Async database session to perform query on.
client : httpx.AsyncClient
HTTP Client to perform the request on.
random_user : app.tests.utils.user.UserWithAuthHeader
@@ -262,7 +264,7 @@ class TestWorkflowExecutionRoutesCreate(_TestWorkflowExecutionRoutes):
random_workflow_version: WorkflowVersion,
) -> None:
"""
- Test for starting a workflow execution with an unknown workflow version.
+ Test for starting a workflow execution with a deprecated workflow version.
Parameters
----------
@@ -296,7 +298,7 @@ class TestWorkflowExecutionRoutesCreate(_TestWorkflowExecutionRoutes):
random_workflow_version: WorkflowVersion,
) -> None:
"""
- Test for starting a workflow execution with a non-existing bucket.
+ Test for starting a workflow execution with a non-existing bucket in the parameters.
Parameters
----------
@@ -323,7 +325,7 @@ class TestWorkflowExecutionRoutesCreate(_TestWorkflowExecutionRoutes):
random_workflow_version: WorkflowVersion,
) -> None:
"""
- Test for starting a workflow execution with an existing bucket.
+ Test for starting a workflow execution with an existing bucket in the parameters.
Parameters
----------
@@ -353,7 +355,7 @@ class TestWorkflowExecutionRoutesCreate(_TestWorkflowExecutionRoutes):
random_workflow_version: WorkflowVersion,
) -> None:
"""
- Test for starting a workflow execution with a permission for the reference bucket.
+ Test for starting a workflow execution with a permission for the referenced bucket.
Parameters
----------
@@ -387,7 +389,7 @@ class TestWorkflowExecutionRoutesCreate(_TestWorkflowExecutionRoutes):
random_workflow_version: WorkflowVersion,
) -> None:
"""
- Test for starting a workflow execution without a permission for the reference bucket.
+ Test for starting a workflow execution without a permission for the referenced bucket.
Parameters
----------
@@ -489,7 +491,7 @@ class TestWorkflowExecutionRoutesCreate(_TestWorkflowExecutionRoutes):
mock_slurm_cluster: MockSlurmCluster,
) -> None:
"""
- Test for starting a workflow execution where the report output bucket is a non-existing bucket.
+ Test for starting a workflow execution with an workflow mode
Parameters
----------
@@ -529,7 +531,7 @@ class TestWorkflowExecutionRoutesCreate(_TestWorkflowExecutionRoutes):
mock_slurm_cluster: MockSlurmCluster,
) -> None:
"""
- Test for starting a workflow execution where the report output bucket is a non-existing bucket.
+ Test for starting a workflow execution with a non-existing workflow mode
Parameters
----------
@@ -552,6 +554,62 @@ class TestWorkflowExecutionRoutesCreate(_TestWorkflowExecutionRoutes):
class TestDevWorkflowExecutionRoutesCreate(_TestWorkflowExecutionRoutes):
+ @pytest.mark.asyncio
+ async def test_start_dev_workflow_execution_from_github_with_mode(
+ self,
+ client: AsyncClient,
+ random_user: UserWithAuthHeader,
+ mock_s3_service: MockS3ServiceResource,
+ mock_slurm_cluster: MockSlurmCluster,
+ ) -> None:
+ """
+ Test for starting a workflow execution with an arbitrary GitHub repository and a workflow mode.
+
+ Parameters
+ ----------
+ client : httpx.AsyncClient
+ HTTP Client to perform the request on.
+ random_user : app.tests.utils.user.UserWithAuthHeader
+ Random user for testing.
+ mock_s3_service : app.tests.mocks.mock_s3_resource.MockS3ServiceResource
+ Mock S3 Service to manipulate objects.
+ mock_slurm_cluster : app.tests.mocks.mock_slurm_cluster.MockSlurmCluster
+ Mock Slurm cluster to inspect submitted jobs.
+ """
+ mode = WorkflowModeIn(
+ name=random_lower_string(10), entrypoint=random_lower_string(16), schema_path=random_lower_string(16)
+ )
+ execution_in = DevWorkflowExecutionIn(
+ git_commit_hash=random_hex_string(),
+ repository_url="https://github.com/example-user/example",
+ parameters={},
+ mode=mode,
+ )
+ response = await client.post(
+ f"{self.base_path}/arbitrary", headers=random_user.auth_headers, json=execution_in.model_dump()
+ )
+ assert response.status_code == status.HTTP_201_CREATED
+ execution_response = response.json()
+ assert execution_response["user_id"] == random_user.user.uid
+ assert execution_response["status"] == WorkflowExecution.WorkflowExecutionStatus.PENDING
+
+ assert (
+ f"params-{UUID(hex=execution_response['execution_id']).hex }.json"
+ in mock_s3_service.Bucket(settings.PARAMS_BUCKET).objects.all_keys()
+ )
+
+ execution_id = UUID(execution_response["execution_id"])
+ job = mock_slurm_cluster.get_job_by_name(str(execution_id))
+ assert job is not None
+ assert job["job"]["environment"]["TOWER_WORKSPACE_ID"] == execution_id.hex[:16]
+ assert "NXF_SCM_FILE" not in job["job"]["environment"].keys()
+
+ nextflow_script = job["script"]
+ assert "-hub github" in nextflow_script
+ assert f"-entry {mode.entrypoint}" in nextflow_script
+ assert f"-revision {execution_in.git_commit_hash}" in nextflow_script
+ assert f"run {execution_in.repository_url}" in nextflow_script
+
@pytest.mark.asyncio
async def test_start_dev_workflow_execution_from_github(
self,
diff --git a/app/tests/api/test_workflow_mode.py b/app/tests/api/test_workflow_mode.py
index 4b98d5ee0e69047eb879c655f7a76dbac5b0b369..be506d55e25106de8d9cbe1086b212d9508e502d 100644
--- a/app/tests/api/test_workflow_mode.py
+++ b/app/tests/api/test_workflow_mode.py
@@ -9,13 +9,15 @@ from app.tests.utils.user import UserWithAuthHeader
class TestWorkflowModeRoutesGet:
+ _base_path = "workflow_modes"
+
@pytest.mark.asyncio
async def test_get_non_existing_workflow_mode(
self,
client: AsyncClient,
random_user: UserWithAuthHeader,
) -> None:
- response = await client.get(f"/{uuid4()}", headers=random_user.auth_headers)
+ response = await client.get(f"{self._base_path}/{uuid4()}", headers=random_user.auth_headers)
assert response.status_code == status.HTTP_404_NOT_FOUND
@pytest.mark.asyncio
@@ -26,7 +28,7 @@ class TestWorkflowModeRoutesGet:
random_workflow_mode: WorkflowMode,
) -> None:
response = await client.get(
- f"workflow_modes/{str(random_workflow_mode.mode_id)}", headers=random_user.auth_headers
+ f"{self._base_path}/{str(random_workflow_mode.mode_id)}", headers=random_user.auth_headers
)
assert response.status_code == status.HTTP_200_OK
mode = response.json()
diff --git a/app/tests/api/test_workflow_version.py b/app/tests/api/test_workflow_version.py
index c403effd5fc91985116cd8bc8b54a94dc12cb77b..c601d70d1bbe9523b3aa669625c4408acff60d10 100644
--- a/app/tests/api/test_workflow_version.py
+++ b/app/tests/api/test_workflow_version.py
@@ -1,10 +1,10 @@
from io import BytesIO
+from uuid import uuid4
import pytest
-from clowmdb.models import WorkflowVersion
+from clowmdb.models import WorkflowMode, WorkflowVersion
from fastapi import status
from httpx import AsyncClient
-from mocks.mock_s3_resource import MockS3ServiceResource
from sqlalchemy import select
from sqlalchemy.ext.asyncio import AsyncSession
@@ -12,6 +12,7 @@ from app.api.endpoints.workflow_version import DocumentationEnum
from app.core.config import settings
from app.schemas.workflow import WorkflowOut
from app.schemas.workflow_version import WorkflowVersionStatus
+from app.tests.mocks.mock_s3_resource import MockS3ServiceResource
from app.tests.utils.user import UserWithAuthHeader
from app.tests.utils.utils import random_hex_string
@@ -227,7 +228,10 @@ class TestWorkflowVersionRoutesUpdate(_TestWorkflowVersionRoutes):
class TestWorkflowVersionRoutesGetDocumentation(_TestWorkflowVersionRoutes):
@pytest.mark.asyncio
async def test_download_workflow_version_documentation(
- self, client: AsyncClient, random_user: UserWithAuthHeader, random_workflow: WorkflowOut
+ self,
+ client: AsyncClient,
+ random_user: UserWithAuthHeader,
+ random_workflow_version: WorkflowVersion,
) -> None:
"""
Test downloading all the different documentation file for a workflow version.
@@ -238,17 +242,17 @@ class TestWorkflowVersionRoutesGetDocumentation(_TestWorkflowVersionRoutes):
HTTP Client to perform the request on.
random_user : app.tests.utils.user.UserWithAuthHeader
Random user for testing.
- random_workflow : app.schemas.workflow.WorkflowOut
- Random workflow for testing.
+ random_workflow_version : clowmdb.models.WorkflowVersion
+ Random workflow version for testing.
"""
for document in DocumentationEnum:
response = await client.get(
"/".join(
[
self.base_path,
- str(random_workflow.workflow_id),
+ str(random_workflow_version.workflow_id),
"versions",
- random_workflow.versions[0].git_commit_hash,
+ random_workflow_version.git_commit_hash,
"documentation",
]
),
@@ -257,6 +261,79 @@ class TestWorkflowVersionRoutesGetDocumentation(_TestWorkflowVersionRoutes):
)
assert response.status_code == status.HTTP_200_OK
+ @pytest.mark.asyncio
+ async def test_download_workflow_version_documentation_with_non_existing_mode(
+ self,
+ client: AsyncClient,
+ random_user: UserWithAuthHeader,
+ random_workflow_version: WorkflowVersion,
+ ) -> None:
+ """
+ Test downloading all the different documentation file for a workflow version with a non-existing workflow mode.
+
+ Parameters
+ ----------
+ client : httpx.AsyncClient
+ HTTP Client to perform the request on.
+ random_user : app.tests.utils.user.UserWithAuthHeader
+ Random user for testing.
+ random_workflow_version : clowmdb.models.WorkflowVersion
+ Random workflow version for testing.
+ """
+ for document in DocumentationEnum:
+ response = await client.get(
+ "/".join(
+ [
+ self.base_path,
+ str(random_workflow_version.workflow_id),
+ "versions",
+ random_workflow_version.git_commit_hash,
+ "documentation",
+ ]
+ ),
+ headers=random_user.auth_headers,
+ params={"document": document.value, "mode_id": str(uuid4())},
+ )
+ assert response.status_code == status.HTTP_404_NOT_FOUND
+
+ @pytest.mark.asyncio
+ async def test_download_workflow_version_documentation_with_existing_mode(
+ self,
+ client: AsyncClient,
+ random_user: UserWithAuthHeader,
+ random_workflow_version: WorkflowVersion,
+ random_workflow_mode: WorkflowMode,
+ ) -> None:
+ """
+ Test downloading all the different documentation file for a workflow version with a workflow mode.
+
+ Parameters
+ ----------
+ client : httpx.AsyncClient
+ HTTP Client to perform the request on.
+ random_user : app.tests.utils.user.UserWithAuthHeader
+ Random user for testing.
+ random_workflow_version : clowmdb.models.WorkflowVersion
+ Random workflow version for testing.
+ random_workflow_mode : clowmdb.models.WorkflowMode
+ Random workflow mode for testing.
+ """
+ for document in DocumentationEnum:
+ response = await client.get(
+ "/".join(
+ [
+ self.base_path,
+ str(random_workflow_version.workflow_id),
+ "versions",
+ random_workflow_version.git_commit_hash,
+ "documentation",
+ ]
+ ),
+ headers=random_user.auth_headers,
+ params={"document": document.value, "mode_id": str(random_workflow_mode.mode_id)},
+ )
+ assert response.status_code == status.HTTP_200_OK
+
class TestWorkflowVersionIconRoutes(_TestWorkflowVersionRoutes):
@pytest.mark.asyncio
@@ -264,7 +341,7 @@ class TestWorkflowVersionIconRoutes(_TestWorkflowVersionRoutes):
self,
client: AsyncClient,
random_user: UserWithAuthHeader,
- random_workflow: WorkflowOut,
+ random_workflow_version: WorkflowVersion,
mock_s3_service: MockS3ServiceResource,
db: AsyncSession,
) -> None:
@@ -277,22 +354,21 @@ class TestWorkflowVersionIconRoutes(_TestWorkflowVersionRoutes):
HTTP Client to perform the request on.
random_user : app.tests.utils.user.UserWithAuthHeader
Random user for testing.
- random_workflow : app.schemas.workflow.WorkflowOut
- Random workflow for testing.
+ random_workflow_version : clowmdb.models.WorkflowVersion
+ Random workflow version for testing.
mock_s3_service : app.tests.mocks.mock_s3_resource.MockS3ServiceResource
Mock S3 Service to manipulate objects.
db : sqlalchemy.ext.asyncio.AsyncSession.
Async database session to perform query on.
"""
files = {"icon": ("RickRoll.txt", BytesIO(b"Never gonna give you up"), "plain/text")}
- version_hash = random_workflow.versions[0].git_commit_hash
response = await client.post(
"/".join(
[
self.base_path,
- str(random_workflow.workflow_id),
+ str(random_workflow_version.workflow_id),
"versions",
- version_hash,
+ random_workflow_version.git_commit_hash,
"icon",
]
),
@@ -302,19 +378,55 @@ class TestWorkflowVersionIconRoutes(_TestWorkflowVersionRoutes):
assert response.status_code == status.HTTP_201_CREATED
icon_slug = response.json()
assert icon_slug in mock_s3_service.Bucket(settings.ICON_BUCKET).objects.all_keys()
- db_version = await db.scalar(select(WorkflowVersion).where(WorkflowVersion.git_commit_hash == version_hash))
+ db_version = await db.scalar(
+ select(WorkflowVersion).where(WorkflowVersion.git_commit_hash == random_workflow_version.git_commit_hash)
+ )
assert db_version is not None
assert db_version.icon_slug == icon_slug
# Clean up
mock_s3_service.Bucket(settings.ICON_BUCKET).Object(icon_slug).delete()
+ @pytest.mark.asyncio
+ async def test_upload_new_icon_as_non_developer(
+ self,
+ client: AsyncClient,
+ random_second_user: UserWithAuthHeader,
+ random_workflow_version: WorkflowVersion,
+ ) -> None:
+ """
+ Test for uploading a new icon for a workflow version
+
+ Parameters
+ ----------
+ client : httpx.AsyncClient
+ HTTP Client to perform the request on.
+ random_second_user : app.tests.utils.user.UserWithAuthHeader
+ Random user for testing.
+ random_workflow_version : clowmdb.models.WorkflowVersion
+ Random workflow version for testing.
+ """
+ files = {"icon": ("RickRoll.txt", BytesIO(b"Never gonna give you up"), "plain/text")}
+ response = await client.post(
+ "/".join(
+ [
+ self.base_path,
+ str(random_workflow_version.workflow_id),
+ "versions",
+ random_workflow_version.git_commit_hash,
+ "icon",
+ ]
+ ),
+ headers=random_second_user.auth_headers,
+ files=files,
+ )
+ assert response.status_code == status.HTTP_403_FORBIDDEN
+
@pytest.mark.asyncio
async def test_delete_icon(
self,
client: AsyncClient,
random_user: UserWithAuthHeader,
- random_workflow: WorkflowOut,
random_workflow_version: WorkflowVersion,
mock_s3_service: MockS3ServiceResource,
db: AsyncSession,
@@ -328,8 +440,6 @@ class TestWorkflowVersionIconRoutes(_TestWorkflowVersionRoutes):
HTTP Client to perform the request on.
random_user : app.tests.utils.user.UserWithAuthHeader
Random user for testing.
- random_workflow : app.schemas.workflow.WorkflowOut
- Random workflow for testing.
random_workflow_version : clowmdb.models.WorkflowVersion
Random workflow version for testing.
mock_s3_service : app.tests.mocks.mock_s3_resource.MockS3ServiceResource
@@ -342,7 +452,7 @@ class TestWorkflowVersionIconRoutes(_TestWorkflowVersionRoutes):
"/".join(
[
self.base_path,
- str(random_workflow.workflow_id),
+ str(random_workflow_version.workflow_id),
"versions",
random_workflow_version.git_commit_hash,
"icon",
@@ -357,3 +467,42 @@ class TestWorkflowVersionIconRoutes(_TestWorkflowVersionRoutes):
)
assert db_version is not None
assert db_version.icon_slug is None
+
+ @pytest.mark.asyncio
+ async def test_delete_icon_as_non_developer(
+ self,
+ client: AsyncClient,
+ random_second_user: UserWithAuthHeader,
+ random_workflow_version: WorkflowVersion,
+ mock_s3_service: MockS3ServiceResource,
+ db: AsyncSession,
+ ) -> None:
+ """
+ Test for deleting a workflow version icon
+
+ Parameters
+ ----------
+ client : httpx.AsyncClient
+ HTTP Client to perform the request on.
+ random_second_user : app.tests.utils.user.UserWithAuthHeader
+ Random user for testing.
+ random_workflow_version : clowmdb.models.WorkflowVersion
+ Random workflow version for testing.
+ mock_s3_service : app.tests.mocks.mock_s3_resource.MockS3ServiceResource
+ Mock S3 Service to manipulate objects.
+ db : sqlalchemy.ext.asyncio.AsyncSession.
+ Async database session to perform query on.
+ """
+ response = await client.delete(
+ "/".join(
+ [
+ self.base_path,
+ str(random_workflow_version.workflow_id),
+ "versions",
+ random_workflow_version.git_commit_hash,
+ "icon",
+ ]
+ ),
+ headers=random_second_user.auth_headers,
+ )
+ assert response.status_code == status.HTTP_403_FORBIDDEN