Fix thumbnails

alembic/env.py

@@ -29,7 +29,14 @@
 
 # importModelsForMetadata
 from app.backend.database import Base  # noqa: E402
-from app.backend.models import user_model, project_model, protocol_model, tag_model, protocol_tag_assignment_model  # noqa: F401,E402
+from app.backend.models import (  # noqa: F401,E402
+    user_model,
+    project_model,
+    protocol_model,
+    tag_model,
+    protocol_tag_assignment_model,
+    protocol_step_model,
+)
 
 target_metadata = Base.metadata
 

alembic/versions/6806b9a72a6e_add_protocol_steps.py

@@ -0,0 +1,54 @@
+"""add protocol steps
+
+Revision ID: 6806b9a72a6e
+Revises: 9b7b3c4d8e21
+Create Date: 2026-06-17 17:40:02.063195
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+from sqlalchemy.dialects import postgresql
+
+# revision identifiers, used by Alembic.
+revision: str = '6806b9a72a6e'
+down_revision: Union[str, None] = '9b7b3c4d8e21'
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    op.create_table(
+        "protocol_steps",
+        sa.Column("id", sa.Integer(), nullable=False),
+        sa.Column("projectId", sa.Integer(), nullable=False),
+        sa.Column("protocolDbId", sa.Integer(), nullable=False),
+        sa.Column("protocolId", sa.String(), nullable=False),
+        sa.Column("stepIndex", sa.Integer(), nullable=False),
+        sa.Column("name", sa.Text(), nullable=False),
+        sa.Column("status", sa.Text(), nullable=False),
+        sa.Column("prerequisites", sa.dialects.postgresql.JSONB(), server_default="[]", nullable=False),
+        sa.Column("args", sa.dialects.postgresql.JSONB(), nullable=True),
+        sa.Column("initTime", sa.DateTime(timezone=True), nullable=True),
+        sa.Column("endTime", sa.DateTime(timezone=True), nullable=True),
+        sa.Column("elapsedSeconds", sa.Float(), nullable=True),
+        sa.Column("error", sa.Text(), nullable=True),
+        sa.Column("interactive", sa.Boolean(), server_default="false", nullable=False),
+        sa.Column("needsGpu", sa.Boolean(), server_default="true", nullable=False),
+        sa.Column("event", sa.Text(), nullable=True),
+        sa.Column("createdAt", sa.DateTime(timezone=True), server_default=sa.func.now(), nullable=False),
+        sa.Column("updatedAt", sa.DateTime(timezone=True), server_default=sa.func.now(), nullable=False),
+        sa.ForeignKeyConstraint(["projectId"], ["projects.id"], ondelete="CASCADE"),
+        sa.ForeignKeyConstraint(["protocolDbId"], ["protocols.id"], ondelete="CASCADE"),
+        sa.PrimaryKeyConstraint("id"),
+        sa.UniqueConstraint("projectId", "protocolDbId", "stepIndex", name="ux_protocol_steps_project_protocol_step"),
+    )
+    op.create_index("idx_protocol_steps_protocol", "protocol_steps", ["projectId", "protocolDbId", "stepIndex"])
+    op.create_index("idx_protocol_steps_protocol_id", "protocol_steps", ["projectId", "protocolId"])
+
+
+def downgrade() -> None:
+    op.drop_index("idx_protocol_steps_protocol_id", table_name="protocol_steps")
+    op.drop_index("idx_protocol_steps_protocol", table_name="protocol_steps")
+    op.drop_table("protocol_steps")

app/backend/api/routers/project_router.py

@@ -348,6 +348,48 @@ async def loadProtocol(
     return service.getProtocolParams(projectId, protocolId)
 
 
+class ProtocolStepStatusUpdate(BaseModel):
+    status: Literal["new", "finished"] = Field(..., description="New status for the selected protocol step")
+
+
+@router.get("/{projectId}/protocols/{protocolId}/steps", response_model=Any)
+def listProtocolSteps(
+    projectId: int,
+    protocolId: int,
+    currentUser=Depends(getCurrentUser),
+    mapper: PostgresqlFlatMapper = Depends(getMapper),
+    service: ProjectService = Depends(getProjectService),
+):
+    project = service.getProjectById(mapper, projectId, currentUser, refresh=False, checkPid=False)
+    if not project:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="Project not found")
+
+    return service.listProtocolStepsService(mapper, projectId, protocolId)
+
+
+@router.patch("/{projectId}/protocols/{protocolId}/steps/{stepIndex}/status", response_model=Any)
+def updateProtocolStepStatus(
+    projectId: int,
+    protocolId: int,
+    stepIndex: int,
+    payload: ProtocolStepStatusUpdate,
+    currentUser=Depends(getCurrentUser),
+    mapper: PostgresqlFlatMapper = Depends(getMapper),
+    service: ProjectService = Depends(getProjectService),
+):
+    project = service.getProjectById(mapper, projectId, currentUser, refresh=False, checkPid=False)
+    if not project:
+        raise HTTPException(status_code=status.HTTP_404_NOT_FOUND, detail="Project not found")
+
+    return service.updateProtocolStepStatusService(
+        mapper=mapper,
+        projectId=projectId,
+        protocolId=protocolId,
+        stepIndex=stepIndex,
+        stepStatus=payload.status,
+    )
+
+
 @router.get("/{projectId}/protclass/{protClassName}", response_model=Any)
 async def loadNewProtocol(
     projectId: int,
@@ -2348,6 +2390,35 @@ def createCoords3dOutputFromPoints(projectId: int,
         raise HTTPException( status_code=500, detail=f"Failed to create coords3d output from points: {e}", )
 
 
+@router.get(
+    "/{projectId}/protocols/{protocolId}/outputs/{outputName}/integrated-context",
+    response_model=Any,
+    status_code=status.HTTP_200_OK,
+)
+def getIntegratedAnalyzeContext(
+    projectId: int,
+    protocolId: int,
+    outputName: str,
+    currentUser=Depends(getCurrentUser),
+    mapper: PostgresqlFlatMapper = Depends(getMapper),
+    service: ProjectService = Depends(getProjectService),
+):
+    project = service.getProjectById(mapper, projectId, currentUser, refresh=False, checkPid=False)
+    if not project:
+        raise HTTPException(status_code=404, detail="Project not found")
+
+    payload = service.getIntegratedAnalyzeContextService(
+        projectId=projectId,
+        protocolId=protocolId,
+        outputName=outputName,
+    )
+
+    resp = JSONResponse(payload)
+    resp.headers["X-Debug-Auth"] = "ok"
+    resp.headers["X-Debug-UserId"] = str(getattr(currentUser, "id", currentUser.get("id", "")))
+    resp.headers["Vary"] = "Authorization"
+    return resp
+
 # ==============================================================================
 #        ANALYZE RESULTS: FSC (SetOfFSCs)
 # ==============================================================================

app/backend/api/schemas/protocols_schema.py

@@ -99,3 +99,19 @@ class WorkflowImportRequest(BaseModel):
     sourceProjectId: Optional[Union[int, str]] = None
     sourceProjectName: Optional[str] = None
 
+
+class ProtocolStepOut(BaseModel):
+    index: int
+    name: str
+    status: str
+    prerequisites: List[int] = []
+    args: Optional[Any] = None
+    initTime: Optional[datetime] = None
+    endTime: Optional[datetime] = None
+    elapsedSeconds: Optional[float] = None
+    error: Optional[str] = None
+    interactive: bool = False
+    needsGpu: bool = True
+    event: Optional[str] = None
+    updatedAt: Optional[datetime] = None
+

app/backend/api/services/environment.py

@@ -52,3 +52,7 @@ def prepareEnvironment():
     scipionHome = variables.get(pyworkflow.SCIPION_HOME_VAR) or os.environ.get(pyworkflow.SCIPION_HOME_VAR)
     if scipionHome:
         os.chdir(scipionHome)
+        os.environ.setdefault(
+            "SCIPION_PROTOCOL_STEPS_NOTIFIER",
+            "app.backend.api.services.protocol_steps_sync:syncProtocolStepsEvent",
+        )