Added views endpoints

pephub/routers/api/v1/namespace.py

@@ -168,7 +168,7 @@ async def create_pep(
     tag: str = Form(DEFAULT_TAG),
     description: Union[str, None] = Form(None),
     pep_schema: str = Form(DEFAULT_PEP_SCHEMA),
-    files: Optional[List[UploadFile]] = File(
+    files: List[UploadFile] = File(
         None  # let the file upload be optional. dont send a file? We instantiate with blank
     ),
     agent: PEPDatabaseAgent = Depends(get_db),

pephub/routers/api/v1/project.py

@@ -2,6 +2,7 @@
 import yaml
 import pandas as pd
 import peppy
+import logging
 from typing import Callable, Literal, Union, Optional, List, Annotated
 from fastapi import APIRouter, Depends, Query, Body
 from fastapi.exceptions import HTTPException
@@ -17,8 +18,17 @@
 )
 
 from pepdbagent import PEPDatabaseAgent
-from pepdbagent.exceptions import ProjectUniqueNameError
-from pepdbagent.models import AnnotationModel, AnnotationList
+from pepdbagent.exceptions import (
+    ProjectUniqueNameError,
+    SampleAlreadyInView,
+    SampleNotFoundError,
+)
+from pepdbagent.models import (
+    AnnotationModel,
+    AnnotationList,
+    CreateViewDictModel,
+    ProjectViews,
+)
 
 from dotenv import load_dotenv
 
@@ -36,6 +46,7 @@
 )
 from ....const import SAMPLE_CONVERSION_FUNCTIONS, VALID_UPDATE_KEYS
 
+_LOGGER = logging.getLogger(__name__)
 
 load_dotenv()
 
@@ -694,6 +705,8 @@ async def fork_pep_to_namespace(
     fork_request: ForkRequest,
     proj_annotation: AnnotationModel = Depends(get_project_annotation),
     agent: PEPDatabaseAgent = Depends(get_db),
+    description: Optional[str] = "",
+    private: Optional[bool] = False,
 ):
     """
     Fork a project for a particular namespace you have write access to.
@@ -712,6 +725,8 @@ async def fork_pep_to_namespace(
             fork_namespace=fork_to,
             fork_name=fork_name,
             fork_tag=fork_tag,
+            description=description or proj_annotation.description,
+            private=private or proj_annotation.is_private,
         )
 
     except ProjectUniqueNameError as _:
@@ -739,3 +754,257 @@ async def get_project_annotation(
     Get project annotation from a certain project and namespace
     """
     return proj_annotation
+
+
+#### Views ####
+@project.get(
+    "/views",
+    summary="get list of views for a project",
+    tags=["views"],
+    response_model=ProjectViews,
+)
+def get_views(
+    namespace: str,
+    project: str,
+    tag: str = DEFAULT_TAG,
+    agent: PEPDatabaseAgent = Depends(get_db),
+):
+    return agent.view.get_views_annotation(namespace, project, tag=tag)
+
+
+@project.get(
+    "/views/{view}",
+    summary="Fetch a project view",
+    response_model=Union[ProjectRawModel, dict],
+    tags=["views"],
+)
+async def get_view_of_the_project(
+    namespace: str,
+    project: str,
+    view: str,
+    tag: str = DEFAULT_TAG,
+    raw: bool = True,
+    agent: PEPDatabaseAgent = Depends(get_db),
+):
+    """
+    Fetch a view of the project.
+    """
+    if raw:
+        return ProjectRawModel(
+            **agent.view.get(
+                namespace=namespace,
+                name=project,
+                view_name=view,
+                tag=tag,
+                raw=raw,
+            )
+        )
+    else:
+        return agent.view.get(
+            namespace=namespace,
+            name=project,
+            view_name=view,
+            tag=tag,
+            raw=raw,
+        ).to_dict()
+
+
+@project.post(
+    "/views/{view}",
+    summary="Create a view",
+    tags=["views"],
+)
+async def create_view_of_the_project(
+    namespace: str,
+    project: str,
+    view: str,
+    tag: str = DEFAULT_TAG,
+    description: str = "",
+    sample_names: List[str] = None,
+    namespace_access_list: List[str] = Depends(get_namespace_access_list),
+    agent: PEPDatabaseAgent = Depends(get_db),
+):
+    """
+    Create a view of the project.
+    """
+    if namespace not in namespace_access_list:
+        raise HTTPException(
+            detail="You do not have permission to create this view.",
+            status_code=401,
+        )
+    try:
+        agent.view.create(
+            view_name=view,
+            description=description,
+            view_dict=CreateViewDictModel(
+                project_namespace=namespace,
+                project_name=project,
+                project_tag=tag,
+                sample_list=sample_names,
+            ),
+        )
+    except Exception as e:
+        _LOGGER.error(f"Could not create view. Error: {e}")
+        raise HTTPException(
+            status_code=400,
+            detail=f"Could not create view. Server error",
+        )
+    return JSONResponse(
+        content={
+            "message": "View created successfully.",
+            "registry": f"{namespace}/{project}:{tag}",
+        },
+        status_code=202,
+    )
+
+
+@project.get(
+    "/views/{view}/zip",
+    summary="Zip a view",
+    tags=["views"],
+)
+async def zip_view_of_the_view(
+    namespace: str,
+    project: str,
+    view: str,
+    tag: str = DEFAULT_TAG,
+    agent: PEPDatabaseAgent = Depends(get_db),
+):
+    """
+    Zip a view of the project.
+    """
+    return zip_pep(
+        agent.view.get(
+            namespace=namespace,
+            name=project,
+            view_name=view,
+            tag=tag,
+            raw=False,
+        )
+    )
+
+
+@project.post(
+    "/views/{view}/{sample_name}",
+    summary="Add sample to the view",
+    tags=["views"],
+)
+async def add_sample_to_view(
+    namespace: str,
+    project: str,
+    view: str,
+    sample_name: str,
+    tag: str = DEFAULT_TAG,
+    namespace_access_list: List[str] = Depends(get_namespace_access_list),
+    agent: PEPDatabaseAgent = Depends(get_db),
+):
+    if namespace not in namespace_access_list:
+        raise HTTPException(
+            detail="You do not have permission to add sample to this view.",
+            status_code=401,
+        )
+    try:
+        agent.view.add_sample(
+            namespace=namespace,
+            name=project,
+            tag=tag,
+            view_name=view,
+            sample_name=sample_name,
+        )
+    except SampleAlreadyInView:
+        raise HTTPException(
+            status_code=400,
+            detail=f"Sample '{sample_name}' already in view '{view}'",
+        )
+    except SampleNotFoundError:
+        raise HTTPException(
+            status_code=400,
+            detail=f"Sample '{sample_name}' not found in project '{namespace}/{project}:{tag}'",
+        )
+    return JSONResponse(
+        content={
+            "message": "Sample added to view successfully.",
+            "registry": f"{namespace}/{project}:{tag}",
+        },
+        status_code=202,
+    )
+
+
+@project.delete(
+    "/views/{view}/{sample_name}",
+    summary="Delete sample from the view",
+    tags=["views"],
+)
+def delete_sample_from_view(
+    namespace: str,
+    project: str,
+    view: str,
+    sample_name: str,
+    tag: str = DEFAULT_TAG,
+    namespace_access_list: List[str] = Depends(get_namespace_access_list),
+    agent: PEPDatabaseAgent = Depends(get_db),
+):
+    if namespace not in namespace_access_list:
+        raise HTTPException(
+            detail="You do not have permission to delete sample from this view.",
+            status_code=401,
+        )
+    try:
+        agent.view.remove_sample(
+            namespace=namespace,
+            name=project,
+            tag=tag,
+            view_name=view,
+            sample_name=sample_name,
+        )
+    except SampleNotFoundError:
+        raise HTTPException(
+            status_code=400,
+            detail=f"Sample '{sample_name}' not found in view '{view}'",
+        )
+    return JSONResponse(
+        content={
+            "message": "Sample deleted from view successfully.",
+            "registry": f"{namespace}/{project}:{tag}",
+        },
+        status_code=202,
+    )
+
+
+@project.delete(
+    "/views/{view}",
+    summary="Delete a view",
+    tags=["views"],
+)
+def delete_view(
+    namespace: str,
+    project: str,
+    view: str,
+    tag: str = DEFAULT_TAG,
+    namespace_access_list: List[str] = Depends(get_namespace_access_list),
+    agent: PEPDatabaseAgent = Depends(get_db),
+):
+    if namespace not in namespace_access_list:
+        raise HTTPException(
+            detail="You do not have permission to delete this view.",
+            status_code=401,
+        )
+    try:
+        agent.view.delete(
+            project_namespace=namespace,
+            project_name=project,
+            project_tag=tag,
+            view_name=view,
+        )
+    except Exception:
+        raise HTTPException(
+            status_code=400,
+            detail=f"Could not delete view. Server error!",
+        )
+    return JSONResponse(
+        content={
+            "message": "View deleted successfully.",
+            "registry": f"{namespace}/{project}:{tag}",
+        },
+        status_code=202,
+    )