Release 0.11.5

docs/changelog.md

@@ -2,11 +2,20 @@
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
 
+## [0.11.5] - 02-02-2024
+
+### Fixed
+
+- POP updated
+- Bug in updating project config file
+- Subsample endpoint
+- Lots more UI bugs that include some security vulnerabilities and stability issues
+
 ## [0.11.4] - 01-22-2024
 
 ### Fixed
-- Downloading zip files
 
+- Downloading zip files
 
 ## [0.11.2] - 01-17-2024
 

pephub/_version.py

@@ -1 +1 @@
-__version__ = "0.11.4"
+__version__ = "0.11.5"

pephub/routers/api/v1/project.py

@@ -1,6 +1,7 @@
 import eido
 import yaml
 import pandas as pd
+import numpy as np
 import peppy
 import logging
 from typing import Callable, Literal, Union, Optional, List, Annotated
@@ -22,6 +23,10 @@
     ProjectUniqueNameError,
     SampleAlreadyInView,
     SampleNotFoundError,
+    ViewNotFoundError,
+    ProjectNotFoundError,
+    ViewAlreadyExistsError,
+    SampleAlreadyExistsError,
 )
 from pepdbagent.models import (
     AnnotationModel,
@@ -303,10 +308,10 @@ async def update_a_pep(
             #     status_code=400,
             #     detail=f"Invalid update key: {k}",
             # )
-    # add params to new_raw_project if update_dict is not empty
-    if len(update_dict) > 0:
-        for k, v in update_dict.items():
-            new_raw_project["_config"][k] = v
+    # # add params to new_raw_project if update_dict is not empty
+    # if len(update_dict) > 0:
+    #     for k, v in update_dict.items():
+    #         new_raw_project["_config"][k] = v
     agent.project.update(
         dict(project=Project().from_dict(new_raw_project), **update_dict),
         namespace,
@@ -397,7 +402,7 @@ async def get_pep_samples(
             return JSONResponse(
                 {
                     "count": df.shape[0],
-                    "items": df.replace({pd.NA: None}).to_dict(orient="records"),
+                    "items": df.replace({np.nan: None}).to_dict(orient="records"),
                 }
             )
         else:
@@ -503,8 +508,8 @@ async def update_sample(
     """
     if namespace not in list_of_admins:
         raise HTTPException(
-            detail="You do not have permission to update this project.",
-            status_code=401,
+            detail="Sample does not exist, or you do not have permission to update this sample.",
+            status_code=404,
         )
     try:
         agent.sample.update(
@@ -521,10 +526,10 @@ async def update_sample(
             },
             status_code=202,
         )
-    except Exception as e:
+    except SampleNotFoundError:
         raise HTTPException(
-            status_code=400,
-            detail=f"Could not update sample. Server error: {e}",
+            status_code=404,
+            detail="Sample does not exist, or you do not have permission to update this sample.",
         )
 
 
@@ -564,10 +569,17 @@ async def upload_sample(
             },
             status_code=202,
         )
-    except Exception:
+
+    except SampleAlreadyExistsError:
+        raise HTTPException(
+            status_code=409,
+            detail="Sample already exists in project. Use 'overwrite' parameter to overwrite.",
+        )
+
+    except Exception as e:
         raise HTTPException(
             status_code=400,
-            detail="Could not upload sample. Server error!",
+            detail=f"Could not upload sample. Server error: {e}",
         )
 
 
@@ -600,6 +612,11 @@ async def delete_sample(
             },
             status_code=202,
         )
+    except SampleNotFoundError:
+        raise HTTPException(
+            status_code=404,
+            detail="Sample not found in project.",
+        )
     except Exception:
         raise HTTPException(
             status_code=400,
@@ -622,8 +639,13 @@ async def get_subsamples(
         project: example
         namespace: databio
     """
-    subsamples = proj[SUBSAMPLE_RAW_LIST_KEY]
-    if subsamples is not None:
+    if isinstance(proj, dict):
+        subsamples = proj[SUBSAMPLE_RAW_LIST_KEY]
+    else:
+        subsamples = proj.to_dict(extended=True, orient="records")[
+            SUBSAMPLE_RAW_LIST_KEY
+        ]
+    if subsamples:
         try:
             subsamples = pd.DataFrame(
                 proj[SUBSAMPLE_RAW_LIST_KEY][0]
@@ -804,24 +826,30 @@ async def get_view_of_the_project(
     """
     Fetch a view of the project.
     """
-    if raw:
-        return ProjectRawModel(
-            **agent.view.get(
+    try:
+        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()
+    except ViewNotFoundError:
+        raise HTTPException(
+            status_code=404,
+            detail=f"View '{view}' not found in project '{namespace}/{project}:{tag}'",
         )
-    else:
-        return agent.view.get(
-            namespace=namespace,
-            name=project,
-            view_name=view,
-            tag=tag,
-            raw=raw,
-        ).to_dict()
 
 
 @project.post(
@@ -858,10 +886,20 @@ async def create_view_of_the_project(
                 sample_list=sample_names,
             ),
         )
-    except Exception as e:
+    except SampleNotFoundError as e:
+        raise HTTPException(
+            status_code=404,
+            detail=f"Sample '{e}' not found in project '{namespace}/{project}:{tag}'",
+        )
+    except ProjectNotFoundError:
+        raise HTTPException(
+            status_code=404,
+            detail=f"Project '{namespace}/{project}:{tag}' not found",
+        )
+    except ViewAlreadyExistsError as e:
         _LOGGER.error(f"Could not create view. Error: {e}")
         raise HTTPException(
-            status_code=400,
+            status_code=409,
             detail="Could not create view. Server error",
         )
     return JSONResponse(
@@ -928,12 +966,12 @@ async def add_sample_to_view(
         )
     except SampleAlreadyInView:
         raise HTTPException(
-            status_code=400,
+            status_code=409,
             detail=f"Sample '{sample_name}' already in view '{view}'",
         )
     except SampleNotFoundError:
         raise HTTPException(
-            status_code=400,
+            status_code=404,
             detail=f"Sample '{sample_name}' not found in project '{namespace}/{project}:{tag}'",
         )
     return JSONResponse(
@@ -974,9 +1012,14 @@ def delete_sample_from_view(
         )
     except SampleNotFoundError:
         raise HTTPException(
-            status_code=400,
+            status_code=404,
             detail=f"Sample '{sample_name}' not found in view '{view}'",
         )
+    except ViewNotFoundError:
+        raise HTTPException(
+            status_code=404,
+            detail=f"View '{view}' not found in project '{namespace}/{project}:{tag}'",
+        )
     return JSONResponse(
         content={
             "message": "Sample deleted from view successfully.",
@@ -1011,6 +1054,11 @@ def delete_view(
             project_tag=tag,
             view_name=view,
         )
+    except ViewNotFoundError:
+        raise HTTPException(
+            status_code=404,
+            detail=f"View '{view}' not found in project '{namespace}/{project}:{tag}'",
+        )
     except Exception:
         raise HTTPException(
             status_code=400,

pephub/routers/models.py

@@ -12,7 +12,6 @@ class ProjectOptional(UpdateItems):
     project_config_yaml: Optional[str] = None
     description: Optional[str] = None
     subsample_tables: Optional[List[List[dict]]] = None
-    pop: Optional[bool] = None
 
     model_config = ConfigDict(populate_by_name=True)
 

requirements/requirements-all.txt

@@ -1,6 +1,6 @@
 fastapi>=0.108.0
 psycopg>=3.1.15
-pepdbagent>=0.7.1
+pepdbagent @ git+https://github.com/pepkit/pepdbagent.git@dev#egg=pepdbagent
 peppy>=0.40.1
 eido>=0.2.2
 jinja2>=3.1.2

web/src/api/namespace.ts

@@ -261,7 +261,7 @@ export const submitPop = (
     });
 };
 
-export const starRepository = (
+export const starProject = (
   namespace: string,
   star_namespace: string,
   star_project: string,