Trigger build to test deployment credentials

.dockerignore

@@ -1,3 +1,3 @@
 .git*
 **/*.pyc
-.venv/
+.venv/

.github/workflows/development_dev-research-index.yml

@@ -49,4 +49,4 @@ jobs:
         app-name: 'dev-research-index'
         slot-name: 'production'
         publish-profile: ${{ secrets.AzureAppService_PublishProfile_a74f0a22a9c3465a91fa629137af0f81 }}
-        images: 'index.docker.io/${{ secrets.AzureAppService_ContainerUsername_9310ce663981441ab232b6b875b913e2 }}/ccg-research-index:${{ github.sha }}'
+        images: 'index.docker.io/${{ secrets.AzureAppService_ContainerUsername_9310ce663981441ab232b6b875b913e2 }}/ccg-research-index:${{ github.sha }}'

.github/workflows/main_research-index.yml

@@ -49,4 +49,4 @@ jobs:
         app-name: 'research-index'
         slot-name: 'production'
         publish-profile: ${{ secrets.AzureAppService_PublishProfile_4b15095a06cc4e57aa33f534f4e54311 }}
-        images: 'index.docker.io/${{ secrets.AzureAppService_ContainerUsername_dce678b65c414723a5c407473fe6c430 }}/ccg-research-index:${{ github.sha }}'
+        images: 'index.docker.io/${{ secrets.AzureAppService_ContainerUsername_dce678b65c414723a5c407473fe6c430 }}/ccg-research-index:${{ github.sha }}'

.gitignore

@@ -31,4 +31,4 @@ build/
 
 research_index_backend/
 data/
-*.bash
+*.bash

.pre-commit-config.yaml

@@ -0,0 +1,43 @@
+exclude: '^docs/conf.py'
+
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v6.0.0
+  hooks:
+  - id: trailing-whitespace
+  - id: check-added-large-files
+  - id: check-ast
+  - id: check-json
+  - id: check-merge-conflict
+  - id: check-xml
+  - id: check-yaml
+  - id: debug-statements
+  - id: end-of-file-fixer
+  - id: requirements-txt-fixer
+  - id: mixed-line-ending
+    args: ['--fix=auto']  # replace 'auto' with 'lf' to enforce Linux/Mac line endings or 'crlf' for Windows
+
+- repo: https://github.com/pycqa/isort
+  rev: 7.0.0
+  hooks:
+  - id: isort
+    args: ["--profile", "black", "--filter-files"]
+
+- repo: https://github.com/psf/black
+  rev: 26.1.0
+  hooks:
+  - id: black
+    language_version: python3
+
+- repo: https://github.com/PyCQA/flake8
+  rev: 7.3.0
+  hooks:
+  - id: flake8
+  ## You can add flake8 plugins via `additional_dependencies`:
+  #  additional_dependencies: [flake8-bugbear]
+
+-   repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.19.1  # Use the sha / tag you want to point at
+    hooks:
+    -   id: mypy
+        additional_dependencies: ['types-requests']

Dockerfile

@@ -15,4 +15,4 @@ EXPOSE 8000
 CMD ["fastapi", "run", "app/main.py", \
      "--port", "8000", \
      "--workers", "4", \
-     "--proxy-headers"]
+     "--proxy-headers"]

README.md

@@ -23,6 +23,7 @@ Once the VM is up and running, SSH into the VM, download and install memgraph
 
     curl -O https://download.memgraph.com/memgraph/v2.14.1/ubuntu-20.04/memgraph_2.14.1-1_amd64.deb
     sudo dpkg -i /memgraph_2.14.1-1_amd64.deb
+
 Set up the Memgraph user to match the credentials specified in the `.env` file.
 
 ### 2. Build Docker container

app/api/author.py

@@ -1,43 +1,41 @@
-from fastapi import APIRouter, HTTPException, Query, Path
 from typing import Annotated
 from uuid import UUID
 
+from fastapi import APIRouter, HTTPException, Path, Query
+
 from app.crud.author import Author
 from app.schemas.author import AuthorListModel, AuthorOutputModel
-from app.schemas.query import FilterWorkstream, FilterParams
+from app.schemas.query import FilterParams, FilterWorkstream
 
 router = APIRouter(prefix="/api/authors", tags=["authors"])
 
 
 @router.get("")
-def api_author_list(query: Annotated[FilterWorkstream, Query()]
-                    ) -> AuthorListModel:
+def api_author_list(query: Annotated[FilterWorkstream, Query()]) -> AuthorListModel:
     try:
         authors = Author()
-        if result := authors.get_authors(skip=query.skip,
-                                         limit=query.limit,
-                                         workstream=query.workstream):
+        if result := authors.get_authors(
+            skip=query.skip, limit=query.limit, workstream=query.workstream
+        ):
             return result
     except Exception as e:
         raise HTTPException(status_code=500, detail=f"Database error: {str(e)}") from e
 
+
 @router.get("/{id}")
-def api_author(id: Annotated[UUID, Path(title="Unique author identifier")],
-               query: Annotated[FilterParams, Query()]
-               ) -> AuthorOutputModel:
+def api_author(
+    id: Annotated[UUID, Path(title="Unique author identifier")],
+    query: Annotated[FilterParams, Query()],
+) -> AuthorOutputModel:
     author = Author()
     try:
-        result = author.get_author(id=id,
-                                   result_type=query.result_type,
-                                   skip=query.skip,
-                                   limit=query.limit)
+        result = author.get_author(
+            id=id, result_type=query.result_type, skip=query.skip, limit=query.limit
+        )
 
     except KeyError:
-        raise HTTPException(status_code=404,
-                            detail=f"Author '{id}' not found")
+        raise HTTPException(status_code=404, detail=f"Author '{id}' not found")
     except ValueError as e:
-        raise HTTPException(status_code=500,
-                            detail=f"Database error: {str(e)}") from e
+        raise HTTPException(status_code=500, detail=f"Database error: {str(e)}") from e
     else:
         return result
-

app/api/country.py

@@ -1,5 +1,7 @@
-from fastapi import APIRouter, HTTPException, Query, Path
 from typing import Annotated
+
+from fastapi import APIRouter, HTTPException, Path, Query
+
 from app.crud.country import Country
 from app.schemas.country import CountryList, CountryOutputListModel
 from app.schemas.query import FilterBase, FilterParams
@@ -8,31 +10,30 @@
 
 
 @router.get("")
-def api_country_list(query: Annotated[FilterBase, Query()]
-                     ) -> CountryList:
+def api_country_list(query: Annotated[FilterBase, Query()]) -> CountryList:
     country_model = Country()
     try:
         return country_model.get_countries(query.skip, query.limit)
     except Exception as e:
-        raise HTTPException(status_code=500,
-                            detail=f"Server error: {str(e)}") from e
+        raise HTTPException(status_code=500, detail=f"Server error: {str(e)}") from e
+
 
 @router.get("/{id}")
-def api_country(id: Annotated[str, Path(examples=['KEN'], title="Country identifier", pattern="^([A-Z]{3})$")],
-                query: Annotated[FilterParams, Query()]
-                ) -> CountryOutputListModel:
+def api_country(
+    id: Annotated[
+        str, Path(examples=["KEN"], title="Country identifier", pattern="^([A-Z]{3})$")
+    ],
+    query: Annotated[FilterParams, Query()],
+) -> CountryOutputListModel:
     country_model = Country()
     try:
-        result = country_model.get_country(id,
-                                           query.skip,
-                                           query.limit,
-                                           query.result_type)
+        result = country_model.get_country(
+            id, query.skip, query.limit, query.result_type
+        )
     except KeyError:
-        raise HTTPException(status_code=404,
-                            detail=f"Country with id {id} not found")
+        raise HTTPException(status_code=404, detail=f"Country with id {id} not found")
     except ValueError as e:
-        raise HTTPException(status_code=500,
-                            detail=f"Database error: {str(e)}") from e
+        raise HTTPException(status_code=500, detail=f"Database error: {str(e)}") from e
 
     else:
         return result

app/api/output.py

@@ -1,39 +1,39 @@
-from fastapi import APIRouter, HTTPException, Query, Path
-from fastapi.logger import logger
 from typing import Annotated
-from app.schemas.query import FilterOutputList
 from uuid import UUID
 
+from fastapi import APIRouter, HTTPException, Path, Query
+from fastapi.logger import logger
+
 from app.crud.output import Output
 from app.schemas.output import OutputListModel, OutputModel
+from app.schemas.query import FilterOutputList
 
 router = APIRouter(prefix="/api/outputs", tags=["outputs"])
 
 
 @router.get("")
-def api_output_list(
-    query: Annotated[FilterOutputList, Query()]
-) -> OutputListModel:
+def api_output_list(query: Annotated[FilterOutputList, Query()]) -> OutputListModel:
     """Return a list of outputs"""
     outputs = Output()
     try:
-        return outputs.get_outputs(query.skip,
-                                   query.limit,
-                                   query.result_type,
-                                   query.country)
+        return outputs.get_outputs(
+            query.skip, query.limit, query.result_type, query.country
+        )
     except ValueError as e:
         raise HTTPException(status_code=500, detail=str(e)) from e
 
 
 @router.get("/{id}")
-def api_output(id: Annotated[UUID, Path(title="Unique output identifier")]) -> OutputModel:
+def api_output(
+    id: Annotated[UUID, Path(title="Unique output identifier")],
+) -> OutputModel:
     output = Output()
     try:
         result = output.get_output(id)
     except KeyError as e:
         raise HTTPException(
-                status_code=404, detail=f"Output with id {id} not found"
-            ) from e
+            status_code=404, detail=f"Output with id {id} not found"
+        ) from e
     except Exception as e:
         logger.error(f"Error in api_output: {str(e)}")
         raise HTTPException(status_code=400, detail=str(e)) from e

app/api/workstream.py

@@ -1,17 +1,16 @@
-from typing import List, Annotated
+from typing import Annotated, List
 
-from fastapi import APIRouter, HTTPException, Query, Path
+from fastapi import APIRouter, HTTPException, Path, Query
 
 from app.crud.workstream import Workstream
-from app.schemas.workstream import WorkstreamDetailModel, WorkstreamListModel
 from app.schemas.query import FilterBase
+from app.schemas.workstream import WorkstreamDetailModel, WorkstreamListModel
 
 router = APIRouter(prefix="/api/workstreams", tags=["workstreams"])
 
 
 @router.get("")
-def list_workstreams(
-    query: Annotated[FilterBase, Query()]) -> WorkstreamListModel:
+def list_workstreams(query: Annotated[FilterBase, Query()]) -> WorkstreamListModel:
     """Return a list of workstreams
 
     Returns
@@ -23,25 +22,21 @@ def list_workstreams(
     try:
         results = model.get_all(skip=query.skip, limit=query.limit)
     except KeyError as e:
-        raise HTTPException(status_code=500,
-                            detail=f"Database error: {str(e)}") from e
+        raise HTTPException(status_code=500, detail=f"Database error: {str(e)}") from e
     else:
         return results
 
 
-
 @router.get("/{id}")
 def get_workstream(
     id: Annotated[str, Path(title="Unique workstream identifier")],
-    query: Annotated[FilterBase, Query()]
-    ) -> WorkstreamDetailModel:
-    """Return a single workstream
-    """
+    query: Annotated[FilterBase, Query()],
+) -> WorkstreamDetailModel:
+    """Return a single workstream"""
     model = Workstream()
     try:
         results = model.get(id, skip=query.skip, limit=query.limit)
     except KeyError:
-        raise HTTPException(status_code=404,
-                            detail=f"Workstream '{id}' not found")
+        raise HTTPException(status_code=404, detail=f"Workstream '{id}' not found")
     else:
-        return results
+        return results

app/core/config.py

@@ -1,4 +1,5 @@
 import os
+
 from dotenv import load_dotenv