diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b7994e1..a3ec43a 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -15,7 +15,7 @@ jobs: steps: # Checkout source code - name: Check out source code - uses: actions/checkout@v2 + uses: actions/checkout@v4 # Calculate some variables that are used later - name: Version information @@ -29,7 +29,7 @@ jobs: fi echo "GITHUB_BRANCH=${BRANCH}" >> $GITHUB_ENV if [ "$BRANCH" == "main" ]; then - version=$(cat package.json | grep \"version\" | head -1 | awk -F= "{ print $2 }" | sed 's/[version:,",]//g' | tr -d '[[:space:]]') + version=$(awk -F= '/^version/ { print $2}' pyproject.toml | sed 's/[ "]//g') tags="latest" oldversion="" while [ "${oldversion}" != "${version}" ]; do @@ -52,6 +52,7 @@ jobs: uses: elgohr/Publish-Docker-Github-Action@3.04 env: BRANCH: ${{ env.GITHUB_BRANCH }} + VERSION: ${{ env.VERSION }} BUILDNUMBER: ${{ github.run_number }} GITSHA1: ${{ github.sha }} with: @@ -60,7 +61,7 @@ jobs: password: ${{ secrets.GITHUB_TOKEN }} registry: ghcr.io tags: "${{ env.TAGS }}" - buildargs: BRANCH,BUILDNUMBER,GITSHA1 + buildargs: BRANCH,VERSION,BUILDNUMBER,GITSHA1 dockerfile: docker/Dockerfile - name: Deploy to prod server diff --git a/.github/workflows/lint.yml b/.github/workflows/lint.yml index aba8aec..0ae01ee 100644 --- a/.github/workflows/lint.yml +++ b/.github/workflows/lint.yml @@ -3,18 +3,18 @@ name: Perform Type and Formatting checks on a new/edited pull requests. on: workflow_dispatch: pull_request: - types: [opened, edited] + types: [opened, edited, synchronize] jobs: - perfrom-type-and-formatting-check: - runs-on: ubuntu-latest + perform-type-and-formatting-check: + runs-on: ubuntu-20.04 steps: - name: Check out repo - uses: actions/checkout@v2 + uses: actions/checkout@v4 - name: Setup Python 3.10 - uses: actions/setup-python@v2 + uses: actions/setup-python@v4 with: python-version: "3.10" diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml index fe62c3d..bb20646 100644 --- a/.github/workflows/pytest.yml +++ b/.github/workflows/pytest.yml @@ -3,7 +3,7 @@ name: Run unit test on: workflow_dispatch: pull_request: - types: [ opened, edited ] + types: [opened, edited, synchronize] jobs: pytest: @@ -37,7 +37,7 @@ jobs: steps: - name: Check out repo - uses: actions/checkout@v2 + uses: actions/checkout@v4 with: submodules: true @@ -68,3 +68,4 @@ jobs: POSTGRES_DB: challenger_expedition FIRST_SUPERUSER: admin@example.com FIRST_SUPERUSER_PASSWORD: secret_password + SECRET_KEY: pytest_secret_key diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8bdf2b2..362bcb7 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,13 +1,13 @@ repos: - repo: https://github.com/PyCQA/isort - rev: 5.10.1 + rev: 5.12.0 hooks: - id: isort - repo: https://github.com/python/black rev: 22.6.0 hooks: - id: black - - repo: https://gitlab.com/pycqa/flake8 + - repo: https://github.com/pycqa/flake8 rev: 5.0.4 hooks: - id: flake8 diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 0000000..c7d2844 --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,27 @@ +# Changelog + +All notable changes to this project will be documented in this file. + +The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), +and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). + +## [1.0.0] - 2023-12-04 + +### Added + +- Added Roboto Bold font (in `fonts` submodule). + +### Fixed + +- Optimized station search. +- Fixed pytest workflow failure. + +### Changed + +- Added temporary binomial name filter at species endpoints. +- Replaced string similarity function for fuzzy search. +- Minor changes to several API endpoints. + +## [0.1.0] - 2022-12-21 + +- The initial release of the Challenger-API. diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md new file mode 100644 index 0000000..0b8c687 --- /dev/null +++ b/CONTRIBUTORS.md @@ -0,0 +1,8 @@ +# Contributors + +- Chris Navarro +- Kaveh Karimi-Asli +- Rashmil Panchani +- Michael Wieck-Sosa +- Olajide Jegede +- Wenqi He diff --git a/app/api/v1/endpoints/species.py b/app/api/v1/endpoints/species.py index cadbfb0..60107fe 100644 --- a/app/api/v1/endpoints/species.py +++ b/app/api/v1/endpoints/species.py @@ -1,11 +1,14 @@ -from typing import Any, List, Optional, Union +from typing import Any, List, Optional, Type, Union from fastapi import APIRouter, Depends, HTTPException, Query +from sqlalchemy import Table from sqlalchemy.orm import Session from app import crud, schemas from app.api import deps -from app.models import SpeciesCommonNames, SpeciesSynonyms +from app.db.base_class import Base +from app.models import SpeciesCommonNames, SpeciesSynonyms, stations_species_table +from app.utils.species import binomial_only router = APIRouter() @@ -28,7 +31,7 @@ def read_all_species( ) -> Any: """Retrieve all species.""" species = crud.species.get_all(db, order_by=order_by) - return species + return binomial_only(species) @router.post("/search/", response_model=List[schemas.SpeciesSummary]) @@ -45,14 +48,15 @@ def read_species_by_search( order_by=order_by, limit=limit, ) - return species + return binomial_only(species) @router.get("/fuzzymatch/", response_model=List[schemas.SpeciesSummary]) def read_fuzzy_species_by_search( query_str: str, + station: Optional[str] = Query(None), db: Session = Depends(deps.get_db), - min_string_similarity_score: float = 0.2, + min_string_similarity_score: float = 0.5, limit: int = 0, order_by: Optional[List[str]] = Query(None), ) -> Any: @@ -91,17 +95,33 @@ def read_fuzzy_species_by_search( ], } + relations: List[Union[Type[Base], Table]] = [SpeciesCommonNames, SpeciesSynonyms] + + if station: + expressions_dict = { + "join": "AND", + "expressions": [ + expressions_dict, + { + "column_name": "station_id", + "search_term": station, + "operator": "eq", + }, + ], + } + relations.append(stations_species_table) + expressions = schemas.ExpressionGroup(**expressions_dict) """Retrieves the species based on the given search expressions.""" species = crud.species.search( db, expressions=expressions, - relations=[SpeciesCommonNames, SpeciesSynonyms], + relations=relations, order_by=order_by, limit=limit, ) - return species + return binomial_only(species) @router.get( diff --git a/app/api/v1/endpoints/stations.py b/app/api/v1/endpoints/stations.py index e999130..691fd8a 100644 --- a/app/api/v1/endpoints/stations.py +++ b/app/api/v1/endpoints/stations.py @@ -1,10 +1,12 @@ -from typing import Any, List, Optional, Union +from typing import Any, List, Optional, Type, Union from fastapi import APIRouter, Depends, HTTPException, Query +from sqlalchemy import Table from sqlalchemy.orm import Session from app import crud, schemas from app.api import deps +from app.db.base_class import Base from app.models import stations_species_table router = APIRouter() @@ -40,10 +42,13 @@ def read_stations_by_search( order_by: Optional[List[str]] = Query(None), ) -> Any: """Retrieves the stations based on the given search expressions.""" + relations: Optional[List[Union[Type[Base], Table]]] = ( + [stations_species_table] if expressions.uses_column("species_id") else None + ) stations = crud.station.search( db, expressions=expressions, - relations=[stations_species_table], + relations=relations, order_by=order_by, limit=limit, ) diff --git a/app/core/config.py b/app/core/config.py index 5719f90..3707206 100644 --- a/app/core/config.py +++ b/app/core/config.py @@ -106,7 +106,7 @@ def get_emails_enabled(cls, v: bool, values: Dict[str, Any]) -> bool: and values.get("EMAILS_FROM_EMAIL") ) - EMAIL_TEST_USER: EmailStr = "test@example.com" # type: ignore + EMAIL_TEST_USER: EmailStr = "test2@example.com" # type: ignore FIRST_SUPERUSER: Optional[EmailStr] = None FIRST_SUPERUSER_PASSWORD: Optional[str] = None @@ -122,6 +122,12 @@ def get_superuser_password(cls, v: Optional[str]) -> Optional[str]: return "test" return v + @validator("ENABLE_AUTH", pre=True) + def get_auth_enable(cls, v: Optional[bool]) -> Optional[bool]: + if os.environ.get("PYTHON_TEST"): + return True + return v + USERS_OPEN_REGISTRATION: bool = False class Config: diff --git a/app/crud/base.py b/app/crud/base.py index 4cf49d5..10e0597 100644 --- a/app/crud/base.py +++ b/app/crud/base.py @@ -168,9 +168,9 @@ def create_search_expressions( raise ValueError(f"Invalid column name: {expression.column_name}") if column.type.python_type == str and expression.fuzzy: # type: ignore - similarity_func = func.similarity(column, expression.search_term) - # TODO: find a better searching function in database. - # similarity_func = func.levenshtein(column, expression.search_term) + + similarity_func = func.word_similarity(expression.search_term, column) + search_expressions["clauses"].append( cast( BinaryExpression, diff --git a/app/crud/crud_station.py b/app/crud/crud_station.py index 732c60d..a24a79f 100644 --- a/app/crud/crud_station.py +++ b/app/crud/crud_station.py @@ -1,17 +1,23 @@ -from typing import Any, Optional +from typing import Any, Optional, cast from sqlalchemy.orm import Session from app.crud.base import CRUDBase from app.models import Station from app.schemas import StationCreate, StationSummaryPagination, StationUpdate +from app.utils.species import binomial_only class CRUDStation( CRUDBase[Station, StationCreate, StationUpdate, StationSummaryPagination] ): def get(self, db: Session, id: Any) -> Optional[Station]: - return db.query(self.model).filter(self.model.name == id).first() + station = cast( + Station, db.query(self.model).filter(self.model.name == id).first() + ) + if station: + station.species = binomial_only(station.species) + return station station = CRUDStation(Station) diff --git a/app/schemas/search.py b/app/schemas/search.py index d303f7a..f18d17c 100644 --- a/app/schemas/search.py +++ b/app/schemas/search.py @@ -27,6 +27,9 @@ class Expression(BaseModel): fuzzy: bool = False min_string_similarity: Optional[float] = Field(default=0.1) + def uses_column(self, name: str) -> bool: + return self.column_name == name + class ExpressionGroup(BaseModel): join: Optional[Join] @@ -46,5 +49,11 @@ def expressions_validator( raise ValueError("a join operator is not needed for one expression") return v + def uses_column(self, name: str) -> bool: + for expression in self.expressions: + if expression.uses_column(name): + return True + return False + ExpressionGroup.update_forward_refs() diff --git a/app/schemas/station.py b/app/schemas/station.py index 1a4ddec..87573d0 100644 --- a/app/schemas/station.py +++ b/app/schemas/station.py @@ -15,6 +15,10 @@ class StationBase(BaseModel): name: str date: date coordinates: List[float] = Field(min_items=2, max_items=2) + fao_area: int + location: str + gear: Optional[str] + sediment_sample: Optional[str] @validator("coordinates", pre=True) def to_point(cls, value: WKBElement) -> List[float]: diff --git a/app/utils/species.py b/app/utils/species.py new file mode 100644 index 0000000..85974ad --- /dev/null +++ b/app/utils/species.py @@ -0,0 +1,17 @@ +from typing import List + +from app.models import Species + + +def binomial_only(species: List[Species]) -> List[Species]: + """ + TODO: This is a temporary fix. In the future, we could consider filtering out genera + when loading data into the database or as part of the OCR workflow. + """ + # Unlike `current_name`, `current_canonical_full_name` doesn't include + # author(s) and year of publication, so for a genus, there won't be any spaces. + return [ + sp + for sp in species + if sp.current_canonical_simple_name and " " in sp.current_canonical_simple_name + ] diff --git a/data b/data index a1db232..11789c9 160000 --- a/data +++ b/data @@ -1 +1 @@ -Subproject commit a1db2329362a5a6103631b15a9f6c5e19edb3d34 +Subproject commit 11789c98f1c96767225143cae4074c56b59b2732 diff --git a/fonts b/fonts index 2df7464..cdfda45 160000 --- a/fonts +++ b/fonts @@ -1 +1 @@ -Subproject commit 2df74649a04ea7b89ea3b71ce4b3697d13a5bfbb +Subproject commit cdfda45cc84a4d3a0adaedbe74e57c92a0b7945c diff --git a/poetry.lock b/poetry.lock index 8d4b27a..15dad94 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,38 +1,134 @@ +# This file is automatically @generated by 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