diff --git a/.circleci/config.yml b/.circleci/config.yml index 2540faf1c8..7691352ee7 100644 --- a/.circleci/config.yml +++ b/.circleci/config.yml @@ -35,7 +35,7 @@ jobs: backend-code-check-PEP8: docker: - - image: cimg/python:3.9 + - image: cimg/python:3.10 steps: - checkout - setup_remote_docker @@ -47,7 +47,7 @@ jobs: backend-code-check-Black: docker: - - image: cimg/python:3.9 + - image: cimg/python:3.10 steps: - checkout - setup_remote_docker @@ -61,12 +61,14 @@ jobs: resource_class: large docker: - - image: cimg/python:3.9 + - image: cimg/python:3.10 environment: SQLALCHEMY_DATABASE_URI: postgresql://taskingmanager@localhost/test_tm POSTGRES_TEST_DB: test_tm POSTGRES_USER: taskingmanager POSTGRES_ENDPOINT: localhost + TM_ORG_CODE: "CICode" + TM_ORG_NAME: "CircleCI Test Organisation" - image: cimg/postgres:14.2-postgis environment: @@ -87,18 +89,19 @@ jobs: -c "CREATE EXTENSION postgis;" - run: pip install --upgrade pip pdm - run: pdm config --global python.use_venv False - - run: pdm export --prod --without-hashes > requirements.txt + - run: pdm export --dev --without-hashes > requirements.txt - run: pip install -r requirements.txt - run: mkdir --mode 766 -p /tmp/logs - run: mkdir ${CIRCLE_WORKING_DIRECTORY}/tests/backend/results - run: find ./tests/backend -name "test*.py" -exec chmod -x {} \; - run: echo "export TM_LOG_DIR=/tmp/logs" >> $BASH_ENV + - run: coverage erase - run: name: Run backend functional tests command: | - nosetests ./tests/backend --with-xunit \ - --xunit-file ${CIRCLE_WORKING_DIRECTORY}/tests/backend/results/unitresults.xml \ - --with-coverage --cover-erase --cover-package=./backend + coverage run --source ./backend -m pytest \ + --rootdir ./tests/backend \ + --junit-xml ${CIRCLE_WORKING_DIRECTORY}/tests/backend/results/unitresults.xml - run: coverage xml -o ${CIRCLE_WORKING_DIRECTORY}/tests/backend/results/coverage.xml - store_test_results: path: tests/backend/results/unitresults.xml @@ -161,10 +164,10 @@ jobs: build: working_directory: /home/circleci/app docker: - - image: cimg/python:3.9.14-node + - image: cimg/python:3.10.7-node environment: SQLALCHEMY_DATABASE_URI: postgresql://taskingmanager@localhost/test_tm - - image: cimg/postgres:14.2-postgis + - image: cimg/postgres:14.7-postgis environment: POSTGRES_USER: taskingmanager POSTGRES_DB: test_tm @@ -184,7 +187,7 @@ jobs: - run: cd ${CIRCLE_WORKING_DIRECTORY} - run: pip install --upgrade pip pdm - run: pdm config --global python.use_venv False - - run: pdm export --prod --without-hashes > requirements.txt + - run: pdm export --dev --without-hashes > requirements.txt - run: pip install -r requirements.txt - run: mkdir ${CIRCLE_WORKING_DIRECTORY}/tests/backend/results - run: find ./tests/backend -name "test*.py" -exec chmod -x {} \; @@ -192,9 +195,9 @@ jobs: - run: name: Run backend tests command: | - nosetests ./tests/backend --with-xunit \ - --xunit-file ${CIRCLE_WORKING_DIRECTORY}/tests/backend/results/unitresults.xml \ - --with-coverage --cover-erase --cover-package=./backend + coverage run --source ./backend -m pytest \ + --rootdir ./tests/backend \ + --junit-xml ${CIRCLE_WORKING_DIRECTORY}/tests/backend/results/unitresults.xml - run: coverage xml -o ${CIRCLE_WORKING_DIRECTORY}/tests/backend/results/coverage.xml - store_test_results: path: tests/backend/results/unitresults.xml @@ -234,7 +237,7 @@ jobs: working_directory: /home/circleci/tasking-manager resource_class: medium docker: - - image: cimg/python:3.9.14-node + - image: cimg/python:3.10.7-node steps: - checkout - setup_remote_docker @@ -271,7 +274,7 @@ jobs: working_directory: /home/circleci/tasking-manager resource_class: large docker: - - image: cimg/python:3.9.14-node + - image: cimg/python:3.10.7-node parameters: stack_name: description: "the name of the stack for cfn-config" diff --git a/.dockerignore b/.dockerignore index 4776b8538f..8155369a49 100644 --- a/.dockerignore +++ b/.dockerignore @@ -4,5 +4,8 @@ **/__pypackages__ **/node_modules **/npm-debug.log -logs/ +**/venv +docs-old/ docs/ +frontend/ +logs/ diff --git a/.flaskenv b/.flaskenv new file mode 100644 index 0000000000..7800b14d16 --- /dev/null +++ b/.flaskenv @@ -0,0 +1,5 @@ +# This file is not read for Tasking Manager variables. Use tasking-manager.env instead. +# Flask (the web server framework) uses this file to figure out what the entry point is, +# if it is non-standard. +# For more information, see https://flask.palletsprojects.com/en/2.0.x/cli/#environment-variables-from-dotenv +FLASK_APP=manage.py diff --git a/Dockerfile b/Dockerfile index b225df4227..e8acc0763a 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,5 +1,5 @@ ARG ALPINE_IMG_TAG=3.17 -ARG PYTHON_IMG_TAG=3.9 +ARG PYTHON_IMG_TAG=3.10 FROM docker.io/python:${PYTHON_IMG_TAG}-alpine${ALPINE_IMG_TAG} as base ARG APP_VERSION=0.1.0 diff --git a/backend/__init__.py b/backend/__init__.py index aa3295566a..c4ab6fd007 100644 --- a/backend/__init__.py +++ b/backend/__init__.py @@ -1,4 +1,18 @@ import logging + +# gevent.monkey.patch_ssl is required. gevent message as follows: +# MonkeyPatchWarning: Monkey-patching ssl after ssl has already been imported may +# lead to errors, including RecursionError on Python 3.6. It may also silently +# lead to incorrect behaviour on Python 3.7. Please monkey-patch earlier. +# See https://github.com/gevent/gevent/issues/1016. +try: + from gevent import monkey + + monkey.patch_ssl() +except ImportError as e: + logging.warning("Not using gevent") + logging.info(e) + import os from logging.handlers import RotatingFileHandler diff --git a/backend/api/interests/__init__.py b/backend/api/interests/__init__.py new file mode 100644 index 0000000000..e69de29bb2 diff --git a/backend/api/organisations/resources.py b/backend/api/organisations/resources.py index 1a7aa2309a..291c57d07c 100644 --- a/backend/api/organisations/resources.py +++ b/backend/api/organisations/resources.py @@ -462,8 +462,8 @@ def get(self): ) # Validate abbreviated. - omit_managers = strtobool(request.args.get("omitManagerList", "false")) - omit_stats = strtobool(request.args.get("omitOrgStats", "true")) + omit_managers = bool(strtobool(request.args.get("omitManagerList", "false"))) + omit_stats = bool(strtobool(request.args.get("omitOrgStats", "true"))) # Obtain organisations try: results_dto = OrganisationService.get_organisations_as_dto( diff --git a/backend/api/projects/actions.py b/backend/api/projects/actions.py index b56f414444..0bdccf5ec4 100644 --- a/backend/api/projects/actions.py +++ b/backend/api/projects/actions.py @@ -15,6 +15,8 @@ from backend.services.users.authentication_service import token_auth, tm from backend.services.interests_service import InterestService from backend.models.postgis.utils import InvalidGeoJson + +from shapely import GEOSException from shapely.errors import TopologicalError @@ -432,6 +434,16 @@ def post(self): "error": "Invalid geometry. Polygon is self intersecting", "SubCode": "SelfIntersectingAOI", }, 400 + except GEOSException as wrapped: + if ( + isinstance(wrapped.args[0], str) + and "Self-intersection" in wrapped.args[0] + ): + return { + "error": "Invalid geometry. Polygon is self intersecting", + "SubCode": "SelfIntersectingAOI", + }, 400 + return {"error": str(wrapped), "SubCode": "InternalServerError"} except Exception as e: error_msg = f"IntersectingTiles GET API - unhandled error: {str(e)}" current_app.logger.critical(error_msg) diff --git a/backend/api/projects/resources.py b/backend/api/projects/resources.py index 4f9de90c94..00bb4e97f0 100644 --- a/backend/api/projects/resources.py +++ b/backend/api/projects/resources.py @@ -106,7 +106,7 @@ def get(self, project_id): io.BytesIO(geojson.dumps(project_dto).encode("utf-8")), mimetype="application/json", as_attachment=True, - attachment_filename=f"project_{str(project_id)}.json", + download_name=f"project_{str(project_id)}.json", ) return project_dto, 200 @@ -1032,7 +1032,7 @@ def get(self, project_id): io.BytesIO(geojson.dumps(project_dto).encode("utf-8")), mimetype="application/json", as_attachment=True, - attachment_filename=f"project_{str(project_id)}.json", + download_name=f"project_{str(project_id)}.json", ) return project_dto, 200 @@ -1154,7 +1154,7 @@ def get(self, project_id): io.BytesIO(geojson.dumps(project_aoi).encode("utf-8")), mimetype="application/json", as_attachment=True, - attachment_filename=f"{str(project_id)}.geojson", + download_name=f"{str(project_id)}.geojson", ) return project_aoi, 200 diff --git a/backend/api/tasks/actions.py b/backend/api/tasks/actions.py index a2f365fbf3..0faea71faf 100644 --- a/backend/api/tasks/actions.py +++ b/backend/api/tasks/actions.py @@ -171,7 +171,9 @@ def post(self, project_id, task_id): description: Internal Server Error """ try: - stop_task = StopMappingTaskDTO(request.get_json()) + stop_task = StopMappingTaskDTO( + request.get_json() if request.is_json else {} + ) stop_task.user_id = token_auth.current_user() stop_task.task_id = task_id stop_task.project_id = project_id diff --git a/backend/api/tasks/resources.py b/backend/api/tasks/resources.py index 8a37634deb..0fda4b8f56 100644 --- a/backend/api/tasks/resources.py +++ b/backend/api/tasks/resources.py @@ -122,7 +122,7 @@ def get(self, project_id): io.BytesIO(tasks_json), mimetype="application/json", as_attachment=True, - attachment_filename=f"{str(project_id)}-tasks.geojson", + download_name=f"{str(project_id)}-tasks.geojson", ) return tasks_json, 200 @@ -268,7 +268,7 @@ def get(self, project_id): io.BytesIO(xml), mimetype="text.xml", as_attachment=True, - attachment_filename=f"HOT-project-{project_id}.osm", + download_name=f"HOT-project-{project_id}.osm", ) return Response(xml, mimetype="text/xml", status=200) @@ -341,7 +341,7 @@ def get(self, project_id): io.BytesIO(xml), mimetype="text.xml", as_attachment=True, - attachment_filename=f"HOT-project-{project_id}.gpx", + download_name=f"HOT-project-{project_id}.gpx", ) return Response(xml, mimetype="text/xml", status=200) diff --git a/backend/models/postgis/custom_editors.py b/backend/models/postgis/custom_editors.py index 58d2f50e1b..5c74cfb4dd 100644 --- a/backend/models/postgis/custom_editors.py +++ b/backend/models/postgis/custom_editors.py @@ -23,7 +23,7 @@ def save(self): @staticmethod def get_by_project_id(project_id: int): """Get custom editor by it's project id""" - return CustomEditor.query.get(project_id) + return db.session.get(CustomEditor, project_id) @classmethod def create_from_dto(cls, project_id: int, dto: CustomEditorDTO): diff --git a/backend/models/postgis/interests.py b/backend/models/postgis/interests.py index bcffe329e8..ba282e9fe2 100644 --- a/backend/models/postgis/interests.py +++ b/backend/models/postgis/interests.py @@ -30,7 +30,7 @@ class Interest(db.Model): @staticmethod def get_by_id(interest_id: int): """Get interest by id""" - interest = Interest.query.get(interest_id) + interest = db.session.get(Interest, interest_id) if interest is None: raise NotFound(f"Interest id {interest_id} not found") diff --git a/backend/models/postgis/licenses.py b/backend/models/postgis/licenses.py index 5a2db77456..3c65de60f8 100644 --- a/backend/models/postgis/licenses.py +++ b/backend/models/postgis/licenses.py @@ -29,7 +29,7 @@ class License(db.Model): @staticmethod def get_by_id(license_id: int): """Get license by id""" - map_license = License.query.get(license_id) + map_license = db.session.get(License, license_id) if map_license is None: raise NotFound() diff --git a/backend/models/postgis/mapping_issues.py b/backend/models/postgis/mapping_issues.py index 135a5d337b..ef7bc8a3d5 100644 --- a/backend/models/postgis/mapping_issues.py +++ b/backend/models/postgis/mapping_issues.py @@ -20,7 +20,7 @@ def __init__(self, name): @staticmethod def get_by_id(category_id: int): """Get category by id""" - return MappingIssueCategory.query.get(category_id) + return db.session.get(MappingIssueCategory, category_id) @classmethod def create_from_dto(cls, dto: MappingIssueCategoryDTO) -> int: diff --git a/backend/models/postgis/organisation.py b/backend/models/postgis/organisation.py index b9b50df084..dff50df8ad 100644 --- a/backend/models/postgis/organisation.py +++ b/backend/models/postgis/organisation.py @@ -131,7 +131,7 @@ def get(organisation_id: int): :param organisation_id: organisation ID in scope :return: Organisation if found otherwise None """ - return Organisation.query.get(organisation_id) + return db.session.get(Organisation, organisation_id) @staticmethod def get_organisation_by_name(organisation_name: str): diff --git a/backend/models/postgis/priority_area.py b/backend/models/postgis/priority_area.py index 033a2ac0a7..c38a950de7 100644 --- a/backend/models/postgis/priority_area.py +++ b/backend/models/postgis/priority_area.py @@ -29,10 +29,9 @@ def from_dict(cls, area_poly: dict): if type(pa_geojson) is not geojson.Polygon: raise InvalidGeoJson("Priority Areas must be supplied as Polygons") - is_valid_geojson = geojson.is_valid(pa_geojson) - if is_valid_geojson["valid"] == "no": + if not pa_geojson.is_valid: raise InvalidGeoJson( - f"Priority Area: Invalid Polygon - {is_valid_geojson['message']}" + "Priority Area: Invalid Polygon - " + ", ".join(pa_geojson.errors()) ) pa = cls() @@ -42,5 +41,6 @@ def from_dict(cls, area_poly: dict): def get_as_geojson(self): """Helper to translate geometry back to a GEOJson Poly""" - pa_geojson = db.engine.execute(self.geometry.ST_AsGeoJSON()).scalar() + with db.engine.connect() as conn: + pa_geojson = conn.execute(self.geometry.ST_AsGeoJSON()).scalar() return geojson.loads(pa_geojson) diff --git a/backend/models/postgis/project.py b/backend/models/postgis/project.py index 307a433c05..8ccff257b6 100644 --- a/backend/models/postgis/project.py +++ b/backend/models/postgis/project.py @@ -9,7 +9,7 @@ from geoalchemy2 import Geometry from geoalchemy2.shape import to_shape from sqlalchemy.sql.expression import cast, or_ -from sqlalchemy import text, desc, func, Time, orm, literal +from sqlalchemy import desc, func, Time, orm, literal from shapely.geometry import shape from sqlalchemy.dialects.postgresql import ARRAY import requests @@ -267,11 +267,18 @@ def set_country_info(self): current_app.config["OSM_NOMINATIM_SERVER_URL"], lat, lng ) try: - country_info = requests.get(url).json() # returns a dict + response = requests.get(url) + response.raise_for_status() + country_info = response.json() # returns a dict if country_info["address"].get("country") is not None: self.country = [country_info["address"]["country"]] - except (KeyError, AttributeError, requests.exceptions.ConnectionError): - pass + except ( + KeyError, + AttributeError, + requests.exceptions.ConnectionError, + requests.exceptions.HTTPError, + ) as e: + current_app.logger.debug(e, exc_info=True) self.save() @@ -288,7 +295,7 @@ def save(self): def clone(project_id: int, author_id: int): """Clone project""" - orig = Project.query.get(project_id) + orig = db.session.get(Project, project_id) if orig is None: raise NotFound() @@ -354,15 +361,21 @@ def clone(project_id: int, author_id: int): return new_proj @staticmethod - def get(project_id: int): + def get(project_id: int) -> Optional["Project"]: """ Gets specified project :param project_id: project ID in scope :return: Project if found otherwise None """ - return Project.query.options( - orm.noload("tasks"), orm.noload("messages"), orm.noload("project_chat") - ).get(project_id) + return db.session.get( + Project, + project_id, + options=[ + orm.noload(Project.tasks), + orm.noload(Project.messages), + orm.noload(Project.project_chat), + ], + ) def update(self, project_dto: ProjectDTO): """Updates project from DTO""" @@ -517,19 +530,19 @@ def exists(project_id): return db.session.query(literal(True)).filter(query).scalar() def is_favorited(self, user_id: int) -> bool: - user = User.query.get(user_id) + user = db.session.get(User, user_id) if user not in self.favorited: return False return True def favorite(self, user_id: int): - user = User.query.get(user_id) + user = db.session.get(User, user_id) self.favorited.append(user) db.session.commit() def unfavorite(self, user_id: int): - user = User.query.get(user_id) + user = db.session.get(User, user_id) if user not in self.favorited: raise ValueError("NotFeatured- Project not been favorited by user") self.favorited.remove(user) @@ -647,10 +660,13 @@ def get_project_stats(self) -> ProjectStatsDTO: """Create Project Stats model for postgis project object""" project_stats = ProjectStatsDTO() project_stats.project_id = self.id - project_area_sql = "select ST_Area(geometry, true)/1000000 as area from public.projects where id = :id" - project_area_result = db.engine.execute(text(project_area_sql), id=self.id) + project_stats.area = ( + db.session.query(func.ST_Area(Project.geometry, True)) + .where(Project.id == self.id) + .first()[0] + / 1000000 + ) - project_stats.area = project_area_result.fetchone()["area"] project_stats.total_mappers = ( db.session.query(User).filter(User.projects_mapped.any(self.id)).count() ) @@ -926,7 +942,8 @@ def get_project_total_contributions(project_id: int) -> int: def get_aoi_geometry_as_geojson(self): """Helper which returns the AOI geometry as a geojson object""" - aoi_geojson = db.engine.execute(self.geometry.ST_AsGeoJSON()).scalar() + with db.engine.connect() as conn: + aoi_geojson = conn.execute(self.geometry.ST_AsGeoJSON()).scalar() return geojson.loads(aoi_geojson) def get_project_teams(self): diff --git a/backend/models/postgis/project_chat.py b/backend/models/postgis/project_chat.py index 790aec9fdb..9070bd917c 100644 --- a/backend/models/postgis/project_chat.py +++ b/backend/models/postgis/project_chat.py @@ -69,7 +69,7 @@ def get_messages(project_id: int, page: int, per_page: int = 20) -> ProjectChatD project_messages = ( ProjectChat.query.filter_by(project_id=project_id) .order_by(ProjectChat.time_stamp.desc()) - .paginate(page, per_page, True) + .paginate(page=page, per_page=per_page, error_out=True) ) dto = ProjectChatDTO() diff --git a/backend/models/postgis/task.py b/backend/models/postgis/task.py index 07db2aa246..3984ceebbc 100644 --- a/backend/models/postgis/task.py +++ b/backend/models/postgis/task.py @@ -563,9 +563,10 @@ def from_geojson_feature(cls, task_id, task_feature): if type(task_geometry) is not geojson.MultiPolygon: raise InvalidGeoJson("MustBeMultiPloygon- Geometry must be a MultiPolygon") - is_valid_geojson = geojson.is_valid(task_geometry) - if is_valid_geojson["valid"] == "no": - raise InvalidGeoJson(f"InvalidMultiPolygon- {is_valid_geojson['message']}") + if not task_geometry.is_valid: + raise InvalidGeoJson( + "InvalidMultiPolygon - " + ", ".join(task_geometry.errors()) + ) task = cls() try: diff --git a/backend/models/postgis/team.py b/backend/models/postgis/team.py index 66ba8a2009..f224965c56 100644 --- a/backend/models/postgis/team.py +++ b/backend/models/postgis/team.py @@ -175,7 +175,7 @@ def get(team_id: int): :param team_id: team ID in scope :return: Team if found otherwise None """ - return Team.query.get(team_id) + return db.session.get(Team, team_id) def get_team_by_name(team_name: str): """ diff --git a/backend/models/postgis/user.py b/backend/models/postgis/user.py index 1d805ddf0a..8541f82062 100644 --- a/backend/models/postgis/user.py +++ b/backend/models/postgis/user.py @@ -69,7 +69,9 @@ class User(db.Model): last_validation_date = db.Column(db.DateTime, default=timestamp) # Relationships - accepted_licenses = db.relationship("License", secondary=user_licenses_table) + accepted_licenses = db.relationship( + "License", secondary=user_licenses_table, overlaps="users" + ) interests = db.relationship(Interest, secondary=user_interests, backref="users") def create(self): @@ -83,7 +85,7 @@ def save(self): @staticmethod def get_by_id(user_id: int): """Return the user for the specified id, or None if not found""" - return User.query.get(user_id) + return db.session.get(User, user_id) @staticmethod def get_by_username(username: str): @@ -158,7 +160,7 @@ def get_all_users(query: UserSearchQuery) -> UserSearchDTO: base = base.filter(User.role.in_(role_array)) if query.pagination: results = base.order_by(User.username).paginate( - query.page, query.per_page, True + page=query.page, per_page=query.per_page, error_out=True ) else: per_page = base.count() @@ -198,7 +200,7 @@ def filter_users(user_filter: str, project_id: int, page: int) -> UserFilterDTO: .order_by(desc("participant").nullslast(), User.username) ) - results = query.paginate(page, 20, True) + results = query.paginate(page=page, per_page=20, error_out=True) if results.total == 0: raise NotFound() diff --git a/backend/services/campaign_service.py b/backend/services/campaign_service.py index a4c4038a6a..6090981aab 100644 --- a/backend/services/campaign_service.py +++ b/backend/services/campaign_service.py @@ -23,7 +23,7 @@ class CampaignService: @staticmethod def get_campaign(campaign_id: int) -> Campaign: """Gets the specified campaign""" - campaign = Campaign.query.get(campaign_id) + campaign = db.session.get(Campaign, campaign_id) if campaign is None: raise NotFound() @@ -42,7 +42,7 @@ def get_campaign_by_name(campaign_name: str) -> Campaign: @staticmethod def delete_campaign(campaign_id: int): """Delete campaign for a project""" - campaign = Campaign.query.get(campaign_id) + campaign = db.session.get(Campaign, campaign_id) campaign.delete() campaign.save() @@ -162,8 +162,8 @@ def campaign_organisation_exists(campaign_id: int, org_id: int): @staticmethod def delete_organisation_campaign(organisation_id: int, campaign_id: int): """Delete campaign for a organisation""" - campaign = Campaign.query.get(campaign_id) - org = Organisation.query.get(organisation_id) + campaign = db.session.get(Campaign, campaign_id) + org = db.session.get(Organisation, organisation_id) try: org.campaign.remove(campaign) except ValueError: @@ -176,7 +176,7 @@ def delete_organisation_campaign(organisation_id: int, campaign_id: int): @staticmethod def update_campaign(campaign_dto: CampaignDTO, campaign_id: int): - campaign = Campaign.query.get(campaign_id) + campaign = db.session.get(Campaign, campaign_id) if not campaign: raise NotFound(f"Campaign id {campaign_id} not found") try: diff --git a/backend/services/grid/grid_service.py b/backend/services/grid/grid_service.py index e7880f19e2..7564f92d8b 100644 --- a/backend/services/grid/grid_service.py +++ b/backend/services/grid/grid_service.py @@ -1,7 +1,7 @@ import geojson import json from shapely.geometry import MultiPolygon, mapping -from shapely.ops import cascaded_union +from shapely.ops import unary_union import shapely.geometry from flask import current_app from backend.models.dtos.grid_dto import GridDTO @@ -26,8 +26,8 @@ def trim_grid_to_aoi(grid_dto: GridDTO) -> geojson.FeatureCollection: :return: geojson.FeatureCollection trimmed task grid """ # get items out of the dto - grid = grid_dto.grid - aoi = grid_dto.area_of_interest + grid = geojson.loads(geojson.dumps(grid_dto.grid)) + aoi = geojson.loads(geojson.dumps(grid_dto.area_of_interest)) clip_to_aoi = grid_dto.clip_to_aoi # create a shapely shape from the aoi @@ -119,10 +119,10 @@ def merge_to_multi_polygon( "MustBeMultiPloygon- Area Of Interest: geometry must be a MultiPolygon" ) - is_valid_geojson = geojson.is_valid(aoi_multi_polygon_geojson) - if is_valid_geojson["valid"] == "no": + if not aoi_multi_polygon_geojson.is_valid: raise InvalidGeoJson( - f"InvalidMultipolygon- Area of Interest: Invalid MultiPolygon - {is_valid_geojson['message']}" + "InvalidMultipolygon- Area of Interest: Invalid MultiPolygon - " + + ", ".join(aoi_multi_polygon_geojson.errors()) ) return aoi_multi_polygon_geojson @@ -183,7 +183,7 @@ def _adapt_feature_geometry(feature: geojson.Feature) -> geojson.Feature: ): # adapt the geometry for use as a shapely geometry # http://toblerity.org/shapely/manual.html#shapely.geometry.asShape - feature.geometry = shapely.geometry.asShape(feature.geometry) + feature.geometry = shapely.geometry.shape(feature.geometry) return feature else: return None @@ -229,7 +229,7 @@ def _dissolve(geoms: MultiPolygon) -> MultiPolygon: :return: Multipolygon """ # http://toblerity.org/shapely/manual.html#shapely.ops.cascaded_union - geometry = cascaded_union(geoms) + geometry = unary_union(geoms) if geometry.geom_type == "Polygon": # shapely may return a POLYGON rather than a MULTIPOLYGON if there is just one shape # force Multipolygon diff --git a/backend/services/grid/split_service.py b/backend/services/grid/split_service.py index d5e6ccb10b..e39252e286 100644 --- a/backend/services/grid/split_service.py +++ b/backend/services/grid/split_service.py @@ -88,9 +88,10 @@ def _create_square(x, y, zoom) -> geojson.MultiPolygon: transformed_geometry = ST_Transform(shape.from_shape(multipolygon, 3857), 4326) # use DB to get the geometry as geojson - return geojson.loads( - db.engine.execute(transformed_geometry.ST_AsGeoJSON()).scalar() - ) + with db.engine.connect() as conn: + return geojson.loads( + conn.execute(transformed_geometry.ST_AsGeoJSON()).scalar() + ) @staticmethod def _create_split_tasks_from_geometry(task) -> list: @@ -127,9 +128,10 @@ def _create_split_tasks_from_geometry(task) -> list: feature = geojson.Feature() # Tasks expect multipolygons. Convert and use the database to get as GeoJSON multipolygon_geometry = shape.from_shape(split_geometry, 4326) - feature.geometry = geojson.loads( - db.engine.execute(multipolygon_geometry.ST_AsGeoJSON()).scalar() - ) + with db.engine.connect() as conn: + feature.geometry = geojson.loads( + conn.execute(multipolygon_geometry.ST_AsGeoJSON()).scalar() + ) feature.properties["x"] = None feature.properties["y"] = None feature.properties["zoom"] = None @@ -147,11 +149,13 @@ def _as_halves(geometries, centroid, axis) -> list: """ first_half = [ g - for g in geometries + for g in geometries.geoms if getattr(g.centroid, axis) <= getattr(centroid, axis) ] second_half = [ - g for g in geometries if getattr(g.centroid, axis) > getattr(centroid, axis) + g + for g in geometries.geoms + if getattr(g.centroid, axis) > getattr(centroid, axis) ] return (MultiPolygon(first_half), MultiPolygon(second_half)) @@ -172,9 +176,10 @@ def split_task(split_task_dto: SplitTaskDTO) -> TaskDTOs: original_geometry = shape.to_shape(original_task.geometry) # Fetch the task geometry in meters - original_task_area_m = db.engine.execute( - ST_Area(ST_GeogFromWKB(original_task.geometry)) - ).scalar() + with db.engine.connect() as conn: + original_task_area_m = conn.execute( + ST_Area(ST_GeogFromWKB(original_task.geometry)) + ).scalar() if ( original_task.zoom and original_task.zoom >= 18 diff --git a/backend/services/mapping_service.py b/backend/services/mapping_service.py index b9e0871776..7178fa681e 100644 --- a/backend/services/mapping_service.py +++ b/backend/services/mapping_service.py @@ -221,9 +221,9 @@ def generate_gpx(project_id: int, task_ids_str: str, timestamp=None): root = ET.Element( "gpx", attrib=dict( - xmlns="http://www.topografix.com/GPX/1/1", version="1.1", creator="HOT Tasking Manager", + xmlns="http://www.topografix.com/GPX/1/1", ), ) @@ -247,7 +247,7 @@ def generate_gpx(project_id: int, task_ids_str: str, timestamp=None): # Construct trkseg elements if task_ids_str is not None: - task_ids = map(int, task_ids_str.split(",")) + task_ids = list(map(int, task_ids_str.split(","))) tasks = Task.get_tasks(project_id, task_ids) if not tasks or len(tasks) == 0: raise NotFound() @@ -258,7 +258,7 @@ def generate_gpx(project_id: int, task_ids_str: str, timestamp=None): for task in tasks: task_geom = shape.to_shape(task.geometry) - for poly in task_geom: + for poly in task_geom.geoms: trkseg = ET.SubElement(trk, "trkseg") for point in poly.exterior.coords: ET.SubElement( @@ -287,7 +287,7 @@ def generate_osm_xml(project_id: int, task_ids_str: str) -> str: ) if task_ids_str: - task_ids = map(int, task_ids_str.split(",")) + task_ids = list(map(int, task_ids_str.split(","))) tasks = Task.get_tasks(project_id, task_ids) if not tasks or len(tasks) == 0: raise NotFound() @@ -304,7 +304,7 @@ def generate_osm_xml(project_id: int, task_ids_str: str) -> str: "way", attrib=dict(id=str((task.id * -1)), action="modify", visible="true"), ) - for poly in task_geom: + for poly in task_geom.geoms: for point in poly.exterior.coords: ET.SubElement( root, diff --git a/backend/services/messaging/message_service.py b/backend/services/messaging/message_service.py index aa166fb782..a056c87458 100644 --- a/backend/services/messaging/message_service.py +++ b/backend/services/messaging/message_service.py @@ -8,7 +8,7 @@ from sqlalchemy import text, func from markdown import markdown -from backend import create_app, db +from backend import db from backend.models.dtos.message_dto import MessageDTO, MessagesDTO from backend.models.dtos.stats_dto import Pagination from backend.models.postgis.message import Message, MessageType, NotFound @@ -122,9 +122,7 @@ def send_message_to_all_contributors(project_id: int, message_dto: MessageDTO): over a minute to run, so this method is expected to be called on its own thread """ - app = ( - create_app() - ) # Because message-all run on background thread it needs it's own app context + app = current_app # Because message-all run on background thread it needs it's own app context with app.app_context(): contributors = Message.get_all_contributors(project_id) @@ -318,9 +316,7 @@ def send_project_transfer_message( transferred_by: str, ): """Will send a message to the manager of the organization after a project is transferred""" - app = ( - create_app() - ) # Because message-all run on background thread it needs it's own app context + app = current_app # Because message-all run on background thread it needs it's own app context with app.app_context(): project = Project.get(project_id) @@ -385,7 +381,7 @@ def send_request_to_join_team( message.message = f"{user_link} has requested to join the {team_link} team.\ Access the team management page to accept or reject that request." MessageService._push_messages( - [dict(message=message, user=User.query.get(to_user))] + [dict(message=message, user=db.session.get(User, to_user))] ) @staticmethod @@ -466,7 +462,7 @@ def send_message_after_chat( ): """Send alert to user if they were @'d in a chat message""" # Because message-all run on background thread it needs it's own app context - app = create_app() + app = current_app with app.app_context(): usernames = MessageService._parse_message_for_username(chat, project_id) if len(usernames) != 0: @@ -496,9 +492,10 @@ def send_message_after_chat( MessageService._push_messages(messages) query = """ select user_id from project_favorites where project_id = :project_id""" - favorited_users_results = db.engine.execute( - text(query), project_id=project_id - ) + with db.engine.connect() as conn: + favorited_users_results = conn.execute( + text(query), project_id=project_id + ) favorited_users = [r[0] for r in favorited_users_results] # Notify all contributors except the user that created the comment. @@ -572,9 +569,10 @@ def send_favorite_project_activities(user_id: int): project_name = ProjectInfo.get_dto_for_locale( project.id, project.default_locale ).name - last_active_users = db.engine.execute( - text(query_last_active_users), project_id=project.id - ) + with db.engine.connect() as conn: + last_active_users = conn.execute( + text(query_last_active_users), project_id=project.id + ) for recent_user_id in last_active_users: recent_user_details = UserService.get_user_by_id(recent_user_id) @@ -615,7 +613,7 @@ def _parse_message_for_bulk_mentions( parsed = parser.findall(message) usernames = [] - project = Project.query.get(project_id) + project = db.session.get(Project, project_id) if project is None: return usernames @@ -719,7 +717,7 @@ def get_all_messages( results = ( query.filter(Message.to_user_id == user_id) .order_by(sort_column) - .paginate(page, page_size, True) + .paginate(page=page, per_page=page_size, error_out=True) ) # if results.total == 0: # raise NotFound() @@ -742,7 +740,7 @@ def get_all_messages( @staticmethod def get_message(message_id: int, user_id: int) -> Message: """Gets the specified message""" - message = Message.query.get(message_id) + message = db.session.get(Message, message_id) if message is None: raise NotFound() diff --git a/backend/services/organisation_service.py b/backend/services/organisation_service.py index 35d5eb59c6..2b000bb018 100644 --- a/backend/services/organisation_service.py +++ b/backend/services/organisation_service.py @@ -205,9 +205,7 @@ def get_organisation_stats( ).filter(Project.organisation_id == organisation_id) if year: start_date = f"{year}/01/01" - projects = projects.filter( - Project.created.between(start_date, datetime.today()) - ) + projects = projects.filter(Project.created.between(start_date, func.now())) published_projects = projects.filter( Project.status == ProjectStatus.PUBLISHED.value diff --git a/backend/services/project_admin_service.py b/backend/services/project_admin_service.py index a9f32def43..a0df1c8837 100644 --- a/backend/services/project_admin_service.py +++ b/backend/services/project_admin_service.py @@ -222,10 +222,9 @@ def _attach_tasks_to_project(draft_project: Project, tasks_geojson): "MustBeFeatureCollection- Invalid: GeoJson must be FeatureCollection" ) - is_valid_geojson = geojson.is_valid(tasks) - if is_valid_geojson["valid"] == "no": + if not tasks.is_valid: raise InvalidGeoJson( - f"InvalidFeatureCollection- {is_valid_geojson['message']}" + "InvalidFeatureCollection - " + ", ".join(tasks.errors()) ) task_count = 1 diff --git a/backend/services/project_search_service.py b/backend/services/project_search_service.py index 74fc5f0193..6f69da1737 100644 --- a/backend/services/project_search_service.py +++ b/backend/services/project_search_service.py @@ -377,12 +377,16 @@ def _filter_projects(search_dto: ProjectSearchDTO, user): if not search_dto.omit_map_results: query_result = query query_result.column_descriptions.clear() - query_result.add_column(Project.id) - query_result.add_column(Project.centroid.ST_AsGeoJSON().label("centroid")) - query_result.add_column(Project.priority) + query_result.add_columns( + Project.id, + Project.centroid.ST_AsGeoJSON().label("centroid"), + Project.priority, + ) all_results = query_result.all() - paginated_results = query.paginate(search_dto.page, 14, True) + paginated_results = query.paginate( + page=search_dto.page, per_page=14, error_out=True + ) return all_results, paginated_results @@ -546,7 +550,8 @@ def _make_4326_polygon_from_bbox(bbox: list, srid: int) -> Polygon: polygon = box(bbox[0], bbox[1], bbox[2], bbox[3]) if not srid == 4326: geometry = shape.from_shape(polygon, srid) - geom_4326 = db.engine.execute(ST_Transform(geometry, 4326)).scalar() + with db.engine.connect() as conn: + geom_4326 = conn.execute(ST_Transform(geometry, 4326)).scalar() polygon = shape.to_shape(geom_4326) except Exception as e: current_app.logger.error(f"InvalidData- error making polygon: {e}") @@ -556,9 +561,10 @@ def _make_4326_polygon_from_bbox(bbox: list, srid: int) -> Polygon: @staticmethod def _get_area_sqm(polygon: Polygon) -> float: """get the area of the polygon in square metres""" - return db.engine.execute( - ST_Area(ST_Transform(shape.from_shape(polygon, 4326), 3857)) - ).scalar() + with db.engine.connect() as conn: + return conn.execute( + ST_Area(ST_Transform(shape.from_shape(polygon, 4326), 3857)) + ).scalar() @staticmethod def validate_bbox_area(polygon: Polygon) -> bool: diff --git a/backend/services/stats_service.py b/backend/services/stats_service.py index 7c7647af27..1f309ac876 100644 --- a/backend/services/stats_service.py +++ b/backend/services/stats_service.py @@ -1,6 +1,6 @@ from cachetools import TTLCache, cached from datetime import date, timedelta -from sqlalchemy import func, desc, cast, extract, or_, tuple_ +from sqlalchemy import func, desc, cast, extract, or_ from sqlalchemy.sql.functions import coalesce from sqlalchemy.types import Time @@ -136,7 +136,7 @@ def get_latest_activity(project_id: int, page: int) -> ProjectActivityDTO: TaskHistory.action != TaskAction.COMMENT.name, ) .order_by(TaskHistory.action_date.desc()) - .paginate(page, 10, True) + .paginate(page=page, per_page=10, error_out=True) ) activity_dto = ProjectActivityDTO() @@ -547,9 +547,7 @@ def get_task_stats( func.DATE(TaskHistory.action_date).label("day"), ) .distinct( - tuple_( - TaskHistory.project_id, TaskHistory.task_id, TaskHistory.action_text - ) + TaskHistory.project_id, TaskHistory.task_id, TaskHistory.action_text ) .filter( TaskHistory.action == "STATE_CHANGE", diff --git a/backend/services/team_service.py b/backend/services/team_service.py index bf59959435..b1df1f3329 100644 --- a/backend/services/team_service.py +++ b/backend/services/team_service.py @@ -288,7 +288,9 @@ def get_all_teams(search_dto: TeamSearchDTO) -> TeamsListDTO: teams_list_dto = TeamsListDTO() if search_dto.paginate: - paginated = query.paginate(search_dto.page, search_dto.per_page, True) + paginated = query.paginate( + page=search_dto.page, per_page=search_dto.per_page, error_out=True + ) teams_list_dto.pagination = Pagination(paginated) teams_list = paginated.items else: diff --git a/backend/services/users/user_service.py b/backend/services/users/user_service.py index f88b08f583..9ebb894cdd 100644 --- a/backend/services/users/user_service.py +++ b/backend/services/users/user_service.py @@ -2,7 +2,7 @@ from flask import current_app import datetime from sqlalchemy.sql.expression import literal -from sqlalchemy import func, or_, desc, and_, distinct, cast, Time +from sqlalchemy import func, or_, desc, and_, distinct, cast, Time, column from backend import db from backend.models.dtos.project_dto import ProjectFavoritesDTO, ProjectSearchResultsDTO from backend.models.dtos.user_dto import ( @@ -291,7 +291,7 @@ def get_tasks_dto( Task.project_id == sq.c.project_id, ), ) - tasks = tasks.add_columns("max", "comments") + tasks = tasks.add_columns(column("max"), column("comments")) if sort_by == "action_date": tasks = tasks.order_by(sq.c.max) @@ -311,7 +311,7 @@ def get_tasks_dto( if project_id: tasks = tasks.filter_by(project_id=project_id) - results = tasks.paginate(page, page_size, True) + results = tasks.paginate(page=page, per_page=page_size, error_out=True) task_list = [] diff --git a/backend/services/validator_service.py b/backend/services/validator_service.py index 47d197b7c0..90ecd8fd75 100644 --- a/backend/services/validator_service.py +++ b/backend/services/validator_service.py @@ -317,7 +317,7 @@ def get_user_invalidated_tasks( query = query.filter_by(project_id=project_id) results = query.order_by(text(sort_by + " " + sort_direction)).paginate( - page, page_size, True + page=page, per_page=page_size, error_out=True ) project_names = {} invalidated_tasks_dto = InvalidatedTasks() diff --git a/docker-compose.yml b/docker-compose.yml index 1032c4b914..28af69935d 100644 --- a/docker-compose.yml +++ b/docker-compose.yml @@ -25,7 +25,7 @@ services: <<: *backend container_name: migration restart: on-failure - command: python manage.py db upgrade + command: flask db upgrade frontend: image: hotosm-tasking-manager:frontend diff --git a/docs-old/migration.md b/docs-old/migration.md index afa485b8f6..e37eb2caf1 100644 --- a/docs-old/migration.md +++ b/docs-old/migration.md @@ -11,7 +11,7 @@ $ `psql -d myDataBase -a -f scripts/database/duplicate-priority-area-cleanup.sql Now, migrating from version 3 to version 4 can be done through the build in alembic migrations by simply running: -$ `python manage.py db upgrade` or `pdm run upgrade` +$ `flask db upgrade` or `pdm run upgrade` Depending on the size of your database this might take a good while. diff --git a/docs-old/review-pr.md b/docs-old/review-pr.md index 75e3aa6b31..eb0e699ad5 100644 --- a/docs-old/review-pr.md +++ b/docs-old/review-pr.md @@ -64,7 +64,7 @@ and ask the person to check on the error. * ```pip install --upgrade pdm``` * ```pdm export --without-hashes > requirements.txt``` * ```pip install requirements.txt``` - b. introduced database migrations: `python manage.py db upgrade` + b. introduced database migrations: `flask db upgrade` c. frontend dependency installation: `cd frontend && yarn && cd ..` d. rebuild the frontend: `cd frontend && yarn build && cd ..` @@ -134,7 +134,7 @@ This is important to do even if there are no frontend changes because you may ha Upgrade the database (it may be wise to back up your database first): -`python manage.py db upgrade` or `pdm run upgrade` +`flask db upgrade` or `pdm run upgrade` If you get an error, you may have an upgraded database from a prior PR. Try downgrading to develop (`python manage.py db downgrade`). @@ -169,7 +169,7 @@ After reviewing, you'll want to downgrade your database, return to develop, and # so if a PR contains multiple revisions, # you may have to run this command more than once -python manage.py db downgrade or pdm run downgrade +flask db downgrade or pdm run downgrade # _now_ you can return to develop. # if you do before downgrading, flask_migrate will not diff --git a/docs-old/setup-development.md b/docs-old/setup-development.md index 42cecbb362..150f5e1460 100644 --- a/docs-old/setup-development.md +++ b/docs-old/setup-development.md @@ -129,7 +129,7 @@ cd frontend && yarn build-locales We use [Flask-Migrate](https://flask-migrate.readthedocs.io/en/latest/) to create the database from the migrations directory. Check the instructions on how to setup a PostGIS database with [docker](#creating-a-local-postgis-database-with-docker) or on your [local system](#non-docker). Then you can execute the following command to apply the migrations: ``` -python3 manage.py db upgrade +flask db upgrade ``` or ``` @@ -150,7 +150,7 @@ To be able to create projects and have full permissions as an admin user inside If you plan to only work on the API you only have to build the backend architecture. Install the backend dependencies, and run the server: -`python3 manage.py runserver -d -r` or `pdm run start` +`flask run --debug --reload` or `pdm run start` You can access the API documentation on [http://localhost:5000/api-docs](http://localhost:5000/api-docs), it also allows you to execute requests on your local TM instance. The API docs is also available on our [production](https://tasks.hotosm.org/api-docs) and [staging](https://tasks-stage.hotosm.org/api-docs/) instances. @@ -158,10 +158,10 @@ You can access the API documentation on [http://localhost:5000/api-docs](http:// In order to authenticate on the API, you need to have an Authorization Token. -1. Run the command line `manage.py` with the `gen_token` option and `-u `. The command line can be run in any shell session as long as you are in the tasking-manager directory. +1. Run the command line `manage.py` via `flask` with the `gen_token` option and `-u `. The command line can be run in any shell session as long as you are in the tasking-manager directory. ``` -python manage.py gen_token -u 99999999 +flask gen_token -u 99999999 ``` This will generate a line that looks like this: diff --git a/docs/developers/development-setup.md b/docs/developers/development-setup.md index 6337814878..2419ffa46e 100644 --- a/docs/developers/development-setup.md +++ b/docs/developers/development-setup.md @@ -137,7 +137,7 @@ cd frontend && yarn build-locales We use [Flask-Migrate](https://flask-migrate.readthedocs.io/en/latest/) to create the database from the migrations directory. Check the instructions on how to setup a PostGIS database with [docker](#creating-a-local-postgis-database-with-docker) or on your [local system](#non-docker). Then you can execute the following command to apply the migrations: ``` -python3 manage.py db upgrade +flask db upgrade ``` or ``` @@ -154,7 +154,7 @@ To be able to create projects and have full permissions as an admin user inside If you plan to only work on the API you only have to build the backend architecture. Install the backend dependencies, and run the server: -`python3 manage.py runserver -d -r ` or `pdm run start` +`flask run --debug --reload` or `pdm run start` You can access the API documentation on [http://localhost:5000/api-docs](http://localhost:5000/api-docs), it also allows you to execute requests on your local TM instance. The API docs is also available on our [production](https://tasks.hotosm.org/api-docs) and [staging](https://tasks-stage.hotosm.org/api-docs/) instances. @@ -162,10 +162,10 @@ You can access the API documentation on [http://localhost:5000/api-docs](http:// In order to authenticate on the API, you need to have an Authorization Token. -1. Run the command line `manage.py` with the `gen_token` option and `-u `. The command line can be run in any shell session as long as you are in the tasking-manager directory. +1. Run the command line `manage.py` via `flask` with the `gen_token` option and `-u `. The command line can be run in any shell session as long as you are in the tasking-manager directory. ``` -python manage.py gen_token -u 99999999 +flask gen_token -u 99999999 ``` This will generate a line that looks like this: diff --git a/manage.py b/manage.py index a2d5d0334e..6a3366945f 100644 --- a/manage.py +++ b/manage.py @@ -4,10 +4,10 @@ import csv import datetime -from flask_migrate import MigrateCommand -from flask_script import Manager +import click +from flask_migrate import Migrate from dotenv import load_dotenv -from backend import create_app, initialise_counters +from backend import create_app, initialise_counters, db from backend.services.users.authentication_service import AuthenticationService from backend.services.users.user_service import UserService from backend.services.stats_service import StatsService @@ -47,14 +47,13 @@ warnings.warn("Homepage counters not initialized.") # Add management commands -manager = Manager(application) # Enable db migrations to be run via the command line -manager.add_command("db", MigrateCommand) +migrate = Migrate(application, db) # Job runs once every 2 hours -@manager.command +@application.cli.command("auto_unlock_tasks") def auto_unlock_tasks(): with application.app_context(): # Identify distinct project IDs that were touched in the last 2 hours @@ -84,7 +83,8 @@ def auto_unlock_tasks(): atexit.register(lambda: cron.shutdown(wait=False)) -@manager.option("-u", "--user_id", help="Test User ID") +@application.cli.command("gen_token") +@click.option("-u", "--user_id", help="Test User ID") def gen_token(user_id): """Helper method for generating valid base64 encoded session tokens""" token = AuthenticationService.generate_session_token_for_user(user_id) @@ -93,21 +93,22 @@ def gen_token(user_id): print(f"Your base64 encoded session token: {b64_token}") -@manager.command +@application.cli.command("refresh_levels") def refresh_levels(): print("Started updating mapper levels...") users_updated = UserService.refresh_mapper_level() print(f"Updated {users_updated} user mapper levels") -@manager.command +@application.cli.command("refresh_project_stats") def refresh_project_stats(): print("Started updating project stats...") StatsService.update_all_project_stats() print("Project stats updated") -@manager.command +@application.cli.command("update_project_categories") +@click.argument("filename") def update_project_categories(filename): with open(filename, "r", encoding="ISO-8859-1", newline="") as csvfile: reader = csv.DictReader(csvfile) @@ -132,4 +133,21 @@ def update_project_categories(filename): if __name__ == "__main__": - manager.run() + # This is compatibility code with previous releases + # People should generally prefer `flask `. + from sys import argv + from flask.cli import FlaskGroup + from click import Command + + cli = FlaskGroup(create_app=lambda: application) + cli.add_command( + cmd=Command( + name="runserver", + callback=application.run, + help='Deprecated, use "flask run" instead', + ) + ) + if argv[1] == "runserver": + application.run() + else: + cli() diff --git a/migrations/alembic.ini b/migrations/alembic.ini index c036ff3eaf..59e0ae6bf6 100644 --- a/migrations/alembic.ini +++ b/migrations/alembic.ini @@ -12,6 +12,7 @@ script_location = /src/migrations # Custom param that enables us to specify tables to ignore when determining migrations [alembic:exclude] tables = spatial_ref_sys +index = idx_username_lower # Logging configuration [loggers] diff --git a/migrations/env.py b/migrations/env.py index 26d4b46068..9a62c50755 100644 --- a/migrations/env.py +++ b/migrations/env.py @@ -1,6 +1,7 @@ from __future__ import with_statement from alembic import context from sqlalchemy import engine_from_config, pool +from geoalchemy2 import alembic_helpers from logging.config import fileConfig from flask import current_app import logging @@ -29,6 +30,7 @@ # my_important_option = config.get_main_option("my_important_option") # ... etc. exclude_tables = config.get_section("alembic:exclude").get("tables", "").split(",") +exclude_index = config.get_section("alembic:exclude").get("index", "").split(",") def include_object(object, name, type_, reflected, compare_to): @@ -37,8 +39,12 @@ def include_object(object, name, type_, reflected, compare_to): """ if type_ == "table" and name in exclude_tables: return False + elif type_ == "index" and name in exclude_index: + return False else: - return True + return alembic_helpers.include_object( + object, name, type_, reflected, compare_to + ) def run_migrations_offline(): @@ -54,7 +60,12 @@ def run_migrations_offline(): """ url = config.get_main_option("sqlalchemy.url") - context.configure(url=url, include_object=include_object) + context.configure( + url=url, + include_object=include_object, + process_revision_directives=alembic_helpers.writer, + render_item=alembic_helpers.render_item, + ) with context.begin_transaction(): context.run_migrations() @@ -72,6 +83,7 @@ def run_migrations_online(): # when there are no changes to the schema # reference: http://alembic.readthedocs.org/en/latest/cookbook.html def process_revision_directives(context, revision, directives): + alembic_helpers.writer(context, revision, directives) if getattr(config.cmd_opts, "autogenerate", False): script = directives[0] if script.upgrade_ops.is_empty(): @@ -90,6 +102,7 @@ def process_revision_directives(context, revision, directives): target_metadata=target_metadata, process_revision_directives=process_revision_directives, include_object=include_object, + render_item=alembic_helpers.render_item, **current_app.extensions["migrate"].configure_args, ) diff --git a/migrations/versions/0a6b82b55983_.py b/migrations/versions/0a6b82b55983_.py index 15695db461..1b2a22790d 100644 --- a/migrations/versions/0a6b82b55983_.py +++ b/migrations/versions/0a6b82b55983_.py @@ -47,7 +47,7 @@ def upgrade(): project_existence = {} # Attempt to classify existing messages - messages = conn.execute("select * from messages") + messages = conn.execute(sa.text("select * from messages")) for message in messages: message_type = None project_id = None @@ -85,7 +85,7 @@ def upgrade(): # If we haven't checked yet if this project exists, check now and cache result if project_id not in project_existence: project = conn.execute( - "select * from projects where id = " + str(project_id) + sa.text("select * from projects where id = " + str(project_id)) ).first() project_existence[project_id] = project is not None diff --git a/migrations/versions/0eee8c1abd3a_.py b/migrations/versions/0eee8c1abd3a_.py index f07ecb96f0..d71c5c5f12 100644 --- a/migrations/versions/0eee8c1abd3a_.py +++ b/migrations/versions/0eee8c1abd3a_.py @@ -27,7 +27,7 @@ def upgrade(): op.add_column("projects", sa.Column("country", ARRAY(sa.String()), nullable=True)) - fetch_all_project_geoms = ( + fetch_all_project_geoms = sa.text( "SELECT id, ST_AsText(ST_GeomFromWKB(ST_AsEWKB(centroid))) from projects;" ) projects = conn.execute(fetch_all_project_geoms) @@ -51,6 +51,9 @@ def upgrade(): print("Geometry Exception: Project " + str(project_id) + " " + str(e)) continue + if not project_centroid: + continue + if not project_centroid.is_valid: project_centroid = project_centroid.buffer(0) diff --git a/migrations/versions/14340f1e0d6b_.py b/migrations/versions/14340f1e0d6b_.py index 13ffde5a7a..79ebc84ecb 100644 --- a/migrations/versions/14340f1e0d6b_.py +++ b/migrations/versions/14340f1e0d6b_.py @@ -6,6 +6,7 @@ """ from alembic import op +import sqlalchemy as sa # revision identifiers, used by Alembic. revision = "14340f1e0d6b" @@ -20,9 +21,11 @@ def upgrade(): tm3_pm_team = "TM3-project-managers" conn = op.get_bind() # Create an undefined organisation - conn.execute("insert into organisations (name) values('" + tm3_org_name + "');") + conn.execute( + sa.text("insert into organisations (name) values('" + tm3_org_name + "');") + ) fetch_org_id = "select * from organisations where name = '" + tm3_org_name + "';" - org_id = [r[0] for r in conn.execute(fetch_org_id)][0] + org_id = [r[0] for r in conn.execute(sa.text(fetch_org_id))][0] # Create two new teams associated to `undefined` organisation create_validator_team = ( @@ -32,9 +35,10 @@ def upgrade(): + tm3_validator_team + "');" ) - conn.execute(create_validator_team) + conn.execute(sa.text(create_validator_team)) validator_team_id = [ - r[0] for r in conn.execute("select id from teams order by id desc limit 1;") + r[0] + for r in conn.execute(sa.text("select id from teams order by id desc limit 1;")) ][0] create_pm_team = ( "insert into teams (visibility,invite_only,organisation_id,name) values (1,true," @@ -43,14 +47,15 @@ def upgrade(): + tm3_pm_team + "');" ) - conn.execute(create_pm_team) + conn.execute(sa.text(create_pm_team)) project_manager_team_id = [ - r[0] for r in conn.execute("select id from teams order by id desc limit 1;") + r[0] + for r in conn.execute(sa.text("select id from teams order by id desc limit 1;")) ][0] # Fetch all TM3 users who are validators; role = 4 # Add them as members to the new team created for validators - existing_validators = conn.execute("select id from users where role = 4;") + existing_validators = conn.execute(sa.text("select id from users where role = 4;")) for validator in existing_validators: validator_user_id = validator[0] # team function = 2(member) backend/models/postgis/statuses.py/TeamMemberFunctions @@ -61,14 +66,14 @@ def upgrade(): + str(validator_user_id) + ");" ) - conn.execute(update_validator_team) + conn.execute(sa.text(update_validator_team)) # Fetch all TM3 projects that has validation_permission = 2(TEAMS) or 3(TEAMS_LEVEL) # Refer to backend/models/postgis/statuses.py/ValidationPermission # Map the validator team to these projects with validator role # This is applicable only for legacy TM3 projects for easy transition existing_projects = conn.execute( - "select id from projects where validation_permission in (2,3)" + sa.text("select id from projects where validation_permission in (2,3)") ) for project in existing_projects: project_id = project[0] @@ -80,12 +85,12 @@ def upgrade(): + str(project_id) + ");" ) - conn.execute(update_project_team) + conn.execute(sa.text(update_project_team)) # Fetch all users who are project managers; role = 2 # Add them as members to the new team created for project managers # This team is only to store legacy information and is not used anywhere internally - existing_pms = conn.execute("select id from users where role = 2;") + existing_pms = conn.execute(sa.text("select id from users where role = 2;")) for project_manager in existing_pms: pm_user_id = project_manager[0] # team function = 2(member) backend/models/postgis/statuses.py/TeamMemberFunctions @@ -96,10 +101,10 @@ def upgrade(): + str(pm_user_id) + ");" ) - conn.execute(update_pm_team) + conn.execute(sa.text(update_pm_team)) # Set all users role = 0 (mapper) - conn.execute("update users set role = 0 where role in (2,4);") + conn.execute(sa.text("update users set role = 0 where role in (2,4);")) def downgrade(): @@ -112,44 +117,60 @@ def downgrade(): validator_team_id = [ r[0] for r in conn.execute( - "select id from teams where name = '" + tm3_validator_team + "';" + sa.text("select id from teams where name = '" + tm3_validator_team + "';") ) ][0] pm_team_id = [ r[0] for r in conn.execute( - "select id from teams where name = '" + tm3_pm_team + "';" + sa.text("select id from teams where name = '" + tm3_pm_team + "';") ) ][0] # Disassociate all projects from the team - conn.execute("delete from project_teams where team_id=" + str(validator_team_id)) + conn.execute( + sa.text("delete from project_teams where team_id=" + str(validator_team_id)) + ) # Get all the users in the undefined-validators # Set role = 4 in users for all the selected users validators = conn.execute( - "select user_id from team_members where team_id=" + str(validator_team_id) + ";" + sa.text( + "select user_id from team_members where team_id=" + + str(validator_team_id) + + ";" + ) ) for validator in validators: - conn.execute("update users set role = 4 where id=" + str(validator[0]) + ";") + conn.execute( + sa.text("update users set role = 4 where id=" + str(validator[0]) + ";") + ) # Get all the users in the undefined-pms # Set role = 2 in users for all the selected users pms = conn.execute( - "select user_id from team_members where team_id=" + str(pm_team_id) + ";" + sa.text( + "select user_id from team_members where team_id=" + str(pm_team_id) + ";" + ) ) for pm in pms: - conn.execute("update users set role = 2 where id=" + str(pm[0]) + ";") + conn.execute(sa.text("update users set role = 2 where id=" + str(pm[0]) + ";")) # Remove all users from both the teams conn.execute( - "delete from team_members where team_id in (" - + str(validator_team_id) - + "," - + str(pm_team_id) - + ");" + sa.text( + "delete from team_members where team_id in (" + + str(validator_team_id) + + "," + + str(pm_team_id) + + ");" + ) ) # Delete the teams and organisation - conn.execute("delete from teams where name = '" + tm3_validator_team + "';") - conn.execute("delete from teams where name = '" + tm3_pm_team + "';") - conn.execute("delete from organisations where name = '" + tm3_org_name + "';") + conn.execute( + sa.text("delete from teams where name = '" + tm3_validator_team + "';") + ) + conn.execute(sa.text("delete from teams where name = '" + tm3_pm_team + "';")) + conn.execute( + sa.text("delete from organisations where name = '" + tm3_org_name + "';") + ) diff --git a/migrations/versions/42c45e74752b_.py b/migrations/versions/42c45e74752b_.py new file mode 100644 index 0000000000..155f8e73b4 --- /dev/null +++ b/migrations/versions/42c45e74752b_.py @@ -0,0 +1,62 @@ +"""empty message + +Revision ID: 42c45e74752b +Revises: a9cbd2c6c213 +Create Date: 2023-03-29 09:07:55.771834 + +""" +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision = "42c45e74752b" +down_revision = "a9cbd2c6c213" +branch_labels = None +depends_on = None + + +def upgrade(): + # ### commands auto generated by Alembic - please adjust! ### + with op.batch_alter_table("application_keys", schema=None) as batch_op: + batch_op.alter_column("id", existing_type=sa.INTEGER(), type_=sa.BigInteger()) + + with op.batch_alter_table("priority_areas", schema=None) as batch_op: + batch_op.create_geospatial_index( + "idx_priority_areas_geometry", + ["geometry"], + unique=False, + postgresql_using="gist", + postgresql_ops={}, + ) + + with op.batch_alter_table("tasks", schema=None) as batch_op: + batch_op.create_geospatial_index( + "idx_tasks_geometry", + ["geometry"], + unique=False, + postgresql_using="gist", + postgresql_ops={}, + ) + + # ### end Alembic commands ### + + +def downgrade(): + # ### commands auto generated by Alembic - please adjust! ### + with op.batch_alter_table("tasks", schema=None) as batch_op: + batch_op.drop_geospatial_index( + "idx_tasks_geometry", postgresql_using="gist", column_name="geometry" + ) + + with op.batch_alter_table("priority_areas", schema=None) as batch_op: + batch_op.drop_geospatial_index( + "idx_priority_areas_geometry", + postgresql_using="gist", + column_name="geometry", + ) + + with op.batch_alter_table("application_keys", schema=None) as batch_op: + batch_op.alter_column("id", existing_type=sa.BigInteger(), type_=sa.INTEGER()) + + # ### end Alembic commands ### diff --git a/migrations/versions/4ed992117718_.py b/migrations/versions/4ed992117718_.py index 63951fed53..b4fef308a3 100644 --- a/migrations/versions/4ed992117718_.py +++ b/migrations/versions/4ed992117718_.py @@ -42,8 +42,8 @@ def downgrade(): sa.Column("invite_only", sa.BOOLEAN(), autoincrement=False, nullable=True), ) op.execute( - f"UPDATE teams SET invite_only = true WHERE join_method = {TeamJoinMethod.BY_REQUEST.value}" - f"UPDATE teams SET invite_only = false WHERE join_method != {TeamJoinMethod.BY_REQUEST.value}" + f"UPDATE teams SET invite_only = true WHERE join_method = {TeamJoinMethod.BY_REQUEST.value};" + f"UPDATE teams SET invite_only = false WHERE join_method != {TeamJoinMethod.BY_REQUEST.value};" ) op.alter_column("teams", "invite_only", nullable=False) op.drop_column("teams", "join_method") diff --git a/migrations/versions/7937dae319b5_.py b/migrations/versions/7937dae319b5_.py index 02e3c20069..91704f216a 100644 --- a/migrations/versions/7937dae319b5_.py +++ b/migrations/versions/7937dae319b5_.py @@ -6,6 +6,7 @@ """ from alembic import op +import sqlalchemy as sa import requests @@ -24,7 +25,7 @@ def upgrade(): fetch_countries = ( "select distinct(unnest(country)) from projects where country is not null;" ) - countries = conn.execute(fetch_countries) + countries = conn.execute(sa.text(fetch_countries)) for country in countries: country = country[0] # search by name @@ -40,7 +41,7 @@ def upgrade(): + "']::varchar[]" + ";" ) - conn.execute(update_project) + conn.execute(sa.text(update_project)) def downgrade(): diff --git a/migrations/versions/7bbc01082457_.py b/migrations/versions/7bbc01082457_.py index d0ac828a91..33db25d568 100644 --- a/migrations/versions/7bbc01082457_.py +++ b/migrations/versions/7bbc01082457_.py @@ -178,7 +178,9 @@ def upgrade(): print("Populating organisation information for Projects....") # Select all existing distinct organisation tags from projects table org_tags = conn.execute( - "select distinct(organisation_tag) from projects where organisation_tag is not null" + sa.text( + "select distinct(organisation_tag) from projects where organisation_tag is not null" + ) ) total_orgs = org_tags.rowcount print("Total distinct organisations in the DB: " + str(total_orgs)) @@ -198,7 +200,7 @@ def upgrade(): mapped_org = mapped_org[:quote_index] + "'" + mapped_org[quote_index:] select_org_id = conn.execute( - "select id from organisations where name ='" + mapped_org + "'" + sa.text("select id from organisations where name ='" + mapped_org + "'") ).scalar() # Create new organisation only if it has not been inserted earlier @@ -208,11 +210,15 @@ def upgrade(): and (mapped_org not in orgs_inserted) ): conn.execute( - "insert into organisations (name) values ('" + mapped_org + "')" + sa.text( + "insert into organisations (name) values ('" + mapped_org + "')" + ) ) # Fetch organisation ID after the insert select_org_id = conn.execute( - "select id from organisations where name ='" + mapped_org + "'" + sa.text( + "select id from organisations where name ='" + mapped_org + "'" + ) ).scalar() org_id = str(select_org_id) @@ -227,31 +233,37 @@ def upgrade(): # Update organisation ID conn.execute( - "update projects set organisation_id=" - + org_id - + " where organisation_tag='" - + original_org_name - + "'" + sa.text( + "update projects set organisation_id=" + + org_id + + " where organisation_tag='" + + original_org_name + + "'" + ) ) # Identify projects related to the org name fetch_first_author_id = conn.execute( - "select author_id from projects where organisation_tag='" - + original_org_name - + "' limit 1" + sa.text( + "select author_id from projects where organisation_tag='" + + original_org_name + + "' limit 1" + ) ).scalar() org_manager = str(fetch_first_author_id) if mapped_org not in orgs_inserted: org_managers[mapped_org] = org_manager conn.execute( - "insert into organisation_managers \ + sa.text( + "insert into organisation_managers \ (organisation_id,user_id) \ values(" - + org_id - + "," - + org_manager - + ")" + + org_id + + "," + + org_manager + + ")" + ) ) print( str(count) @@ -273,22 +285,28 @@ def downgrade(): conn = op.get_bind() op.add_column("projects", sa.Column("organisation_tag", sa.String(), nullable=True)) # Remove all mappings made - org_ids = conn.execute("select id, name from organisations") + org_ids = conn.execute(sa.text("select id, name from organisations")) for org_id, org_name in org_ids: quote_index = org_name.find("'") if quote_index > -1: org_name = org_name[:quote_index] + "'" + org_name[quote_index:] conn.execute( - "update projects set organisation_tag='" - + str(org_name) - + "' where organisation_id=" - + str(org_id) + sa.text( + "update projects set organisation_tag='" + + str(org_name) + + "' where organisation_id=" + + str(org_id) + ) ) - conn.execute("delete from project_teams where team_id is not null") - conn.execute("delete from team_members where team_id is not null") - conn.execute("delete from teams where organisation_id is not null") - conn.execute("delete from organisation_managers where organisation_id is not null") + conn.execute(sa.text("delete from project_teams where team_id is not null")) + conn.execute(sa.text("delete from team_members where team_id is not null")) + conn.execute(sa.text("delete from teams where organisation_id is not null")) conn.execute( - "update projects set organisation_id = null where organisation_id is not null" + sa.text("delete from organisation_managers where organisation_id is not null") + ) + conn.execute( + sa.text( + "update projects set organisation_id = null where organisation_id is not null" + ) ) - conn.execute("delete from organisations where name is not null") + conn.execute(sa.text("delete from organisations where name is not null")) diff --git a/migrations/versions/7d55a089b5bc_.py b/migrations/versions/7d55a089b5bc_.py index de62c80d29..f2699e1e2e 100644 --- a/migrations/versions/7d55a089b5bc_.py +++ b/migrations/versions/7d55a089b5bc_.py @@ -30,17 +30,17 @@ def upgrade(): # Content migration: Check the amount of zoom levels in tasks of a project and set # task_creation_mode to 1 or 0 accordingly. - projects = conn.execute("select * from projects") + projects = conn.execute(sa.text("select * from projects")) for project in projects: query = "select distinct zoom from tasks where project_id = " + str(project.id) - zooms = conn.execute(query).fetchall() + zooms = conn.execute(sa.text(query)).fetchall() if len(zooms) == 1 and zooms[0] == (None,): query = "update projects set task_creation_mode = 1 where id = " + str( project.id ) - op.execute(query) + op.execute(sa.text(query)) def downgrade(): diff --git a/migrations/versions/84c793a951b2_.py b/migrations/versions/84c793a951b2_.py index a20382f590..8ee3aaa577 100644 --- a/migrations/versions/84c793a951b2_.py +++ b/migrations/versions/84c793a951b2_.py @@ -32,10 +32,10 @@ def upgrade(): "idx_notifications_user_id", "notifications", ["user_id"], unique=False ) fetch_all_users = "select id from users;" - all_users = conn.execute(fetch_all_users) + all_users = conn.execute(sa.text(fetch_all_users)) for user in all_users: user_id = user[0] - insert_user_info = ( + insert_user_info = sa.text( "insert into notifications (user_id,unread_count,date) values (" + str(user_id) + "," @@ -47,7 +47,7 @@ def upgrade(): op.execute(insert_user_info) fetch_all_unread_counts = "select to_user_id, count(*) from messages where read = false group by to_user_id;" - unread_counts = conn.execute(fetch_all_unread_counts) + unread_counts = conn.execute(sa.text(fetch_all_unread_counts)) for unread_count in unread_counts: user_id = unread_count[0] user_unread_count = unread_count[1] diff --git a/migrations/versions/a43b9748ceee_.py b/migrations/versions/a43b9748ceee_.py index 9538fd894b..010d5f621e 100644 --- a/migrations/versions/a43b9748ceee_.py +++ b/migrations/versions/a43b9748ceee_.py @@ -6,6 +6,7 @@ """ from alembic import op +import sqlalchemy as sa from backend.models.postgis.statuses import TaskStatus @@ -32,7 +33,7 @@ def upgrade(): # Recalculate tasks stats based on the task states in projects conn = op.get_bind() - projects = conn.execute("select id from projects") + projects = conn.execute(sa.text("select id from projects")) print("Recalculating projects' tasks stats... can take a bit") for project_id in projects: _set_project_counters_from_task_states(project_id[0]) @@ -43,8 +44,10 @@ def _set_project_counters_from_task_states(project_id: int): conn = op.get_bind() tasks_statuses = conn.execute( - "SELECT task_status, count(task_status) FROM tasks WHERE project_id={0} GROUP BY task_status" - "".format(project_id) + sa.text( + "SELECT task_status, count(task_status) FROM tasks WHERE project_id={0} GROUP BY task_status" + "".format(project_id) + ) ) tasks_statuses = [r for r in tasks_statuses] diff --git a/migrations/versions/bfcf4182dcb5_.py b/migrations/versions/bfcf4182dcb5_.py index b3af370bd7..63f34b5ae2 100644 --- a/migrations/versions/bfcf4182dcb5_.py +++ b/migrations/versions/bfcf4182dcb5_.py @@ -24,7 +24,7 @@ def upgrade(): op.add_column( "organisations", sa.Column("slug", sa.String(length=255), nullable=True) ) - orgs = conn.execute("select name from organisations;") + orgs = conn.execute(sa.text("select name from organisations;")) for org in orgs: name = handle_special_chars(org[0]) query = ( diff --git a/migrations/versions/c40e1fdf6b70_.py b/migrations/versions/c40e1fdf6b70_.py index f467478555..93d64de31e 100644 --- a/migrations/versions/c40e1fdf6b70_.py +++ b/migrations/versions/c40e1fdf6b70_.py @@ -6,6 +6,7 @@ """ from alembic import op +import sqlalchemy as sa # revision identifiers, used by Alembic. revision = "c40e1fdf6b70" @@ -41,11 +42,11 @@ def determine_validation_permission(self, val, reverse=False): def upgrade(): conn = op.get_bind() - conn.execute("ALTER TABLE projects ADD mapping_permission Integer;") - conn.execute("ALTER TABLE projects ADD validation_permission Integer;") + conn.execute(sa.text("ALTER TABLE projects ADD mapping_permission Integer;")) + conn.execute(sa.text("ALTER TABLE projects ADD validation_permission Integer;")) fetch_all_projects = "select id, restrict_mapping_level_to_project, \ restrict_validation_role, restrict_validation_level_intermediate from projects;" - all_projects = conn.execute(fetch_all_projects) + all_projects = conn.execute(sa.text(fetch_all_projects)) for project in all_projects: mapping_permission = None validation_permission = None @@ -80,15 +81,19 @@ def upgrade(): def downgrade(): conn = op.get_bind() - conn.execute("ALTER TABLE projects ADD restrict_mapping_level_to_project boolean;") - conn.execute("ALTER TABLE projects ADD restrict_validation_role boolean;") conn.execute( - "ALTER TABLE projects ADD restrict_validation_level_intermediate boolean;" + sa.text("ALTER TABLE projects ADD restrict_mapping_level_to_project boolean;") + ) + conn.execute(sa.text("ALTER TABLE projects ADD restrict_validation_role boolean;")) + conn.execute( + sa.text( + "ALTER TABLE projects ADD restrict_validation_level_intermediate boolean;" + ) ) fetch_all_projects = ( "select id, mapping_permission, validation_permission from projects;" ) - all_projects = conn.execute(fetch_all_projects) + all_projects = conn.execute(sa.text(fetch_all_projects)) for project in all_projects: project_id = project[0] mapping_permission = project[1] diff --git a/migrations/versions/deec8123583d_.py b/migrations/versions/deec8123583d_.py index dfed4b0ab8..36d5ebfa56 100644 --- a/migrations/versions/deec8123583d_.py +++ b/migrations/versions/deec8123583d_.py @@ -6,6 +6,7 @@ """ from alembic import op +import sqlalchemy as sa # revision identifiers, used by Alembic. @@ -18,7 +19,7 @@ def upgrade(): conn = op.get_bind() - projects = conn.execute("select * from projects") + projects = conn.execute(sa.text("select * from projects")) # Content migration: Check the amount of zoom levels in tasks of a project and set # task_creation_mode to 1 or 0 accordingly. @@ -26,7 +27,7 @@ def upgrade(): select_query = "select distinct zoom from tasks where project_id = " + str( project.id ) - zooms = conn.execute(select_query) + zooms = conn.execute(sa.text(select_query)) zooms = zooms.fetchall() if len(zooms) == 1 and zooms[0] == (None,): @@ -40,7 +41,7 @@ def upgrade(): + str(project.id) ) - op.execute(update_query) + op.execute(sa.text(update_query)) def downgrade(): diff --git a/migrations/versions/f86698c827cc_.py b/migrations/versions/f86698c827cc_.py index 9c45bb6d9c..8ae21cfd1c 100644 --- a/migrations/versions/f86698c827cc_.py +++ b/migrations/versions/f86698c827cc_.py @@ -19,7 +19,7 @@ def upgrade(): conn = op.get_bind() campaign_tags = conn.execute( - "select distinct(campaigns) from tags where campaigns is not null" + sa.text("select distinct(campaigns) from tags where campaigns is not null") ) total_campaigns = campaign_tags.rowcount @@ -36,11 +36,13 @@ def upgrade(): for project_id in projects: project_id = project_id[0] conn.execute( - "insert into campaign_projects (campaign_id, project_id) values (" - + str(new_campaign_id) - + "," - + str(project_id) - + ")" + sa.text( + "insert into campaign_projects (campaign_id, project_id) values (" + + str(new_campaign_id) + + "," + + str(project_id) + + ")" + ) ) op.drop_table("tags") op.drop_index("ix_projects_campaign_tag", table_name="projects") @@ -65,25 +67,36 @@ def downgrade(): sa.UniqueConstraint("campaigns", name="tags_campaigns_key"), sa.UniqueConstraint("organisations", name="tags_organisations_key"), ) - campaigns = conn.execute("select id, name from campaigns") + campaigns = conn.execute(sa.text("select id, name from campaigns")) for campaign_id, campaign_tag in campaigns: - conn.execute("insert into tags (campaigns) values ('" + campaign_tag + "')") + conn.execute( + sa.text("insert into tags (campaigns) values ('" + campaign_tag + "')") + ) projects = conn.execute( - "select project_id from campaign_projects where campaign_id=" - + str(campaign_id) + sa.text( + "select project_id from campaign_projects where campaign_id=" + + str(campaign_id) + ) ) for project in projects: project_id = project[0] conn.execute( - "update projects set campaign_tag='" - + campaign_tag - + "' where id=" - + str(project_id) + sa.text( + "update projects set campaign_tag='" + + campaign_tag + + "' where id=" + + str(project_id) + ) ) conn.execute( - "delete from campaign_organisations where campaign_id=" + str(campaign_id) + sa.text( + "delete from campaign_organisations where campaign_id=" + + str(campaign_id) + ) ) conn.execute( - "delete from campaign_projects where campaign_id=" + str(campaign_id) + sa.text( + "delete from campaign_projects where campaign_id=" + str(campaign_id) + ) ) - conn.execute("delete from campaigns where id=" + str(campaign_id)) + conn.execute(sa.text("delete from campaigns where id=" + str(campaign_id))) diff --git a/pdm.lock b/pdm.lock index 38f6717636..9cbef9f27f 100644 --- a/pdm.lock +++ b/pdm.lock @@ -3,44 +3,32 @@ [[package]] name = "alembic" -version = "1.4.3" -requires_python = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +version = "1.11.1" +requires_python = ">=3.7" summary = "A database migration tool for SQLAlchemy." dependencies = [ "Mako", - "SQLAlchemy>=1.1.0", - "python-dateutil", - "python-editor>=0.3", + "SQLAlchemy>=1.3.0", + "typing-extensions>=4", ] [[package]] name = "aniso8601" -version = "8.0.0" +version = "9.0.1" summary = "A library for parsing ISO 8601 strings." -[[package]] -name = "appdirs" -version = "1.4.4" -summary = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." - [[package]] name = "apscheduler" -version = "3.7.0" -requires_python = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4" +version = "3.10.1" +requires_python = ">=3.6" summary = "In-process task scheduler with Cron-like capabilities" dependencies = [ "pytz", "setuptools>=0.7", "six>=1.4.0", - "tzlocal~=2.0", + "tzlocal!=3.*,>=2.0", ] -[[package]] -name = "attrs" -version = "20.2.0" -requires_python = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" -summary = "Classes Without Boilerplate" - [[package]] name = "black" version = "23.3.0" @@ -58,7 +46,7 @@ dependencies = [ [[package]] name = "bleach" -version = "5.0.1" +version = "6.0.0" requires_python = ">=3.7" summary = "An easy safelist-based HTML-sanitizing tool." dependencies = [ @@ -68,19 +56,20 @@ dependencies = [ [[package]] name = "blinker" -version = "1.5" -requires_python = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +version = "1.6.2" +requires_python = ">=3.7" summary = "Fast, simple object-to-object and broadcast signaling" [[package]] name = "cachetools" -version = "4.1.1" -requires_python = "~=3.5" +version = "5.3.0" +requires_python = "~=3.7" summary = "Extensible memoizing collections and decorators" [[package]] name = "certifi" -version = "2020.6.20" +version = "2023.5.7" +requires_python = ">=3.6" summary = "Python package for providing Mozilla's CA Bundle." [[package]] @@ -91,15 +80,10 @@ dependencies = [ "pycparser", ] -[[package]] -name = "chardet" -version = "3.0.4" -summary = "Universal encoding detector for Python 2 and 3" - [[package]] name = "charset-normalizer" -version = "2.0.12" -requires_python = ">=3.5.0" +version = "3.1.0" +requires_python = ">=3.7.0" summary = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." [[package]] @@ -119,42 +103,44 @@ summary = "Cross-platform colored terminal text." [[package]] name = "coverage" -version = "6.4" +version = "7.2.5" requires_python = ">=3.7" summary = "Code coverage measurement for Python" [[package]] -name = "entrypoints" -version = "0.3" -requires_python = ">=2.7" -summary = "Discover and load entry points from installed packages." +name = "exceptiongroup" +version = "1.1.1" +requires_python = ">=3.7" +summary = "Backport of PEP 654 (exception groups)" [[package]] name = "flake8" -version = "3.8.4" -requires_python = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,>=2.7" +version = "6.0.0" +requires_python = ">=3.8.1" summary = "the modular source code checker: pep8 pyflakes and co" dependencies = [ - "mccabe<0.7.0,>=0.6.0", - "pycodestyle<2.7.0,>=2.6.0a1", - "pyflakes<2.3.0,>=2.2.0", + "mccabe<0.8.0,>=0.7.0", + "pycodestyle<2.11.0,>=2.10.0", + "pyflakes<3.1.0,>=3.0.0", ] [[package]] name = "flask" -version = "1.1.2" -requires_python = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +version = "2.3.2" +requires_python = ">=3.8" summary = "A simple framework for building complex web applications." dependencies = [ - "Jinja2>=2.10.1", - "Werkzeug>=0.15", - "click>=5.1", - "itsdangerous>=0.24", + "Jinja2>=3.1.2", + "Werkzeug>=2.3.3", + "blinker>=1.6.2", + "click>=8.1.3", + "importlib-metadata>=3.6.0; python_version < \"3.10\"", + "itsdangerous>=2.1.2", ] [[package]] name = "flask-cors" -version = "3.0.9" +version = "3.0.10" summary = "A Flask extension adding a decorator for CORS support" dependencies = [ "Flask>=0.9", @@ -163,10 +149,10 @@ dependencies = [ [[package]] name = "flask-httpauth" -version = "4.1.0" -summary = "Basic and Digest HTTP authentication for Flask routes" +version = "4.8.0" +summary = "HTTP authentication for Flask routes" dependencies = [ - "Flask", + "flask", ] [[package]] @@ -180,17 +166,18 @@ dependencies = [ [[package]] name = "flask-migrate" -version = "2.5.3" -summary = "SQLAlchemy database migrations for Flask applications using Alembic" +version = "4.0.4" +requires_python = ">=3.6" +summary = "SQLAlchemy database migrations for Flask applications using Alembic." dependencies = [ "Flask-SQLAlchemy>=1.0", "Flask>=0.9", - "alembic>=0.7", + "alembic>=1.9.0", ] [[package]] name = "flask-restful" -version = "0.3.8" +version = "0.3.9" summary = "Simple framework for creating REST APIs" dependencies = [ "Flask>=0.8", @@ -199,22 +186,14 @@ dependencies = [ "six>=1.3.0", ] -[[package]] -name = "flask-script" -version = "2.0.6" -summary = "Scripting support for Flask" -dependencies = [ - "Flask", -] - [[package]] name = "flask-sqlalchemy" -version = "2.4.4" -requires_python = ">= 2.7, != 3.0.*, != 3.1.*, != 3.2.*, != 3.3.*" -summary = "Adds SQLAlchemy support to your Flask application." +version = "3.0.3" +requires_python = ">=3.7" +summary = "Add SQLAlchemy support to your Flask application." dependencies = [ - "Flask>=0.10", - "SQLAlchemy>=0.8.0", + "Flask>=2.2", + "SQLAlchemy>=1.4.18", ] [[package]] @@ -228,83 +207,98 @@ dependencies = [ [[package]] name = "geoalchemy2" -version = "0.8.4" +version = "0.13.3" +requires_python = ">=3.7" summary = "Using SQLAlchemy with Spatial Databases" dependencies = [ - "SQLAlchemy>=0.8", + "SQLAlchemy>=1.4", + "packaging", ] [[package]] name = "geojson" -version = "1.3.4" +version = "3.0.1" +requires_python = ">=3.7, <3.12" summary = "Python bindings and utilities for GeoJSON" [[package]] name = "gevent" -version = "21.12.0" +version = "22.10.2" requires_python = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5" summary = "Coroutine-based network library" dependencies = [ "cffi>=1.12.2; platform_python_implementation == \"CPython\" and sys_platform == \"win32\"", - "greenlet<2.0,>=1.1.0; platform_python_implementation == \"CPython\"", + "greenlet>=2.0.0; platform_python_implementation == \"CPython\"", "setuptools", "zope-event", "zope-interface", ] -[[package]] -name = "glob2" -version = "0.7" -summary = "Version of the glob module that can capture patterns and supports recursive wildcards" - [[package]] name = "greenlet" -version = "1.1.2" +version = "2.0.2" requires_python = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*" summary = "Lightweight in-process concurrent programming" [[package]] name = "gunicorn" -version = "20.0.4" -requires_python = ">=3.4" +version = "20.1.0" +requires_python = ">=3.5" summary = "WSGI HTTP Server for UNIX" dependencies = [ "setuptools>=3.0", ] +[[package]] +name = "gunicorn" +version = "20.1.0" +extras = ["gevent"] +requires_python = ">=3.5" +summary = "WSGI HTTP Server for UNIX" +dependencies = [ + "gevent>=1.4.0", + "gunicorn==20.1.0", +] + [[package]] name = "idna" -version = "2.10" -requires_python = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +version = "3.4" +requires_python = ">=3.5" summary = "Internationalized Domain Names in Applications (IDNA)" [[package]] name = "importlib-metadata" -version = "4.13.0" +version = "6.6.0" requires_python = ">=3.7" summary = "Read metadata from Python packages" dependencies = [ "zipp>=0.5", ] +[[package]] +name = "iniconfig" +version = "2.0.0" +requires_python = ">=3.7" +summary = "brain-dead simple config-ini parsing" + [[package]] name = "itsdangerous" -version = "1.1.0" -requires_python = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" -summary = "Various helpers to pass data to untrusted environments and back." +version = "2.1.2" +requires_python = ">=3.7" +summary = "Safely pass data to untrusted environments and back." [[package]] name = "jinja2" -version = "2.11.3" -requires_python = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +version = "3.1.2" +requires_python = ">=3.7" summary = "A very fast and expressive template engine." dependencies = [ - "MarkupSafe>=0.23", + "MarkupSafe>=2.0", ] [[package]] name = "mako" -version = "1.2.2" +version = "1.2.4" requires_python = ">=3.7" summary = "A super-fast templating language that borrows the best ideas from the existing templating languages." dependencies = [ @@ -313,19 +307,23 @@ dependencies = [ [[package]] name = "markdown" -version = "3.3.3" -requires_python = ">=3.6" -summary = "Python implementation of Markdown." +version = "3.4.3" +requires_python = ">=3.7" +summary = "Python implementation of John Gruber's Markdown." +dependencies = [ + "importlib-metadata>=4.4; python_version < \"3.10\"", +] [[package]] name = "markupsafe" -version = "1.1.1" -requires_python = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*" +version = "2.1.2" +requires_python = ">=3.7" summary = "Safely add untrusted strings to HTML/XML markup." [[package]] name = "mccabe" -version = "0.6.1" +version = "0.7.0" +requires_python = ">=3.6" summary = "McCabe checker, plugin for flake8" [[package]] @@ -335,19 +333,14 @@ requires_python = ">=3.5" summary = "Type system extensions for programs checked with the mypy type checker." [[package]] -name = "newrelic" -version = "8.8.0" -requires_python = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*" -summary = "New Relic Python Agent" - -[[package]] -name = "nose" -version = "1.3.7" -summary = "nose extends unittest to make testing easier" +name = "numpy" +version = "1.24.3" +requires_python = ">=3.8" +summary = "Fundamental package for array computing in Python" [[package]] name = "oauthlib" -version = "3.2.0" +version = "3.2.2" requires_python = ">=3.6" summary = "A generic, spec-compliant, thorough implementation of the OAuth request-signing logic" @@ -365,20 +358,26 @@ summary = "Utility library for gitignore style pattern matching of file paths." [[package]] name = "platformdirs" -version = "3.5.0" +version = "3.5.1" requires_python = ">=3.7" summary = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." +[[package]] +name = "pluggy" +version = "1.0.0" +requires_python = ">=3.6" +summary = "plugin and hook calling mechanisms for python" + [[package]] name = "psycopg2" -version = "2.8.6" -requires_python = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*" +version = "2.9.6" +requires_python = ">=3.6" summary = "psycopg2 - Python-PostgreSQL Database Adapter" [[package]] name = "pycodestyle" -version = "2.6.0" -requires_python = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +version = "2.10.0" +requires_python = ">=3.6" summary = "Python style guide checker" [[package]] @@ -389,28 +388,27 @@ summary = "C parser in Python" [[package]] name = "pyflakes" -version = "2.2.0" -requires_python = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" +version = "3.0.1" +requires_python = ">=3.6" summary = "passive checker of Python programs" [[package]] -name = "pyparsing" -version = "2.4.7" -requires_python = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*" -summary = "Python parsing module" - -[[package]] -name = "pyproj" -version = "3.5.0" -requires_python = ">=3.8" -summary = "Python interface to PROJ (cartographic projections and coordinate transformations library)" +name = "pytest" +version = "7.3.1" +requires_python = ">=3.7" +summary = "pytest: simple powerful testing with Python" dependencies = [ - "certifi", + "colorama; sys_platform == \"win32\"", + "exceptiongroup>=1.0.0rc8; python_version < \"3.11\"", + "iniconfig", + "packaging", + "pluggy<2.0,>=0.12", + "tomli>=1.0.0; python_version < \"3.11\"", ] [[package]] name = "python-dateutil" -version = "2.8.1" +version = "2.8.2" requires_python = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7" summary = "Extensions to the standard Python datetime module" dependencies = [ @@ -419,50 +417,40 @@ dependencies = [ [[package]] name = "python-dotenv" -version = "0.14.0" -summary = "Add .env support to your django/flask apps in development and deployments" - -[[package]] -name = "python-editor" -version = "1.0.4" -summary = "Programmatically open an editor, capture the result." +version = "1.0.0" +requires_python = ">=3.8" +summary = "Read key-value pairs from a .env file and set them as environment variables" [[package]] name = "python-slugify" -version = "4.0.1" -requires_python = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" -summary = "A Python Slugify application that handles Unicode" +version = "8.0.1" +requires_python = ">=3.7" +summary = "A Python slugify application that also handles Unicode" dependencies = [ "text-unidecode>=1.3", ] [[package]] name = "pytz" -version = "2020.1" +version = "2023.3" summary = "World timezone definitions, modern and historical" [[package]] name = "pyyaml" -version = "5.4" -requires_python = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" -summary = "YAML parser and emitter for Python" - -[[package]] -name = "regex" -version = "2022.10.31" +version = "6.0" requires_python = ">=3.6" -summary = "Alternative regular expression module, to replace re." +summary = "YAML parser and emitter for Python" [[package]] name = "requests" -version = "2.27.1" -requires_python = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" +version = "2.30.0" +requires_python = ">=3.7" summary = "Python HTTP for Humans." dependencies = [ "certifi>=2017.4.17", - "charset-normalizer~=2.0.0; 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"Werkzeug==0.16.1", - "zipp==3.15.0", - "zope-event==4.6", - "zope-interface==6.0", + "sentry-sdk[flask]==1.23.1", + "shapely==2.0.1", + "SQLAlchemy==2.0.13", + "Werkzeug==2.3.4", + # Indirect, but required dependencies (often required for efficient deployments) + "gevent==22.10.2", + "greenlet==2.0.2", + "gunicorn[gevent]==20.1.0", + "importlib-metadata==6.6.0" # See https://github.com/hotosm/tasking-manager/issues/5395 ] requires-python = ">=3.9,<=3.11" readme = "README.md" license = {text = "BSD-2-Clause"} [tool] -[tool.pdm] +[tool.pdm.dev-dependencies] +test = ["coverage==7.2.5", "pytest==7.3.1"] +lint = ["black==23.3.0", "flake8==6.0.0"] [tool.pdm.scripts] -start = "python manage.py runserver -d -r" -migrate = "python manage.py db migrate" -upgrade = "python manage.py db upgrade" -downgrade = "python manage.py db downgrade" +start = "flask run --debug --reload" +migrate = "flask db migrate" +upgrade = "flask db upgrade" +downgrade = "flask db downgrade" test = "python -m unittest discover" lint = "black manage.py backend tests migrations" flake8 = "flake8 manage.py backend tests migrations" diff --git a/requirements.txt b/requirements.txt index 9d41de92f4..014752a3e4 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,80 +1,82 @@ -alembic==1.4.3 -aniso8601==8.0.0 -appdirs==1.4.4 -APScheduler==3.7.0 -attrs==20.2.0 -black==23.3.0 -bleach==5.0.1 -blinker==1.5 -cachetools==4.1.1 -certifi==2020.6.20 -chardet==3.0.4 -charset-normalizer==2.0.12 -click==8.1.3 -coverage==6.4 -entrypoints==0.3 -flake8==3.8.4 -Flask==1.1.2 -Flask-Cors==3.0.9 -Flask-HTTPAuth==4.1.0 +# Update instructions: +# 1. Delete the virtual environment +# 2. Create a new clean virtual environment +# 3. Remove all unnecessary indirect dependencies in this file ("Indirect dependencies (these can be blown away at any time)") +# 4. Update the relevant packages +# 5. Run `pip install -r requirements.txt` +# 6. Run `pip freeze -r requirements.txt > requirements.new.txt` +# 7. Run `mv requirements.new.txt requirements.txt` +# 8. Run tests +# +# Direct dependencies (at least one import requires it) +APScheduler==3.10.1 +alembic==1.11.1 +bleach==6.0.0 +cachetools==5.3.0 +Flask==2.3.2 +Flask-Cors==3.0.10 +Flask-HTTPAuth==4.8.0 +Flask-Migrate==4.0.4 Flask-Mail==0.9.1 -Flask-Migrate==2.5.3 -Flask-RESTful==0.3.8 -Flask-Script==2.0.6 -Flask-SQLAlchemy==2.4.4 +Flask-RESTful==0.3.9 +Flask-SQLAlchemy==3.0.3 flask-swagger==0.2.14 -GeoAlchemy2==0.8.4 -geojson==1.3.4 -gevent==21.12.0 -glob2==0.7 -greenlet==1.1.2 -gunicorn==20.0.4 -idna==2.10 -importlib-metadata==4.13.0 # See https://github.com/hotosm/tasking-manager/issues/5395 -itsdangerous==1.1.0 -Jinja2==2.11.3 -Mako==1.2.2 -Markdown==3.3.3 -MarkupSafe==1.1.1 -mccabe==0.6.1 +GeoAlchemy2==0.13.3 +geojson==3.0.1 +itsdangerous==2.1.2 +Markdown==3.4.3 +oauthlib==3.2.2 +psycopg2==2.9.6 +python-dateutil==2.8.2 +python-dotenv==1.0.0 +python-slugify==8.0.1 +requests==2.30.0 +requests-oauthlib==1.3.1 +schematics==2.1.1 +sentry-sdk[flask]==1.23.1 +shapely==2.0.1 +SQLAlchemy==2.0.13 +Werkzeug==2.3.4 +# Dev dependencies (stuff useful for development) +black==23.3.0 +coverage==7.2.5 +flake8==6.0.0 +pytest==7.3.1 +# Indirect, but required dependencies (often required for efficient deployments) +gevent==22.10.2 +greenlet==2.0.2 +gunicorn==20.1.0 +importlib-metadata==6.6.0 # See https://github.com/hotosm/tasking-manager/issues/5395 +# Indirect dependencies (these can be blown away at any time) + +## The following requirements were added by pip freeze: +aniso8601==9.0.1 +blinker==1.6.2 +certifi==2023.5.7 +charset-normalizer==3.1.0 +click==8.1.3 +idna==3.4 +iniconfig==2.0.0 +Jinja2==3.1.2 +Mako==1.2.4 +MarkupSafe==2.1.2 +mccabe==0.7.0 mypy-extensions==1.0.0 -newrelic==8.8.0 -nose==1.3.7 -oauthlib==3.2.0 +numpy==1.24.3 packaging==23.1 pathspec==0.11.1 -platformdirs==3.5.0 -psycopg2==2.8.6 -pycodestyle==2.6.0 -pyflakes==2.2.0 -pyparsing==2.4.7 -pyproj==3.5.0 -python-dateutil==2.8.1 -python-dotenv==0.14.0 -python-editor==1.0.4 -python-slugify==4.0.1 -pytz==2020.1 -PyYAML==5.4 -regex==2022.10.31 -requests==2.27.1 -requests-oauthlib==1.3.1 -schematics==2.1.1 -sentry-sdk[flask]==1.5.8 -setuptools==67.7.2 -Shapely==1.7.1 -six==1.15.0 -SQLAlchemy==1.3.20 +platformdirs==3.5.1 +pluggy==1.0.0 +pycodestyle==2.10.0 +pyflakes==3.0.1 +pytz==2023.3 +PyYAML==6.0 +six==1.16.0 text-unidecode==1.3 -toml==0.10.1 -tomli==2.0.1 -typed-ast==1.5.4 -typing-extensions==4.5.0 -tzlocal==2.1 -Unidecode==1.1.1 -urllib3==1.26.9 +typing_extensions==4.5.0 +tzlocal==5.0.1 +urllib3==1.26.15 webencodings==0.5.1 -Werkzeug==0.16.1 zipp==3.15.0 -zope-event==4.6 -zope-interface==6.0 - +zope.event==4.6 +zope.interface==6.0 diff --git a/scripts/aws/cloudformation/tasking-manager.template.js b/scripts/aws/cloudformation/tasking-manager.template.js index b92ddd9e17..e03637dc9e 100644 --- a/scripts/aws/cloudformation/tasking-manager.template.js +++ b/scripts/aws/cloudformation/tasking-manager.template.js @@ -417,7 +417,7 @@ const Resources = { cf.sub('export TM_IMAGE_UPLOAD_API_KEY="${TaskingManagerImageUploadAPIKey}"'), 'psql "host=$POSTGRES_ENDPOINT dbname=$POSTGRES_DB user=$POSTGRES_USER password=$POSTGRES_PASSWORD" -c "CREATE EXTENSION IF NOT EXISTS postgis"', cf.if('DatabaseDumpFileGiven', cf.sub('aws s3 cp ${DatabaseDump} dump.sql; sudo -u postgres psql "postgresql://$POSTGRES_USER:$POSTGRES_PASSWORD@$POSTGRES_ENDPOINT/$POSTGRES_DB" < dump.sql'), ''), - 'python3 manage.py db upgrade', + 'pdm run flask db upgrade', 'echo "------------------------------------------------------------"', cf.sub('export NEW_RELIC_LICENSE_KEY="${NewRelicLicense}"'), cf.sub('export TM_SENTRY_BACKEND_DSN="${SentryBackendDSN}"'), diff --git a/scripts/database/export-import-projects/README b/scripts/database/export-import-projects/README index 976930a85b..c8e6a5c6b3 100644 --- a/scripts/database/export-import-projects/README +++ b/scripts/database/export-import-projects/README @@ -2,7 +2,7 @@ These migration scripts allow to restore deleted projects using postgres commands. For now, there are two scripts: 1. dbtocsv.sh: By setting the required variables, this script reads the defined project ids within the PROJECT_IDS variable and starts saving the required information for each table in a csv file. -2. restart_table.sh: which destroys and then creates with postgis extension the desired database. However, migration tables are not executed within this script. You need to run `python manage.py db upgrade` yourself every time the database is restarted. +2. restart_table.sh: which destroys and then creates with postgis extension the desired database. However, migration tables are not executed within this script. You need to run `flask db upgrade` yourself every time the database is restarted. Tables to migrate and verify if they are necessary to: [x] projects diff --git a/scripts/database/migration-from-tm2-postgres.sql b/scripts/database/migration-from-tm2-postgres.sql index 527d2894db..6e652fed45 100644 --- a/scripts/database/migration-from-tm2-postgres.sql +++ b/scripts/database/migration-from-tm2-postgres.sql @@ -5,7 +5,7 @@ -- Also, we assume you have created the TM3 database by following the README or migration guide, -- meaning you will have a database named "taskingmanager" already. Make sure you have run the alembic -- database upgrades to load the schema of "taskingmanager". As a refresher, this is done in the base --- TM3 directory via: python manage.py db upgrade +-- TM3 directory via: flask db upgrade -- If you run into errors, make sure your environmental variable is set for TM_DB. -- -- Now to the migration... diff --git a/scripts/docker/Dockerfile.backend b/scripts/docker/Dockerfile.backend index b225df4227..e8acc0763a 100644 --- a/scripts/docker/Dockerfile.backend +++ b/scripts/docker/Dockerfile.backend @@ -1,5 +1,5 @@ ARG ALPINE_IMG_TAG=3.17 -ARG PYTHON_IMG_TAG=3.9 +ARG PYTHON_IMG_TAG=3.10 FROM docker.io/python:${PYTHON_IMG_TAG}-alpine${ALPINE_IMG_TAG} as base ARG APP_VERSION=0.1.0 diff --git a/scripts/docker/tasking-manager/Dockerfile b/scripts/docker/tasking-manager/Dockerfile index cd176dfd8d..9424962b4c 100644 --- a/scripts/docker/tasking-manager/Dockerfile +++ b/scripts/docker/tasking-manager/Dockerfile @@ -1,10 +1,11 @@ -FROM python:3.7-buster +ARG PYTHON_IMG_TAG=3.10 +FROM python:${PYTHON_IMG_TAG}-bullseye RUN mkdir -p /usr/src/app WORKDIR /usr/src/app -ENV PATH="/usr/src/app/__pypackages__/3.7/bin:$PATH" \ - PYTHONPATH="/usr/src/app/__pypackages__/3.7/lib" +ENV PATH="/usr/src/app/__pypackages__/${PYTHON_IMG_TAG}/bin:$PATH" \ + PYTHONPATH="/usr/src/app/__pypackages__/${PYTHON_IMG_TAG}/lib" # INSTALLATION @@ -39,4 +40,4 @@ RUN cd frontend && npm install && npm run build # INITIALIZATION EXPOSE 5000 -CMD ["python", "manage.py", "runserver", "-h", "0.0.0.0"] +CMD ["pdm", "run", "flask", "run", "-h", "0.0.0.0"] diff --git a/scripts/install/install_on_debian_10_buster.sh b/scripts/install/install_on_debian_10_buster.sh index e8571c1caa..6590350837 100755 --- a/scripts/install/install_on_debian_10_buster.sh +++ b/scripts/install/install_on_debian_10_buster.sh @@ -67,7 +67,7 @@ do sudo -u postgres psql -c "alter table \"$tbl\" owner to $POSTGRES_USER" $POS cd ../../ && # Upgrade database -python3 manage.py db upgrade && +pdm run flask db upgrade && # Assamble the tasking manager interface cd frontend/ && @@ -78,4 +78,4 @@ cd ../ && ## Please edit the tasking-manager.env as indicated in the README.md ## # Start the tasking manager -python3 manage.py runserver -d +pdm run flask run -d diff --git a/scripts/install/install_on_ubuntu_18_04.sh b/scripts/install/install_on_ubuntu_18_04.sh index e24598eb8c..1f4ce43b41 100755 --- a/scripts/install/install_on_ubuntu_18_04.sh +++ b/scripts/install/install_on_ubuntu_18_04.sh @@ -68,9 +68,9 @@ do sudo -u postgres psql -c "alter table \"$tbl\" owner to $POSTGRES_USER" $POS cd ../../ && # Upgrade database -python3 manage.py db upgrade && +pdm run flask db upgrade && -# Assamble the tasking manager interface +# Assemble the tasking manager interface cd frontend/ && npm install && npm run build && @@ -79,4 +79,4 @@ cd ../ && ## Please edit the tasking-manager.env as indicated in the README.md ## # Start the tasking manager -python3 manage.py runserver -d +pdm run flask run -d diff --git a/tests/backend/base.py b/tests/backend/base.py index a0b4b9a6e8..c8fa9b4756 100644 --- a/tests/backend/base.py +++ b/tests/backend/base.py @@ -1,6 +1,11 @@ import unittest +from typing import Optional +from shapely.geometry import shape from backend import create_app, db +import geojson +from flask import Flask +from flask_sqlalchemy import SQLAlchemy def clean_db(db): @@ -9,19 +14,36 @@ def clean_db(db): class BaseTestCase(unittest.TestCase): + DEFAULT_PRECISION: Optional[int] + app: Optional[Flask] + db: Optional[SQLAlchemy] + @classmethod def setUpClass(cls): super(BaseTestCase, cls).setUpClass() + cls.DEFAULT_PRECISION = geojson.geometry.DEFAULT_PRECISION + # OSM uses 7, which means the worst error of longitude is ±5.56595 mm + # at the equator. The worst error for 6 decimal places of longitude is + # ±5.56595 cm at the equator. This is the default, and realistically + # is probably more than enough for the TM. + geojson.geometry.DEFAULT_PRECISION = 7 cls.app = create_app("backend.config.TestEnvironmentConfig") + cls.app.config.update({"TESTING": True}) cls.db = db cls.db.app = cls.app - cls.db.create_all() + with cls.app.app_context(): + cls.db.create_all() @classmethod def tearDownClass(cls): - db.session.remove() - cls.db.drop_all() - cls.db.get_engine(cls.app).dispose() + geojson.geometry.DEFAULT_PRECISION = cls.DEFAULT_PRECISION + with cls.app.app_context(): + db.session.remove() + cls.db.drop_all() + if cls.app in cls.db.engines: + cls.db.engines[cls.app].dispose() + if None in cls.db.engines: + cls.db.engines[None].dispose() super(BaseTestCase, cls).tearDownClass() def setUp(self): @@ -29,7 +51,6 @@ def setUp(self): self.client = self.app.test_client() self.app_context = self.app.app_context() self.app_context.push() - self.db.session.begin(subtransactions=True) clean_db(self.db) def tearDown(self): @@ -37,3 +58,45 @@ def tearDown(self): self.db.session.rollback() self.db.session.close() self.app_context.pop() + + # Code modified from https://github.com/larsbutler/oq-engine/blob/master/tests/utils/helpers.py + # Note: Was originally in test_resources.py (author Aadesh-Baral) + def assertDeepAlmostEqual(self, expected, actual, *args, **kwargs): + """ + Assert that two complex structures have almost equal contents. + + Compares lists, dicts and tuples recursively. Checks numeric values + using test_case's :py:meth:`unittest.TestCase.assertAlmostEqual` and + checks all other values with :py:meth:`unittest.TestCase.assertEqual`. + Accepts additional positional and keyword arguments and pass those + intact to assertAlmostEqual() (that's how you specify comparison + precision). + + :type test_case: :py:class:`unittest.TestCase` object + """ + kwargs.pop("__trace", "ROOT") + if ( + hasattr(expected, "__geo_interface__") + and hasattr(actual, "__geo_interface__") + and expected.__geo_interface__["type"] == actual.__geo_interface__["type"] + and expected.__geo_interface__["type"] + not in ["Feature", "FeatureCollection"] + ): + shape_expected = shape(expected) + shape_actual = shape(actual) + assert shape_expected.equals(shape_actual) + elif isinstance(expected, (int, float, complex)): + self.assertAlmostEqual(expected, actual, *args, **kwargs) + elif isinstance(expected, (list, tuple)): + self.assertEqual(len(expected), len(actual)) + for index in range(len(expected)): + v1, v2 = expected[index], actual[index] + self.assertDeepAlmostEqual(v1, v2, __trace=repr(index), *args, **kwargs) + elif isinstance(expected, dict): + self.assertEqual(set(expected), set(actual)) + for key in expected: + self.assertDeepAlmostEqual( + expected[key], actual[key], __trace=repr(key), *args, **kwargs + ) + else: + self.assertEqual(expected, actual) diff --git a/tests/backend/helpers/test_files/clipped_feature_collection.json b/tests/backend/helpers/test_files/clipped_feature_collection.json index 2302f9ae17..c81c2f4eb2 100644 --- a/tests/backend/helpers/test_files/clipped_feature_collection.json +++ b/tests/backend/helpers/test_files/clipped_feature_collection.json @@ -1,1259 +1,1145 @@ { + "type":"FeatureCollection", "features":[ { + "type":"Feature", "geometry":{ + "type":"MultiPolygon", "coordinates":[ [ [ [ - 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}, - "type":"Feature" + } }, { + "type":"Feature", "geometry":{ + "type":"MultiPolygon", "coordinates":[ [ [ [ - 1275122.5056249015, - 2828781.542271093 + 1275046.0685966, + 2828781.5422711 ], [ - 1275046.0685966313, - 2828781.542271093 + 1275046.0685966, + 2828857.9792994 ], [ - 1275046.0685966313, - 2828857.9792993665 + 1275122.5056249, + 2828857.9792994 ], [ - 1275122.5056249015, - 2828857.9792993665 + 1275122.5056249, + 2828781.5422711 ], [ - 1275122.5056249015, - 2828781.542271093 + 1275046.0685966, + 2828781.5422711 ] ] ] - ], - "type":"MultiPolygon" + ] }, "properties":{ - "isSquare":false, + "isSquare":true, "x":278825, "y":299152, "zoom":19 - }, - "type":"Feature" + } }, { + "type":"Feature", "geometry":{ + "type":"MultiPolygon", "coordinates":[ [ [ [ - 1275046.0685966313, - 2828908.286806327 + 1275052.1344223, + 2828934.4163276 ], [ - 1275052.1344222624, - 2828934.4163276367 + 1275122.5056249, + 2828934.4163276 ], [ - 1275122.5056249015, - 2828934.4163276367 + 1275122.5056249, + 2828857.9792994 ], [ - 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152.401607946, - -31.311279627 + 152.401608, + -31.3112796 ], [ - 152.401607946, - -31.952162233 + 152.401608, + -31.9521622 ] ] ] @@ -43,24 +43,24 @@ [ [ [ - 151.874999973, - -31.311279627 + 151.875, + -31.3112796 ], [ - 151.874999973, - -30.751277771 + 151.875, + -30.7512778 ], [ - 152.401607946, - -30.751277771 + 152.401608, + -30.7512778 ], [ - 152.401607946, - -31.311279627 + 152.401608, + -31.3112796 ], [ - 151.874999973, - -31.311279627 + 151.875, + -31.3112796 ] ] ] @@ -81,56 +81,56 @@ [ [ [ - 152.964694643, - -31.311279627 + 152.9646946, + -31.3112796 ], [ - 152.964694643, - -31.314876311 + 152.9646946, + -31.3148763 ], [ - 152.94092667, - -31.360552708 + 152.9409267, + -31.3605527 ], [ - 152.949562214, - -31.445384196 + 152.9495622, + -31.4453842 ], [ - 152.905274711, - -31.47718046 + 152.9052747, + -31.4771805 ], [ - 152.857738766, - -31.573415644 + 152.8577388, + -31.5734156 ], [ - 152.804260827, - -31.669551593 + 152.8042608, + -31.6695516 ], [ - 152.732956909, - -31.816093707 + 152.7329569, + -31.8160937 ], [ - 152.673536977, - -31.881709671 + 152.673537, + -31.8817097 ], [ 152.5951471, - -31.952162233 + -31.9521622 ], [ - 152.401607946, - -31.952162233 + 152.401608, + -31.9521622 ], [ - 152.401607946, - -31.311279627 + 152.401608, + -31.3112796 ], [ - 152.964694643, - -31.311279627 + 152.9646946, + -31.3112796 ] ] ] @@ -151,52 +151,52 @@ [ [ [ - 153.002629854, - -30.751277771 + 153.0026299, + -30.7512778 ], [ - 153.012230588, - -30.800769981 + 153.0122306, + -30.80077 ], [ - 153.041940554, + 153.0419406, -30.8568964 ], [ 153.0894765, - -30.912989989 + -30.91299 ], [ - 153.047882548, - -30.994521987 + 153.0478825, + -30.994522 ], [ - 153.041940554, - -31.065805365 + 153.0419406, + -31.0658054 ], [ - 153.000346602, - -31.126862915 + 153.0003466, + -31.1268629 ], [ - 152.964694643, - -31.223457045 + 152.9646946, + -31.223457 ], [ - 152.964694643, - -31.311279627 + 152.9646946, + -31.3112796 ], [ - 152.401607946, - -31.311279627 + 152.401608, + -31.3112796 ], [ - 152.401607946, - -30.751277771 + 152.401608, + -30.7512778 ], [ - 153.002629854, - -30.751277771 + 153.0026299, + -30.7512778 ] ] ] @@ -211,4 +211,4 @@ }, "type": "Feature" } -] \ No newline at end of file +] diff --git a/tests/backend/integration/api/projects/test_actions.py b/tests/backend/integration/api/projects/test_actions.py index 8a42d91092..08e0415eb3 100644 --- a/tests/backend/integration/api/projects/test_actions.py +++ b/tests/backend/integration/api/projects/test_actions.py @@ -65,7 +65,7 @@ def test_returns_clipped_grid_if_clip_to_aoi_set_true(self): ) # Assert self.assertEqual(response.status_code, 200) - self.assertDictEqual(response.json, expected_response) + self.assertDeepAlmostEqual(expected_response, geojson.loads(response.text)) def test_returns_not_clipped_grid_if_clip_to_aoi_set_false(self): """Test that the endpoint returns a not clipped grid if clipToAoi is set to false""" @@ -83,7 +83,7 @@ def test_returns_not_clipped_grid_if_clip_to_aoi_set_false(self): ) # Assert self.assertEqual(response.status_code, 200) - self.assertDictEqual(response.json, expected_response) + self.assertDeepAlmostEqual(expected_response, geojson.loads(response.text)) def test_raises_invalid_geojson_exception_if_invalid_aoi(self): """Test that the endpoint raises an InvalidGeoJson exception if the grid is invalid""" diff --git a/tests/backend/integration/api/projects/test_resources.py b/tests/backend/integration/api/projects/test_resources.py index 416618ba79..dd4dfcebed 100644 --- a/tests/backend/integration/api/projects/test_resources.py +++ b/tests/backend/integration/api/projects/test_resources.py @@ -259,14 +259,16 @@ def assert_project_response(project_response, expected_project, assert_type="ful assert expected_project.id == project_response["projectId"] # Since some of the fields are not returned in summary mode we need to skip them if assert_type != "summary": - assert geojson.is_valid(project_response["areaOfInterest"]) + assert geojson.loads( + geojson.dumps(project_response["areaOfInterest"]) + ).is_valid assert ["type", "coordinates"] == list( project_response["areaOfInterest"].keys() ) if assert_type == "notasks": assert "tasks" not in project_response else: - assert geojson.is_valid(project_response["tasks"]) + assert geojson.loads(geojson.dumps(project_response["tasks"])).is_valid assert ( is_known_task_creation_mode(project_response["taskCreationMode"]) is None @@ -1996,37 +1998,6 @@ def setUp(self): self.test_project.save() self.url = f"/api/v2/projects/{self.test_project.id}/queries/priority-areas/" - # Code modified from https://github.com/larsbutler/oq-engine/blob/master/tests/utils/helpers.py - def assertDeepAlmostEqual(self, expected, actual, *args, **kwargs): - """ - Assert that two complex structures have almost equal contents. - - Compares lists, dicts and tuples recursively. Checks numeric values - using test_case's :py:meth:`unittest.TestCase.assertAlmostEqual` and - checks all other values with :py:meth:`unittest.TestCase.assertEqual`. - Accepts additional positional and keyword arguments and pass those - intact to assertAlmostEqual() (that's how you specify comparison - precision). - - :type test_case: :py:class:`unittest.TestCase` object - """ - kwargs.pop("__trace", "ROOT") - if isinstance(expected, (int, float, complex)): - self.assertAlmostEqual(expected, actual, *args, **kwargs) - elif isinstance(expected, (list, tuple)): - self.assertEqual(len(expected), len(actual)) - for index in range(len(expected)): - v1, v2 = expected[index], actual[index] - self.assertDeepAlmostEqual(v1, v2, __trace=repr(index), *args, **kwargs) - elif isinstance(expected, dict): - self.assertEqual(set(expected), set(actual)) - for key in expected: - self.assertDeepAlmostEqual( - expected[key], actual[key], __trace=repr(key), *args, **kwargs - ) - else: - self.assertEqual(expected, actual) - def returns_404_if_project_doesnt_exist(self): """ Test 404 is returned if project doesn't exist @@ -2050,7 +2021,7 @@ def test_authentication_is_not_required(self): self.assertEqual(response.status_code, 200) self.assertEqual(len(response.json), 1) self.assertDeepAlmostEqual( - response.json[0], json_data["priorityAreas"][0], places=8 + response.json[0], json_data["priorityAreas"][0], places=6 ) diff --git a/tests/backend/integration/api/users/test_actions.py b/tests/backend/integration/api/users/test_actions.py index 745bfd9e91..a9e9f06e92 100644 --- a/tests/backend/integration/api/users/test_actions.py +++ b/tests/backend/integration/api/users/test_actions.py @@ -116,7 +116,7 @@ def setUp(self): def test_returns_400_if_no_data(self): """Test that the API returns 400 if no data is provided""" # Act - response = self.client.post(self.url) + response = self.client.post(self.url, content_type="application/json") # Assert self.assertEqual(response.status_code, 400) diff --git a/tests/backend/integration/services/grid/test_split_service.py b/tests/backend/integration/services/grid/test_split_service.py index fea3b5433c..8bd61ac617 100644 --- a/tests/backend/integration/services/grid/test_split_service.py +++ b/tests/backend/integration/services/grid/test_split_service.py @@ -35,7 +35,7 @@ def test_split_geom_returns_split_geometries(self): # act result = SplitService._create_split_tasks(x, y, zoom, task_stub) # assert - self.assertEqual(str(expected), str(result)) + self.assertDeepAlmostEqual(expected, result) def test_split_geom_raise_grid_service_error_when_task_not_usable(self): with self.assertRaises(SplitServiceError): @@ -115,4 +115,4 @@ def test_split_non_square_task(self, mock_task): json.dumps(get_canned_json("non_square_split_results.json")) ) result = SplitService._create_split_tasks(task.x, task.y, task.zoom, task) - self.assertEqual(str(expected), str(result)) + self.assertDeepAlmostEqual(expected, result) diff --git a/tests/backend/unit/models/postgis/test_project.py b/tests/backend/unit/models/postgis/test_project.py index 1d9186f925..5698852725 100644 --- a/tests/backend/unit/models/postgis/test_project.py +++ b/tests/backend/unit/models/postgis/test_project.py @@ -61,4 +61,7 @@ def test_set_country_info(self): # Act test_project.set_country_info() # Assert - self.assertNotEqual(0, len(test_project.country)) + self.assertNotEqual( + 0, len(test_project.country), "Nominatim may have given a bad response" + ) + self.assertEqual(["United Kingdom"], test_project.country) diff --git a/tests/backend/unit/services/grid/test_grid_service.py b/tests/backend/unit/services/grid/test_grid_service.py index 9d008878b0..cc78e73724 100644 --- a/tests/backend/unit/services/grid/test_grid_service.py +++ b/tests/backend/unit/services/grid/test_grid_service.py @@ -23,7 +23,7 @@ def test_feature_collection_to_multi_polygon_dissolve(self): result = GridService.merge_to_multi_polygon(aoi_geojson, True) # assert - self.assertEqual(str(expected), str(result)) + self.assertDeepAlmostEqual(expected, result) def test_feature_collection_to_multi_polygon_nodissolve(self): # arrange @@ -52,7 +52,7 @@ def test_trim_grid_to_aoi_clip(self): result = GridService.trim_grid_to_aoi(grid_dto) # assert - self.assertEqual(str(expected), str(result)) + self.assertDeepAlmostEqual(expected, result, places=6) def test_trim_grid_to_aoi_noclip(self): # arrange @@ -67,7 +67,7 @@ def test_trim_grid_to_aoi_noclip(self): result = GridService.trim_grid_to_aoi(grid_dto) # assert - self.assertEqual(str(expected), str(result)) + self.assertDeepAlmostEqual(expected, result) def test_tasks_from_aoi_features(self): # arrange diff --git a/tests/backend/unit/services/test_project_admin_service.py b/tests/backend/unit/services/test_project_admin_service.py index 43f86d11a1..6ab65612ae 100644 --- a/tests/backend/unit/services/test_project_admin_service.py +++ b/tests/backend/unit/services/test_project_admin_service.py @@ -111,7 +111,7 @@ def test_attempting_to_attach_non_existant_license_raise_error(self, license_moc ProjectAdminService._validate_imagery_licence(1) @patch.object(ProjectAdminService, "_get_project_by_id") - @patch("flask_sqlalchemy._QueryProperty.__get__") + @patch("flask_sqlalchemy.model._QueryProperty.__get__") @patch.object(Task, "set_task_history") def test_reset_all_tasks(self, mock_set_task_history, mock_query, mock_get_project): user_id = 123