From 30e9c7c1faacb0517a49a137a0cc356dda34f0fc Mon Sep 17 00:00:00 2001 From: Ronan Date: Sun, 11 Feb 2024 22:01:51 +0100 Subject: [PATCH 1/3] fix: use "dockercompose" instead of "docker-compose" command --- Makefile | 2 +- poetry.lock | 2699 ++++++++++++++++++++++-------------------------- pyproject.toml | 2 +- 3 files changed, 1260 insertions(+), 1443 deletions(-) diff --git a/Makefile b/Makefile index c6efb7d0..130eff61 100644 --- a/Makefile +++ b/Makefile @@ -8,7 +8,7 @@ build: @docker tag d4g/bloom:${VERSION} d4g/bloom:latest launch-dev-db: - @docker-compose -f docker-env/docker-compose-db.yaml up -d + @docker compose -f docker-env/docker-compose-db.yaml up -d @sleep 10 $(BLOOM_DEV_DOCKER) --rm d4g/bloom:${VERSION} alembic upgrade head $(BLOOM_DEV_DOCKER) --rm d4g/bloom:${VERSION} /venv/bin/python3 alembic/init_script/load_vessels_data.py diff --git a/poetry.lock b/poetry.lock index 3b7bdfaf..e885b610 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,15 +1,14 @@ -# This file is automatically @generated by Poetry 1.4.0 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand. 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"f08a9b1a827467964de915c57bf166bff6f87e3b2e0a43494fb9fbce7fc69b95" +content-hash = "0ca2a9293ef31f71ff506062e5c14f8a62eeff0f9cffd0eec434a518aebe95c0" diff --git a/pyproject.toml b/pyproject.toml index 17ce4fca..50dbed04 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -25,7 +25,7 @@ geoalchemy2 = "^0.13.1" psycopg2-binary = "^2.9.6" dependency-injector = "^4.41.0" dependency_injection = "1.2.0" -requests = "2.31.0" +requests = "2.28.1" gql = "^3.4.0" requests-toolbelt = "^0.10.1" slack-sdk = "^3.21.3" From be4a1947c0ba6e996746d2b47de84b8ba8d0d18d Mon Sep 17 00:00:00 2001 From: Ronan Date: Sun, 11 Feb 2024 22:47:02 +0100 Subject: [PATCH 2/3] feat: add init script in order to load amp data in database --- .gitignore | 2 + Makefile | 3 ++ ...load_geometry_data.py => load_amp_data.py} | 34 ++++++++------- .../versions/961cee5426d6_create_amp_table.py | 43 +++++++++++++++++++ 4 files changed, 66 insertions(+), 16 deletions(-) rename alembic/init_script/{load_geometry_data.py => load_amp_data.py} (50%) create mode 100644 alembic/versions/961cee5426d6_create_amp_table.py diff --git a/.gitignore b/.gitignore index 2f593c69..a9b7efb4 100644 --- a/.gitignore +++ b/.gitignore @@ -28,6 +28,8 @@ share/python-wheels/ .installed.cfg *.egg MANIFEST +zones_subset_02022024.csv + # PyInstaller # Usually these files are written by a python script from a template diff --git a/Makefile b/Makefile index 130eff61..2a926404 100644 --- a/Makefile +++ b/Makefile @@ -13,6 +13,9 @@ launch-dev-db: $(BLOOM_DEV_DOCKER) --rm d4g/bloom:${VERSION} alembic upgrade head $(BLOOM_DEV_DOCKER) --rm d4g/bloom:${VERSION} /venv/bin/python3 alembic/init_script/load_vessels_data.py +load-amp-data: + $(BLOOM_DEV_DOCKER) --rm d4g/bloom:${VERSION} /venv/bin/python3 alembic/init_script/load_amp_data.py + launch-dev-container: $(BLOOM_DEV_DOCKER) -dti d4g/bloom:${VERSION} /bin/bash diff --git a/alembic/init_script/load_geometry_data.py b/alembic/init_script/load_amp_data.py similarity index 50% rename from alembic/init_script/load_geometry_data.py rename to alembic/init_script/load_amp_data.py index fd67f23f..532fcd64 100644 --- a/alembic/init_script/load_geometry_data.py +++ b/alembic/init_script/load_amp_data.py @@ -1,21 +1,9 @@ -""" -This script presents a method to load geometry data in a local DB. -First, you will need 4 shape files present in the data directory : -data/Nonterrestrial_WDPA_Jan2023.dbf -data/Nonterrestrial_WDPA_Jan2023.prj -data/Nonterrestrial_WDPA_Jan2023.shp -data/Nonterrestrial_WDPA_Jan2023.shx -The, you will have to spawn a database and a pgadmin containers locally, -using the db.yaml docker compose file. -#! docker compose up -d postgres pgadmin - -Once images are built and running, you can run the following -python script from the root of the bloom project. -""" import logging import os import geopandas as gpd +import pandas as pd +from shapely import wkb from sqlalchemy import create_engine logging.basicConfig() @@ -42,6 +30,20 @@ + postgres_db ) engine = create_engine(db_url, echo=False) -gdf = gpd.read_file("data/Nonterrestrial_WDPA_Jan2023.shp") -gdf.to_postgis("mpa", con=engine, if_exists="append", index=False) +df = pd.read_csv("zones_subset_02022024.csv") +df = df.rename(columns={"Geometry": "geometry", + "Index": "index", "Wdpaid": "WDPAID", + "Name": "name", + "Desig Eng": "DESIG_ENG", + "Desig Type": "DESIG_TYPE", + "Iucn Cat": "IUCN_CAT", + "Parent Iso": "PARENT_ISO", + "Iso3": "ISO3", + "Beneficiaries": "BENEFICIARIES"}) + +df['geometry'] = df['geometry'].apply(wkb.loads) +gdf = gpd.GeoDataFrame(df, crs='epsg:4326') +gdf.head() + +gdf.to_postgis("mpa_fr_with_mn", con=engine, if_exists="replace", index=False) \ No newline at end of file diff --git a/alembic/versions/961cee5426d6_create_amp_table.py b/alembic/versions/961cee5426d6_create_amp_table.py new file mode 100644 index 00000000..0cfe991b --- /dev/null +++ b/alembic/versions/961cee5426d6_create_amp_table.py @@ -0,0 +1,43 @@ +"""create amp table + +Revision ID: 961cee5426d6 +Revises: 1fd83d22bd1e +Create Date: 2024-02-11 22:10:19.010986 + +""" +from alembic import op +import sqlalchemy as sa +import geoalchemy2 + +# revision identifiers, used by Alembic. +revision = '961cee5426d6' +down_revision = '1fd83d22bd1e' +branch_labels = None +depends_on = None + + +def upgrade() -> None: + op.create_table("mpa_fr_with_mn", + sa.Column("index", sa.Integer, primary_key=True), + sa.Column("wdpaid", sa.Integer), + sa.Column("name", sa.String, nullable=False), + sa.Column("desig_eng", sa.String), + sa.Column("desig_type", sa.String), + sa.Column("iucn_cat", sa.String), + sa.Column("parent_iso", sa.String), + sa.Column("iso3", sa.String), + sa.Column("geometry", geoalchemy2.types.Geometry(geometry_type="GEOMETRY", srid=4326)), + sa.Column("benificiaries", sa.String) + ) + + +def downgrade() -> None: + conn = op.get_bind() + inspector = Inspector.from_engine(conn) + sql_tables = inspector.get_table_names() + tables = [ + "mpa_fr_with_mn", + ] + for t in tables: + if t in sql_tables: + op.drop_table(t) From 52526b116a27ad457955894f80401ee094765c58 Mon Sep 17 00:00:00 2001 From: Ronan Date: Mon, 12 Feb 2024 10:03:26 +0100 Subject: [PATCH 3/3] feat : add script for loading positions of the test dataset --- .gitignore | 2 +- Makefile | 3 ++ alembic/init_script/load_positions_data.py | 36 ++++++++++++++++++++++ 3 files changed, 40 insertions(+), 1 deletion(-) create mode 100644 alembic/init_script/load_positions_data.py diff --git a/.gitignore b/.gitignore index a9b7efb4..339b6bcf 100644 --- a/.gitignore +++ b/.gitignore @@ -29,7 +29,7 @@ share/python-wheels/ *.egg MANIFEST zones_subset_02022024.csv - +spire_positions_subset_02022024.csv # PyInstaller # Usually these files are written by a python script from a template diff --git a/Makefile b/Makefile index 2a926404..f8fdea66 100644 --- a/Makefile +++ b/Makefile @@ -16,6 +16,9 @@ launch-dev-db: load-amp-data: $(BLOOM_DEV_DOCKER) --rm d4g/bloom:${VERSION} /venv/bin/python3 alembic/init_script/load_amp_data.py +load-test-positions-data: + $(BLOOM_DEV_DOCKER) --rm d4g/bloom:${VERSION} /venv/bin/python3 alembic/init_script/load_positions_data.py + launch-dev-container: $(BLOOM_DEV_DOCKER) -dti d4g/bloom:${VERSION} /bin/bash diff --git a/alembic/init_script/load_positions_data.py b/alembic/init_script/load_positions_data.py new file mode 100644 index 00000000..9a1e2a9f --- /dev/null +++ b/alembic/init_script/load_positions_data.py @@ -0,0 +1,36 @@ +import logging +import os +from pathlib import Path + +import pandas as pd +from sqlalchemy import create_engine + +logging.basicConfig() +logging.getLogger("sqlalchemy.engine").setLevel(logging.INFO) + +postgres_user = os.environ.get("POSTGRES_USER") +postgres_password = os.environ.get("POSTGRES_PASSWORD") +postgres_hostname = os.environ.get("POSTGRES_HOSTNAME") +postgres_db = os.environ.get("POSTGRES_DB") +postgres_port = os.environ.get("POSTGRES_PORT") + +# The db url is configured with the db connexion variables declared in the db.yaml file. +db_url = ( + "postgresql://" + + postgres_user + + ":" + + postgres_password + + "@" + + postgres_hostname + + ":" + + postgres_port + + "/" + + postgres_db +) +engine = create_engine(db_url) +df = pd.read_csv( + Path.joinpath(Path.cwd(), "spire_positions_subset_02022024.csv"), + sep="," +) + +df.to_sql("spire_vessel_positions", engine, if_exists="append", index=False) \ No newline at end of file