diff --git a/.github/workflows/build_and_test.yaml b/.github/workflows/build_and_test.yaml index c44f3c76..bedd9ff0 100644 --- a/.github/workflows/build_and_test.yaml +++ b/.github/workflows/build_and_test.yaml @@ -11,23 +11,23 @@ jobs: runs-on: ubuntu-latest strategy: matrix: - python-version: [3.9] + python-version: ["3.10"] steps: - name: Checkout - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Start containers run: | mv .env.sample .env - docker-compose -f "docker-compose.production.yaml" up -d --build --quiet-pull + docker compose -f "docker-compose.production.yaml" up -d --build --quiet-pull - name: Set up Python ${{ matrix.python-version }} - uses: actions/setup-python@v2 + uses: actions/setup-python@v5 with: python-version: ${{ matrix.python-version }} - - name: Install ERDDAP harvester and db loader - run: pip install -q ./harvester ./db-loader + - name: Install Python environment + run: pip install . - name: Run ERDDAP harvester on sample dataset run: python -m cde_harvester --urls https://data.cioospacific.ca/erddap/ --dataset_ids DFO_MEDS_BUOYS --folder erddap_harvest @@ -54,4 +54,4 @@ jobs: - name: Stop containers if: always() - run: docker-compose -f "docker-compose.production.yaml" down + run: docker compose -f "docker-compose.production.yaml" down diff --git a/README.md b/README.md index 1427ceba..0b1132d0 100644 --- a/README.md +++ b/README.md @@ -7,9 +7,9 @@ If you just want to see how a dataset is harvested by CDE: 1. Start your python environment environment, `conda create -n cde python=3.10;conda activate cde` -1. `pip install -e ./harvester` -1. `python -m cde_harvester --urls https://data.cioospacific.ca/erddap --dataset_ids ECCC_MSC_BUOYS` -1. See files in `harvest` folder +2. `pip install -e .` +3. `python -m cde_harvester --urls https://data.cioospacific.ca/erddap --dataset_ids ECCC_MSC_BUOYS` +4. See files in `harvest` folder ## Starting using docker diff --git a/db-loader/cde_db_loader/__main__.py b/db-loader/cde_db_loader/__main__.py index 492ab887..a34c9a76 100644 --- a/db-loader/cde_db_loader/__main__.py +++ b/db-loader/cde_db_loader/__main__.py @@ -6,13 +6,31 @@ import numpy as np import pandas as pd +import sentry_sdk from cde_harvester.utils import df_cde_eov_to_standard_name from dotenv import load_dotenv +from sentry_sdk.integrations.logging import LoggingIntegration from sqlalchemy import create_engine from sqlalchemy.dialects.postgresql import ARRAY, INTEGER, TEXT logging.getLogger("urllib3").setLevel(logging.WARNING) +logging.basicConfig( + level=logging.DEBUG, format="%(asctime)s - %(levelname)-8s - %(name)s : %(message)s" +) +logger = logging.getLogger() + +sentry_sdk.init( + dsn=os.environ.get("SENTRY_DSN"), + integrations=[ + LoggingIntegration( + level=logging.INFO, # Capture info and above as breadcrumbs + event_level=logging.WARNING, # Send records as events + ), + ], + environment=os.environ.get("ENVIRONMENT", "development"), +) + def main(folder): # setup database connection @@ -26,13 +44,15 @@ def main(folder): engine = create_engine(database_link) # test connection engine.connect() - print("Connected to ", envs["DB_HOST_EXTERNAL"]) + logger.info("Connected to %s", envs["DB_HOST_EXTERNAL"]) datasets_file = f"{folder}/datasets.csv" profiles_file = f"{folder}/profiles.csv" skipped_datasets_file = f"{folder}/skipped.csv" - print("Reading", datasets_file, profiles_file, skipped_datasets_file) + logger.info( + "Reading %s,%s, %s", datasets_file, profiles_file, skipped_datasets_file + ) # ckan_file = f"ckan_{uuid_suffix}.csv" @@ -47,22 +67,22 @@ def main(folder): ) if datasets.empty: - print("No datasets found") + logger.info("No datasets found") sys.exit(1) # this gets a list of all the standard names schema = "cde" with engine.begin() as transaction: - print("Writing to DB:") + logger.info("Writing to DB:") - print("Dropping constraints") + logger.info("Dropping constraints") transaction.execute("SELECT drop_constraints();") - print("Clearing tables") + logger.info("Clearing tables") transaction.execute("SELECT remove_all_data();") - print("Writing datasets") + logger.info("Writing datasets") datasets.to_sql( "datasets", @@ -80,7 +100,7 @@ def main(folder): profiles = profiles.replace("", np.NaN) - print("Writing profiles") + logger.info("Writing profiles") # profiles has some columns to fix up first profiles.to_sql( @@ -92,7 +112,7 @@ def main(folder): # method="multi", ) - print("Writing skipped_datasets") + logger.info("Writing skipped_datasets") skipped_datasets.to_sql( "skipped_datasets", con=transaction, @@ -101,20 +121,20 @@ def main(folder): index=False, ) - print("Processing new records") + logger.info("Processing new records") transaction.execute("SELECT profile_process();") transaction.execute("SELECT ckan_process();") - print("Creating hexes") + logger.info("Creating hexes") transaction.execute("SELECT create_hexes();") # This ensures that all fields were set successfully - print("Setting constraints") + logger.info("Setting constraints") transaction.execute("SELECT set_constraints();") - print("Wrote to db:", f"{schema}.datasets") - print("Wrote to db:", f"{schema}.profiles") - print("Wrote to db:", f"{schema}.skipped_datasets") + logger.info("Wrote to db: %s", f"{schema}.datasets") + logger.info("Wrote to db: %s", f"{schema}.profiles") + logger.info("Wrote to db: %s", f"{schema}.skipped_datasets") if __name__ == "__main__": @@ -127,5 +147,8 @@ def main(folder): ) args = parser.parse_args() - - main(args.folder) + try: + main(args.folder) + except Exception: + logger.error("Failed to write to db", exc_info=True) + sys.exit(1) diff --git a/db-loader/setup.py b/db-loader/setup.py index 27d1ac4d..029cc6f1 100644 --- a/db-loader/setup.py +++ b/db-loader/setup.py @@ -14,5 +14,6 @@ "psycopg2-binary", "python-dotenv", "numpy", + "sentry_sdk", ], ) diff --git a/download_scheduler/Dockerfile b/download_scheduler/Dockerfile index c6fef844..c24d2f11 100644 --- a/download_scheduler/Dockerfile +++ b/download_scheduler/Dockerfile @@ -1,4 +1,4 @@ -FROM python:3.9-slim-buster +FROM python:3.10.2 # for shapely, pdf creation RUN apt-get -y -qq update @@ -14,7 +14,8 @@ WORKDIR /usr/src/app COPY . . -RUN pip install -q ./downloader ./download_scheduler ./harvester +RUN pip install --upgrade pip +RUN pip install -q . # -u seems to be needed to get it to print to stdout CMD [ "python", "-u","-m","download_scheduler" ] diff --git a/harvester/Dockerfile b/harvester/Dockerfile index 6bf2c4d6..453541c3 100644 --- a/harvester/Dockerfile +++ b/harvester/Dockerfile @@ -2,9 +2,14 @@ FROM python:3.10.2 WORKDIR /usr/src/app -COPY ./harvester ./harvester -COPY ./db-loader ./db-loader - -RUN pip install -q ./db-loader ./harvester +COPY harvester /usr/src/app/harvester +COPY downloader /usr/src/app/downloader +COPY db-loader /usr/src/app/db-loader +COPY pyproject.toml /usr/src/app/pyproject.toml +COPY poetry.lock /usr/src/app/poetry.lock +COPY README.md /usr/src/app/README.md + +RUN pip install --upgrade pip +RUN pip install -q . CMD [ "sh","./harvester/run.sh" ] diff --git a/harvester/cde_harvester/platform_ioos_to_l06.py b/harvester/cde_harvester/platform_ioos_to_l06.py index 9e730f6a..3a88df2c 100644 --- a/harvester/cde_harvester/platform_ioos_to_l06.py +++ b/harvester/cde_harvester/platform_ioos_to_l06.py @@ -26,14 +26,15 @@ def get_l06_codes_and_labels(): for platform in platforms: # first entry describes the vocabulary, skip it - if not "identifier" in platform: + if not "dce:identifier" in platform: continue - label = platform["prefLabel"]["@value"] - broader = platform.get("broader", []) + label = platform["skos:prefLabel"]["@value"] + broader = platform.get("skos:broader", []) id = platform["@id"] found_parent_platform = False for url in broader: + url = url["@id"] if "L06" in url: platforms_parsed[id] = {"broader_L06_url": url, "l06_label": label} found_parent_platform = True diff --git a/harvester/setup.py b/harvester/setup.py index 6b43db4a..15a776c5 100644 --- a/harvester/setup.py +++ 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