Data sources from S3 (#769)

* Started 535

* Data sources from S3

* lint

* renove breakpoints

* PR comments

* lint

* census data completed

* lint

* renaming data source

.github/workflows/combine-tilefy.yml

@@ -0,0 +1,62 @@
+name: Combine and Tilefy
+on:
+  workflow_dispatch:
+    inputs:
+      confirm-action:
+        description: This will rebuild the data sources and regenerate the score, are you sure you want to proceed? (Y/n)
+        default: n
+        required: true
+
+jobs:
+  deploy_data:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: data/data-pipeline
+    strategy:
+      matrix:
+        python-version: [3.9]
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v2
+      - name: Print variables to help debug
+        uses: hmarr/debug-action@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Setup Poetry
+        uses: Gr1N/setup-poetry@v7
+      - name: Print poetry version
+        run: poetry --version
+      - name: Install dependencies
+        run: poetry install
+      - name: Install GDAL/ogr2ogr
+        run: |
+          sudo apt-add-repository ppa:ubuntugis/ubuntugis-unstable
+          sudo apt-get update
+          sudo apt-get install gdal-bin libgdal-dev
+          pip install GDAL==3.2.3
+      - name: Run Scripts
+        run: |
+          poetry run download_census
+          poetry run etl_and_score
+      - name: Configure AWS Credentials
+        uses: aws-actions/configure-aws-credentials@v1
+        with:
+          aws-access-key-id: ${{ secrets.DATA_DEV_AWS_ACCESS_KEY_ID }}
+          aws-secret-access-key: ${{ secrets.DATA_DEV_AWS_SECRET_ACCESS_KEY }}
+          aws-region: us-east-1
+      - name: Deploy to Geoplatform AWS
+        run: |
+          aws s3 sync ./data_pipeline/data/dataset/ s3://justice40-data/data-pipeline/data/dataset --acl public-read --delete
+          aws s3 sync ./data_pipeline/data/score/csv/ s3://justice40-data/data-pipeline/data/score/csv --acl public-read --delete
+          aws s3 sync ./data_pipeline/data/score/downloadable/ s3://justice40-data/data-pipeline/data/score/downloadable --acl public-read --delete
+      - name: Update PR with Comment about deployment
+        uses: mshick/add-pr-comment@v1
+        with:
+          message: |
+            Data Synced! Find it here: s3://justice40-data/data-pipeline/data/
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          repo-token-user-login: "github-actions[bot]" # The user.login for temporary GitHub tokens
+          allow-repeats: false # This is the default

.github/workflows/generate-census.yml

@@ -0,0 +1,59 @@
+name: Generate Census
+on: 
+  workflow_dispatch:
+    inputs:
+      confirm-action:
+        description: This will rebuild the census data and upload it to S3, are you sure you want to proceed? (Y/n)
+        default: n
+        required: true
+
+jobs:
+  deploy_data:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: data/data-pipeline
+    strategy:
+      matrix:
+        python-version: [3.9]
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v2
+      - name: Print variables to help debug
+        uses: hmarr/debug-action@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Setup Poetry
+        uses: Gr1N/setup-poetry@v7
+      - name: Print poetry version
+        run: poetry --version
+      - name: Install dependencies
+        run: poetry install
+      - name: Install GDAL/ogr2ogr
+        run: |
+          sudo apt-add-repository ppa:ubuntugis/ubuntugis-unstable
+          sudo apt-get update
+          sudo apt-get install gdal-bin libgdal-dev
+          pip install GDAL==3.2.3
+      - name: Run Census Script
+        run: |
+          poetry run python3 data_pipeline/application.py census-data-download -zc
+      - name: Configure AWS Credentials
+        uses: aws-actions/configure-aws-credentials@v1
+        with:
+          aws-access-key-id: ${{ secrets.DATA_DEV_AWS_ACCESS_KEY_ID }}
+          aws-secret-access-key: ${{ secrets.DATA_DEV_AWS_SECRET_ACCESS_KEY }}
+          aws-region: us-east-1
+      - name: Upload Census Zip to Geoplatform AWS
+        run: |
+          aws s3 sync ./data_pipeline/data/tmp/census.zip s3://justice40-data/data-sources/census.zip --acl public-read --delete
+      - name: Update PR with Comment about deployment
+        uses: mshick/add-pr-comment@v1
+        with:
+          message: |
+            Data Synced! Find it here: s3://justice40-data/data-pipeline/data/
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+          repo-token-user-login: 'github-actions[bot]' # The user.login for temporary GitHub tokens
+          allow-repeats: false # This is the default

.github/workflows/generate-score.yml

@@ -31,16 +31,9 @@ jobs:
         run: poetry --version
       - name: Install dependencies
         run: poetry install
-      - name: Install GDAL/ogr2ogr
-        run: |
-          sudo apt-add-repository ppa:ubuntugis/ubuntugis-unstable
-          sudo apt-get update
-          sudo apt-get install gdal-bin libgdal-dev
-          pip install GDAL==3.2.3
       - name: Run Scripts
         run: |
-          poetry run download_census
-          poetry run etl_and_score
+          poetry run python3 data_pipeline/application.py score_full_run
       - name: Configure AWS Credentials
         uses: aws-actions/configure-aws-credentials@v1
         with:
@@ -49,14 +42,13 @@ jobs:
           aws-region: us-east-1
       - name: Deploy to Geoplatform AWS
         run: |
-          aws s3 sync ./data_pipeline/data/dataset/ s3://justice40-data/data-pipeline/data/dataset --acl public-read --delete
           aws s3 sync ./data_pipeline/data/score/csv/ s3://justice40-data/data-pipeline/data/score/csv --acl public-read --delete
           aws s3 sync ./data_pipeline/data/score/downloadable/ s3://justice40-data/data-pipeline/data/score/downloadable --acl public-read --delete
       - name: Update PR with Comment about deployment
         uses: mshick/add-pr-comment@v1
         with:
           message: |
-            Data Synced! Find it here: s3://justice40-data/data-pipeline/data/
+            Data Synced! Find it here: s3://justice40-data/data-pipeline/data/score
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           repo-token-user-login: 'github-actions[bot]' # The user.login for temporary GitHub tokens
           allow-repeats: false # This is the default

data/data-pipeline/data_pipeline/application.py

@@ -11,6 +11,7 @@ from data_pipeline.etl.runner import (
 )
 from data_pipeline.etl.sources.census.etl_utils import (
     reset_data_directories as census_reset,
+    zip_census_data,
 )
 from data_pipeline.tile.generate import generate_tiles
 from data_pipeline.utils import (
@@ -64,18 +65,27 @@ def data_cleanup():
 @cli.command(
     help="Census data download",
 )
-def census_data_download():
+@click.option(
+    "-zc",
+    "--zip-compress",
+    is_flag=True,
+    help="Upload to AWS S3 a zipped archive of the census data.",
+)
+def census_data_download(zip_compress):
     """CLI command to download all census shape files from the Census FTP and extract the geojson
     to generate national and by state Census Block Group CSVs"""
 
-    data_path = settings.APP_ROOT / "data"
-
     logger.info("Initializing all census data")
+
+    data_path = settings.APP_ROOT / "data"
     census_reset(data_path)
 
     logger.info("Downloading census data")
     etl_runner("census")
 
+    if zip_compress:
+        zip_census_data()
+
     logger.info("Completed downloading census data")
     sys.exit()
 
@@ -124,10 +134,21 @@ def score_full_run():
 
 
 @cli.command(help="Generate Geojson files with scores baked in")
-def geo_score():
-    """CLI command to generate the score"""
+@click.option("-d", "--data-source", default="local", required=False, type=str)
+def geo_score(data_source: str):
+    """CLI command to generate the score
 
-    score_geo()
+    Args:
+        data_source (str): Source for the census data (optional)
+                           Options:
+                           - local: fetch census and score data from the local data directory
+                           - aws: fetch census and score from AWS S3 J40 data repository
+
+    Returns:
+        None
+    """
+
+    score_geo(data_source=data_source)
     sys.exit()
 
 

data/data-pipeline/data_pipeline/etl/runner.py

@@ -104,18 +104,21 @@ def score_post() -> None:
     score_post.cleanup()
 
 
-def score_geo() -> None:
+def score_geo(data_source: str = "local") -> None:
     """Generates the geojson files with score data baked in
 
     Args:
-        None
+        census_data_source (str): Source for the census data (optional)
+                                  Options:
+                                  - local (default): fetch census data from the local data directory
+                                  - aws: fetch census from AWS S3 J40 data repository
 
     Returns:
         None
     """
 
     # Score Geo
-    score_geo = GeoScoreETL()
+    score_geo = GeoScoreETL(data_source=data_source)
     score_geo.extract()
     score_geo.transform()
     score_geo.load()

data/data-pipeline/data_pipeline/etl/score/etl_score.py

@@ -315,6 +315,7 @@ class ScoreETL(ExtractTransformLoad):
 
     def extract(self) -> None:
         logger.info("Loading data sets from disk.")
+
         # EJSCreen csv Load
         ejscreen_csv = self.DATA_PATH / "dataset" / "ejscreen_2019" / "usa.csv"
         self.ejscreen_df = pd.read_csv(

data/data-pipeline/data_pipeline/etl/score/etl_score_geo.py

@@ -1,9 +1,11 @@
 import math
-
 import pandas as pd
 import geopandas as gpd
 
 from data_pipeline.etl.base import ExtractTransformLoad
+from data_pipeline.etl.sources.census.etl_utils import (
+    check_census_data_source,
+)
 from data_pipeline.utils import get_module_logger
 
 logger = get_module_logger(__name__)
@@ -14,7 +16,7 @@ class GeoScoreETL(ExtractTransformLoad):
     A class used to generate per state and national GeoJson files with the score baked in
     """
 
-    def __init__(self):
+    def __init__(self, data_source: str = None):
         self.SCORE_GEOJSON_PATH = self.DATA_PATH / "score" / "geojson"
         self.SCORE_LOW_GEOJSON = self.SCORE_GEOJSON_PATH / "usa-low.json"
         self.SCORE_HIGH_GEOJSON = self.SCORE_GEOJSON_PATH / "usa-high.json"
@@ -22,6 +24,7 @@ class GeoScoreETL(ExtractTransformLoad):
         self.SCORE_CSV_PATH = self.DATA_PATH / "score" / "csv"
         self.TILE_SCORE_CSV = self.SCORE_CSV_PATH / "tiles" / "usa.csv"
 
+        self.DATA_SOURCE = data_source
         self.CENSUS_USA_GEOJSON = (
             self.DATA_PATH / "census" / "geojson" / "us.json"
         )
@@ -37,6 +40,12 @@ class GeoScoreETL(ExtractTransformLoad):
         self.geojson_score_usa_low: gpd.GeoDataFrame
 
     def extract(self) -> None:
+        # check census data
+        check_census_data_source(
+            census_data_path=self.DATA_PATH / "census",
+            census_data_source=self.DATA_SOURCE,
+        )
+
         logger.info("Reading US GeoJSON (~6 minutes)")
         self.geojson_usa_df = gpd.read_file(
             self.CENSUS_USA_GEOJSON,

data/data-pipeline/data_pipeline/etl/score/etl_score_post.py

@@ -1,22 +1,10 @@
-import json
-import zipfile
 from pathlib import Path
-
 import pandas as pd
 from data_pipeline.etl.base import ExtractTransformLoad
-from data_pipeline.utils import get_module_logger, get_zip_info
+from data_pipeline.utils import get_module_logger, zip_files
 
 from . import constants
 
-## zlib is not available on all systems
-try:
-    import zlib  # noqa # pylint: disable=unused-import
-
-    compression = zipfile.ZIP_DEFLATED
-except (ImportError, AttributeError):
-    compression = zipfile.ZIP_STORED
-
-
 logger = get_module_logger(__name__)
 
 
@@ -268,11 +256,7 @@ class PostScoreETL(ExtractTransformLoad):
 
         logger.info("Compressing files")
         files_to_compress = [csv_path, excel_path, pdf_path]
-        with zipfile.ZipFile(zip_path, "w") as zf:
-            for f in files_to_compress:
-                zf.write(f, arcname=Path(f).name, compress_type=compression)
-        zip_info = get_zip_info(zip_path)
-        logger.info(json.dumps(zip_info, indent=4, sort_keys=True, default=str))
+        zip_files(zip_path, files_to_compress)
 
     def load(self) -> None:
         self._load_score_csv(

data/data-pipeline/data_pipeline/etl/sources/census/etl_utils.py

@@ -1,5 +1,6 @@
 import csv
 import os
+import sys
 from pathlib import Path
 
 import pandas as pd
@@ -9,12 +10,14 @@ from data_pipeline.utils import (
     remove_all_dirs_from_dir,
     remove_files_from_dir,
     unzip_file_from_url,
+    zip_directory,
 )
 
 logger = get_module_logger(__name__)
 
 
 def reset_data_directories(data_path: Path) -> None:
+    """Empties all census folders"""
     census_data_path = data_path / "census"
 
     # csv
@@ -31,6 +34,7 @@ def reset_data_directories(data_path: Path) -> None:
 
 
 def get_state_fips_codes(data_path: Path) -> list:
+    """Returns a list with state data"""
     fips_csv_path = data_path / "census" / "csv" / "fips_states_2010.csv"
 
     # check if file exists
@@ -69,3 +73,50 @@ def get_state_information(data_path: Path) -> pd.DataFrame:
     df["fips"] = df["fips"].astype(str).apply(lambda x: x.zfill(2))
 
     return df
+
+
+def check_census_data_source(
+    census_data_path: Path, census_data_source: str
+) -> None:
+    """Checks if census data is present, and exits gracefully if it doesn't exist. It will download it from S3
+       if census_data_source is set to "aws"
+
+    Args:
+        census_data_path (str): Path for Census data
+        census_data_source (str): Source for the census data
+                                  Options:
+                                  - local: fetch census data from the local data directory
+                                  - aws: fetch census from AWS S3 J40 data repository
+
+    Returns:
+        None
+
+    """
+    CENSUS_DATA_S3_URL = settings.AWS_JUSTICE40_DATASOURCES_URL + "/census.zip"
+    DATA_PATH = settings.APP_ROOT / "data"
+
+    # download from s3 if census_data_source is aws
+    if census_data_source == "aws":
+        logger.info("Fetching Census data from AWS S3")
+        unzip_file_from_url(
+            CENSUS_DATA_S3_URL,
+            DATA_PATH / "tmp",
+            DATA_PATH,
+        )
+    else:
+        # check if census data is found locally
+        if not os.path.isfile(census_data_path / "geojson" / "us.json"):
+            logger.info(
+                "No local census data found. Please use '-cds aws` to fetch from AWS"
+            )
+            sys.exit()
+
+
+def zip_census_data():
+    logger.info("Compressing and uploading census files to AWS S3")
+
+    CENSUS_DATA_PATH = settings.APP_ROOT / "data" / "census"
+    TMP_PATH = settings.APP_ROOT / "data" / "tmp"
+
+    # zip folder
+    zip_directory(CENSUS_DATA_PATH, TMP_PATH)

data/data-pipeline/data_pipeline/utils.py

@@ -1,17 +1,27 @@
+from typing import List
 import datetime
+import json
 import logging
 import os
 import sys
 import shutil
 import zipfile
 from pathlib import Path
-
-import requests
 import urllib3
+import requests
 
 from data_pipeline.config import settings
 
 
+## zlib is not available on all systems
+try:
+    import zlib  # noqa # pylint: disable=unused-import
+
+    compression = zipfile.ZIP_DEFLATED
+except (ImportError, AttributeError):
+    compression = zipfile.ZIP_STORED
+
+
 def get_module_logger(module_name: str) -> logging.Logger:
     """Instantiates a logger object on stdout
 
@@ -219,6 +229,90 @@ def check_first_run() -> bool:
     return False
 
 
+def get_zip_info(archive_path: Path) -> list:
+    """
+    Returns information about a provided archive
+
+    Args:
+        archive_path (pathlib.Path): Path of the archive to be inspected
+
+    Returns:
+        a list of information about every file in the zipfile
+
+    """
+    zf = zipfile.ZipFile(archive_path)
+    info_list = []
+    for info in zf.infolist():
+        info_dict = {}
+        info_dict["Filename"] = info.filename
+        info_dict["Comment"] = info.comment.decode("utf8")
+        info_dict["Modified"] = datetime.datetime(*info.date_time).isoformat()
+        info_dict["System"] = f"{info.create_system} (0 = Windows, 3 = Unix)"
+        info_dict["ZIP version"] = info.create_version
+        info_dict["Compressed"] = f"{info.compress_size} bytes"
+        info_dict["Uncompressed"] = f"{info.file_size} bytes"
+        info_list.append(info_dict)
+    return info_list
+
+
+def zip_files(zip_file_path: Path, files_to_compress: List[Path]):
+    """
+    Zips a list of files in a path
+
+    Args:
+        zip_file_path (pathlib.Path): Path of the zip file where files are compressed
+
+    Returns:
+        None
+    """
+    with zipfile.ZipFile(zip_file_path, "w") as zf:
+        for f in files_to_compress:
+            zf.write(f, arcname=Path(f).name, compress_type=compression)
+    zip_info = get_zip_info(zip_file_path)
+    logger.info(json.dumps(zip_info, indent=4, sort_keys=True, default=str))
+
+
+def zip_directory(
+    origin_zip_directory: Path, destination_zip_directory: Path
+) -> None:
+    """
+    Zips a whole directory
+
+    Args:
+        path (pathlib.Path): Path of the directory to be archived
+    Returns:
+        None
+
+    """
+
+    def zipdir(origin_directory: Path, ziph: zipfile.ZipFile):
+        for root, dirs, files in os.walk(origin_directory):
+            for file in files:
+                logger.info(f"Compressing file: {file}")
+                ziph.write(
+                    os.path.join(root, file),
+                    os.path.relpath(
+                        os.path.join(root, file),
+                        os.path.join(origin_directory, ".."),
+                    ),
+                    compress_type=compression,
+                )
+
+    logger.info(f"Compressing {Path(origin_zip_directory).name} directory")
+    zip_file_name = f"{Path(origin_zip_directory).name}.zip"
+
+    # start archiving
+    zipf = zipfile.ZipFile(
+        destination_zip_directory / zip_file_name, "w", zipfile.ZIP_DEFLATED
+    )
+    zipdir(f"{origin_zip_directory}/", zipf)
+    zipf.close()
+
+    logger.info(
+        f"Completed compression of {Path(origin_zip_directory).name} directory"
+    )
+
+
 def get_excel_column_name(index: int) -> str:
     """Map a numeric index to the appropriate column in Excel. E.g., column #95 is "CR".
     Only works for the first 1000 columns.
@@ -1232,29 +1326,3 @@ def get_excel_column_name(index: int) -> str:
     ]
 
     return excel_column_names[index]
-
-
-def get_zip_info(archive_path: Path) -> list:
-    """
-    Returns information about a provided archive
-
-    Args:
-        archive_path (pathlib.Path): Path of the archive to be inspected
-
-    Returns:
-        a list of information about every file in the zipfile
-
-    """
-    zf = zipfile.ZipFile(archive_path)
-    info_list = []
-    for info in zf.infolist():
-        info_dict = {}
-        info_dict["Filename"] = info.filename
-        info_dict["Comment"] = info.comment.decode("utf8")
-        info_dict["Modified"] = datetime.datetime(*info.date_time).isoformat()
-        info_dict["System"] = f"{info.create_system} (0 = Windows, 3 = Unix)"
-        info_dict["ZIP version"] = info.create_version
-        info_dict["Compressed"] = f"{info.compress_size} bytes"
-        info_dict["Uncompressed"] = f"{info.file_size} bytes"
-        info_list.append(info_dict)
-    return info_list