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Based on Python type hints." category = "main" optional = false python-versions = ">=3.6" files = [ - {file = "typer-0.7.0-py3-none-any.whl", hash = "sha256:b5e704f4e48ec263de1c0b3a2387cd405a13767d2f907f44c1a08cbad96f606d"}, - {file = "typer-0.7.0.tar.gz", hash = "sha256:ff797846578a9f2a201b53442aedeb543319466870fbe1c701eab66dd7681165"}, + {file = "typer-0.9.0-py3-none-any.whl", hash = "sha256:5d96d986a21493606a358cae4461bd8cdf83cbf33a5aa950ae629ca3b51467ee"}, + {file = "typer-0.9.0.tar.gz", hash = "sha256:50922fd79aea2f4751a8e0408ff10d2662bd0c8bbfa84755a699f3bada2978b2"}, ] [package.dependencies] click = ">=7.1.1,<9.0.0" colorama = {version = ">=0.4.3,<0.5.0", optional = true, markers = "extra == \"all\""} -rich = {version = ">=10.11.0,<13.0.0", optional = true, markers = "extra == \"all\""} +rich = {version = ">=10.11.0,<14.0.0", optional = true, markers = "extra == \"all\""} shellingham = {version = ">=1.3.0,<2.0.0", optional = true, markers = "extra == \"all\""} +typing-extensions = ">=3.7.4.3" [package.extras] -all = ["colorama (>=0.4.3,<0.5.0)", "rich (>=10.11.0,<13.0.0)", "shellingham (>=1.3.0,<2.0.0)"] +all = ["colorama (>=0.4.3,<0.5.0)", "rich (>=10.11.0,<14.0.0)", "shellingham (>=1.3.0,<2.0.0)"] dev = ["autoflake (>=1.3.1,<2.0.0)", "flake8 (>=3.8.3,<4.0.0)", "pre-commit (>=2.17.0,<3.0.0)"] doc = ["cairosvg (>=2.5.2,<3.0.0)", "mdx-include (>=1.4.1,<2.0.0)", "mkdocs (>=1.1.2,<2.0.0)", "mkdocs-material (>=8.1.4,<9.0.0)", "pillow (>=9.3.0,<10.0.0)"] -test = ["black (>=22.3.0,<23.0.0)", "coverage (>=6.2,<7.0)", "isort (>=5.0.6,<6.0.0)", "mypy (==0.910)", "pytest (>=4.4.0,<8.0.0)", "pytest-cov (>=2.10.0,<5.0.0)", "pytest-sugar (>=0.9.4,<0.10.0)", "pytest-xdist (>=1.32.0,<4.0.0)", "rich (>=10.11.0,<13.0.0)", "shellingham (>=1.3.0,<2.0.0)"] +test = ["black (>=22.3.0,<23.0.0)", "coverage (>=6.2,<7.0)", "isort (>=5.0.6,<6.0.0)", "mypy (==0.910)", "pytest (>=4.4.0,<8.0.0)", "pytest-cov (>=2.10.0,<5.0.0)", "pytest-sugar (>=0.9.4,<0.10.0)", "pytest-xdist (>=1.32.0,<4.0.0)", "rich (>=10.11.0,<14.0.0)", "shellingham (>=1.3.0,<2.0.0)"] [[package]] name = "typing-extensions" @@ -4472,40 +4826,46 @@ files = [ [[package]] name = "urllib3" -version = "1.26.14" +version = "2.0.4" description = "HTTP library with thread-safe connection pooling, file post, and more." category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*" +python-versions = ">=3.7" files = [ - {file = "urllib3-1.26.14-py2.py3-none-any.whl", hash = "sha256:75edcdc2f7d85b137124a6c3c9fc3933cdeaa12ecb9a6a959f22797a0feca7e1"}, - {file = "urllib3-1.26.14.tar.gz", hash = "sha256:076907bf8fd355cde77728471316625a4d2f7e713c125f51953bb5b3eecf4f72"}, + {file = "urllib3-2.0.4-py3-none-any.whl", hash = "sha256:de7df1803967d2c2a98e4b11bb7d6bd9210474c46e8a0401514e3a42a75ebde4"}, + {file = "urllib3-2.0.4.tar.gz", hash = "sha256:8d22f86aae8ef5e410d4f539fde9ce6b2113a001bb4d189e0aed70642d602b11"}, ] [package.dependencies] -PySocks = {version = ">=1.5.6,<1.5.7 || >1.5.7,<2.0", optional = true, markers = "extra == \"socks\""} +pysocks = {version = ">=1.5.6,<1.5.7 || >1.5.7,<2.0", optional = true, markers = "extra == \"socks\""} [package.extras] -brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)", "brotlipy (>=0.6.0)"] -secure = ["certifi", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "ipaddress", "pyOpenSSL (>=0.14)", "urllib3-secure-extra"] -socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] +brotli = ["brotli (>=1.0.9)", "brotlicffi (>=0.8.0)"] +secure = ["certifi", "cryptography (>=1.9)", "idna (>=2.0.0)", "pyopenssl (>=17.1.0)", "urllib3-secure-extra"] +socks = ["pysocks (>=1.5.6,!=1.5.7,<2.0)"] +zstd = ["zstandard (>=0.18.0)"] [[package]] name = "validators" -version = "0.20.0" -description = "Python Data Validation for Humans™." +version = "0.21.2" +description = "Python Data Validation for Humans™" category = "main" optional = false -python-versions = ">=3.4" +python-versions = ">=3.8" files = [ - {file = "validators-0.20.0.tar.gz", hash = "sha256:24148ce4e64100a2d5e267233e23e7afeb55316b47d30faae7eb6e7292bc226a"}, + {file = "validators-0.21.2-py3-none-any.whl", hash = "sha256:6ad95131005a9d4c734a69dd4ef08cf66961e61222e60da25a9b5137cecd6fd4"}, + {file = "validators-0.21.2.tar.gz", hash = "sha256:002ba1552076535176824e43149c18c06f6b611bc8b597ddbcf8770bcf5f9f5c"}, ] -[package.dependencies] -decorator = ">=3.4.0" - [package.extras] -test = ["flake8 (>=2.4.0)", "isort (>=4.2.2)", "pytest (>=2.2.3)"] +docs-offline = ["myst-parser (>=2.0.0)", "pypandoc-binary (>=1.11)", "sphinx (>=7.1.1)"] +docs-online = ["mkdocs (>=1.5.2)", "mkdocs-material (>=9.1.21)", "mkdocstrings[python] (>=0.22.0)", "pyaml (>=23.7.0)"] +hooks = ["pre-commit (>=3.3.3)"] +runner = ["tox (>=4.6.4)"] +sast = ["bandit[toml] (>=1.7.5)"] +testing = ["pytest (>=7.4.0)"] +tooling = ["black (>=23.7.0)", "pyright (>=1.1.320)", "ruff (>=0.0.280)"] +tooling-extras = ["pyaml (>=23.7.0)", "pypandoc-binary (>=1.11)", "pytest (>=7.4.0)"] [[package]] name = "wcwidth" @@ -4533,46 +4893,46 @@ files = [ [[package]] name = "websocket-client" -version = "1.5.0" +version = "1.6.2" description = "WebSocket client for Python with low level API options" category = "main" optional = false -python-versions = ">=3.7" +python-versions = ">=3.8" files = [ - {file = "websocket-client-1.5.0.tar.gz", hash = "sha256:561ca949e5bbb5d33409a37235db55c279235c78ee407802f1d2314fff8a8536"}, - {file = "websocket_client-1.5.0-py3-none-any.whl", hash = "sha256:fb5d81b95d350f3a54838ebcb4c68a5353bbd1412ae8f068b1e5280faeb13074"}, + {file = "websocket-client-1.6.2.tar.gz", hash = "sha256:53e95c826bf800c4c465f50093a8c4ff091c7327023b10bfaff40cf1ef170eaa"}, + {file = "websocket_client-1.6.2-py3-none-any.whl", hash = "sha256:ce54f419dfae71f4bdba69ebe65bf7f0a93fe71bc009ad3a010aacc3eebad537"}, ] [package.extras] -docs = ["Sphinx (>=3.4)", "sphinx-rtd-theme (>=0.5)"] +docs = ["Sphinx (>=6.0)", "sphinx-rtd-theme (>=1.1.0)"] optional = ["python-socks", "wsaccel"] test = ["websockets"] [[package]] name = "wheel" -version = "0.38.4" +version = "0.41.2" description = "A built-package format for Python" category = "main" optional = false python-versions = ">=3.7" files = [ - {file = "wheel-0.38.4-py3-none-any.whl", hash = "sha256:b60533f3f5d530e971d6737ca6d58681ee434818fab630c83a734bb10c083ce8"}, - {file = "wheel-0.38.4.tar.gz", hash = "sha256:965f5259b566725405b05e7cf774052044b1ed30119b5d586b2703aafe8719ac"}, + {file = "wheel-0.41.2-py3-none-any.whl", hash = "sha256:75909db2664838d015e3d9139004ee16711748a52c8f336b52882266540215d8"}, + {file = "wheel-0.41.2.tar.gz", hash = "sha256:0c5ac5ff2afb79ac23ab82bab027a0be7b5dbcf2e54dc50efe4bf507de1f7985"}, ] [package.extras] -test = ["pytest (>=3.0.0)"] +test = ["pytest (>=6.0.0)", "setuptools (>=65)"] [[package]] name = "widgetsnbextension" -version = "4.0.5" +version = "4.0.8" description = "Jupyter interactive widgets for Jupyter Notebook" category = "main" optional = false python-versions = ">=3.7" files = [ - {file = "widgetsnbextension-4.0.5-py3-none-any.whl", hash = "sha256:eaaaf434fb9b08bd197b2a14ffe45ddb5ac3897593d43c69287091e5f3147bf7"}, - {file = "widgetsnbextension-4.0.5.tar.gz", hash = "sha256:003f716d930d385be3fd9de42dd9bf008e30053f73bddde235d14fbeaeff19af"}, + {file = "widgetsnbextension-4.0.8-py3-none-any.whl", hash = "sha256:2e37f0ce9da11651056280c7efe96f2db052fe8fc269508e3724f5cbd6c93018"}, + {file = "widgetsnbextension-4.0.8.tar.gz", hash = "sha256:9ec291ba87c2dfad42c3d5b6f68713fa18be1acd7476569516b2431682315c17"}, ] [[package]] @@ -4669,15 +5029,15 @@ docs = ["sphinx"] test = ["pytest", "pytest-cov"] [[package]] -name = "XlsxWriter" -version = "3.0.7" +name = "xlsxwriter" +version = "3.1.2" description = "A Python module for creating Excel XLSX files." category = "main" optional = false python-versions = ">=3.6" files = [ - {file = "XlsxWriter-3.0.7-py3-none-any.whl", hash = "sha256:d79dadac9dcbff3c24281764b052b46bcdb391f3184f337c4c4e6ed8d2738d7d"}, - {file = "XlsxWriter-3.0.7.tar.gz", hash = "sha256:1239958b12da12be6abf05b32f64ff162eb75fff0fdf00d901ca0f46dc0557cf"}, + {file = "XlsxWriter-3.1.2-py3-none-any.whl", hash = "sha256:331508ff39d610ecdaf979e458840bc1eab6e6a02cfd5d08f044f0f73636236f"}, + {file = "XlsxWriter-3.1.2.tar.gz", hash = "sha256:78751099a770273f1c98b8d6643351f68f98ae8e6acf9d09d37dc6798f8cd3de"}, ] [[package]] @@ -4695,4 +5055,4 @@ files = [ [metadata] lock-version = "2.0" python-versions = ">=3.10,<3.11" -content-hash = "3839561ca2068feddc97e917911e39760f27645af1c84a2430c3a9f1bcec4f4d" +content-hash = "de6c7fb86b9c9bd35102629e19f111d0f2f403f30db5f75e5f67c9bd3166ef0b" diff --git a/pyproject.toml b/pyproject.toml index aa52717..a70ad02 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -46,6 +46,7 @@ pyarrow = "^11.0.0" duckdb = "^0.6.1" sqlfluff = "^1.4.5" pydantic = "^2.3.0" +geopandas = "^0.13.2" [build-system] requires = ["poetry-core>=1.0.0"] diff --git a/src/data_common/charting/download.py b/src/data_common/charting/download.py index 76e6852..df56f50 100644 --- a/src/data_common/charting/download.py +++ b/src/data_common/charting/download.py @@ -39,12 +39,12 @@ def json_to_chart(json_spec: str) -> alt.Chart: del di_copy["datasets"] del di_copy["width"] c = Chart.from_dict(di_copy) - chart += c + chart += c # type: ignore else: del di["width"] del di["config"]["view"] chart = Chart.from_dict(di) - return chart + return chart # type: ignore def get_chart_from_url(url: str, n: int = 0) -> alt.Chart: diff --git a/src/data_common/charting/sw_theme.py b/src/data_common/charting/sw_theme.py index bc6d292..6ca81ae 100644 --- a/src/data_common/charting/sw_theme.py +++ b/src/data_common/charting/sw_theme.py @@ -118,7 +118,7 @@ def color_scale( use_palette = palette[: len(domain)] if reverse: use_palette = use_palette[::-1] - return alt.Scale(domain=domain, range=use_palette) + return alt.Scale(domain=domain, range=use_palette) # type: ignore font = "Lato" diff --git a/src/data_common/charting/theme.py b/src/data_common/charting/theme.py index 3b2935a..2e1316a 100644 --- a/src/data_common/charting/theme.py +++ b/src/data_common/charting/theme.py @@ -131,7 +131,7 @@ def color_scale( use_palette = palette[: len(domain)] if reverse: use_palette = use_palette[::-1] - return alt.Scale(domain=domain, range=use_palette) + return alt.Scale(domain=domain, range=use_palette) # type: ignore font = "Source Sans Pro" diff --git a/src/data_common/dataset/jekyll_management.py b/src/data_common/dataset/jekyll_management.py index ec0012c..39985ab 100644 --- a/src/data_common/dataset/jekyll_management.py +++ b/src/data_common/dataset/jekyll_management.py @@ -12,7 +12,6 @@ def markdown_with_frontmatter( data: dict[str, Any], dest: Path, content: str = "", from_file: Path | None = None ): - if content and from_file: raise ValueError("Trying to use contents and from_file arguments") @@ -31,7 +30,6 @@ def markdown_with_frontmatter( def render_download_format_to_dir(items: list[dict[str, Any]], output_dir: Path): - if output_dir.exists() is False: output_dir.mkdir() # remove existing files @@ -52,7 +50,6 @@ def render_download_format_to_dir(items: list[dict[str, Any]], output_dir: Path) def render_sources_to_dir(items: list[dict[str, Any]], output_dir: Path): - if output_dir.exists() is False: output_dir.mkdir() # remove existing files @@ -103,7 +100,7 @@ def make_version_info_page(items: list[dict[str, Any]], output_dir: Path): df = pd.DataFrame(items)[["name", "title", "version", "full_version"]] for name, d in df.groupby("name"): - safe_name = name.replace("-", "_") + safe_name = str(name).replace("-", "_") data_dict = { "name": name, "title": d["title"].iloc[0], diff --git a/src/data_common/dataset/resource_management.py b/src/data_common/dataset/resource_management.py index 898831d..4f8bd75 100644 --- a/src/data_common/dataset/resource_management.py +++ b/src/data_common/dataset/resource_management.py @@ -11,8 +11,9 @@ from dataclasses import dataclass from pathlib import Path from shutil import copyfile -from typing import Any, Callable, Dict, Literal, TypedDict, TypeVar, cast +from typing import Any, Callable, Literal, TypedDict, TypeVar, cast from urllib.parse import urlencode +import geopandas as gpd import pandas as pd import pytest @@ -20,9 +21,7 @@ import xlsxwriter import re -from frictionless import Schema, describe, validate -from pyparsing import any_open_tag -from rich.markdown import Markdown +from frictionless import describe, validate from rich.table import Table from ruamel.yaml import YAML @@ -168,16 +167,18 @@ def get_df(self) -> pd.DataFrame: else: raise ValueError(f"Unhandled file type {self.path.suffix}") - def get_resource(self, inline_data: bool = False) -> dict[str, Any]: - + def get_resource( + self, inline_data: bool = False, is_geodata: bool = False + ) -> dict[str, Any]: if self.has_resource_yaml: yaml = YAML(typ="safe") - with open(self.resource_path, "r") as f: + with self.resource_path.open("r") as f: resource = yaml.load(f) if inline_data: - resource["data"] = ( - self.get_df().fillna(value="").to_dict(orient="records") - ) + df = self.get_df() + if is_geodata and "geometry" in df.columns: + df = df.drop(columns=["geometry"]) + resource["data"] = df.fillna(value="").to_dict(orient="records") resource["format"] = "json" del resource["scheme"] del resource["path"] @@ -205,12 +206,10 @@ def get_schema_from_file( ) -> SchemaValidator: return update_table_schema(self.path, existing_schema) - def rebuild_yaml(self): + def rebuild_yaml(self, is_geodata: bool = False): """ Recreate yaml file from source file, preserving any custom values from previously existing yaml file """ - from frictionless.resource.resource import Resource - existing_desc = self.get_resource() desc = describe(self.path) desc.update(existing_desc) @@ -218,6 +217,15 @@ def rebuild_yaml(self): desc["schema"] = self.get_schema_from_file(existing_desc.get("schema", None)) desc["path"] = self.path.name + # if geodata - drop geometry example from schema + if is_geodata: + new_fields = [] + for f in desc["schema"]["fields"]: + if f["name"] == "geometry": + f["example"] = "" + new_fields.append(f) + desc["schema"]["fields"] = new_fields + # ensure a blank title and description new_dict = {"title": None, "description": None, "custom": {}} @@ -262,7 +270,7 @@ def rebuild_yaml(self): yaml_str = yaml_str.replace("- no\n", "- 'no'\n") yaml_str = yaml_str.replace("- yes\n", "- 'yes'\n") - with open(self.resource_path, "w") as f: + with self.resource_path.open("w") as f: f.write(yaml_str) print(f"Updated config for {self.slug} to {self.resource_path}") @@ -337,7 +345,6 @@ def build_from_function(self): ) return None if ":" in build_module and " " not in build_module: - module, function = build_module.split(":") module = importlib.import_module(module) function = getattr(module, function) @@ -680,7 +687,6 @@ def derive_bump_rule_from_change(self) -> tuple[version_rules, str] | None: ) if current_data != previous_data: - dict_diff = diff_dicts(previous_data, current_data) rich.print(dict_diff) @@ -809,8 +815,13 @@ def rebuild_resource(self, slug: str): resource.rebuild_yaml() def rebuild_all_resources(self): + is_geodata = self.is_geodata() for resource in self.resources().values(): - resource.rebuild_yaml() + resource.rebuild_yaml(is_geodata=is_geodata) + + def is_geodata(self) -> bool: + desc = self.get_datapackage() + return desc["custom"].get("is_geodata", False) def get_datapackage(self) -> dict[str, Any]: yaml = YAML(typ="safe") @@ -897,15 +908,24 @@ def copy_resources(self): """ desc = self.get_datapackage() - csv_value = desc.get("custom", {}).get("formats", {}).get("csv", True) - parquet_value = desc.get("custom", {}).get("formats", {}).get("parquet", True) + formats = desc.get("custom", {}).get("formats", {}) + csv_value = formats.get("csv", True) + parquet_value = formats.get("parquet", True) + geojson_value = formats.get("geojson", False) + geopackage_value = formats.get("gpkg", False) csv_copy_query = """ copy (select * from {{ source }}) to {{ dest }} (format PARQUET); """ + # __index_level_0__ is an internal parquet column that duckdb has access to + # but we don't want to export + exclude = "EXCLUDE (__index_level_0__)" + if desc["custom"].get("is_geodata", False): + exclude = "EXCLUDE (__index_level_0__, geometry)" + parquet_copy_query = """ - copy (select * from {{ source }}) to {{ dest }} (HEADER, DELIMITER ','); + copy (select * {{ exclude }} from {{ source }}) to {{ dest }} (HEADER, DELIMITER ','); """ for r in self.resources().values(): @@ -915,13 +935,30 @@ def copy_resources(self): copyfile(r.path, self.build_path() / r.path.name) if parquet_value: parquet_file = self.build_path() / (r.path.stem + ".parquet") - duck_query(csv_copy_query, source=r.path, dest=parquet_file) + duck_query(csv_copy_query, source=r.path, dest=parquet_file).run() + if geojson_value or geopackage_value: + raise ValueError( + "Writing to geojson/geopackage from csv source not supported. Use parquet internally." + ) elif r.path.suffix == ".parquet": if parquet_value: copyfile(r.path, self.build_path() / r.path.name) if csv_value: csv_file = self.build_path() / (r.path.stem + ".csv") - duck_query(parquet_copy_query, source=r.path, dest=csv_file) + duck_query( + parquet_copy_query, + exclude=exclude, + source=r.path, + dest=csv_file, + ).run() + if geojson_value: + geojson_path = self.build_path() / (r.path.stem + ".geojson") + gdf = gpd.read_parquet(r.path) + gdf.to_file(geojson_path, driver="GeoJSON") + if geopackage_value: + geopackage_path = self.build_path() / (r.path.stem + ".gpkg") + gdf = gpd.read_parquet(r.path) + gdf.to_file(geopackage_path, driver="GPKG") def get_datapackage_order(self) -> int: """ @@ -1103,7 +1140,7 @@ def get_composite_options( return composite_options - def build_excel(self): + def build_excel(self, is_geodata: bool = False): """ Build a single excel file for all resources """ @@ -1134,6 +1171,9 @@ def build_excel(self): for sheet_name, df in sheets.items(): short_sheet_name = sheet_name[-31:] # only allow 31 characters + # if geometry is column - remove it + if is_geodata and "geometry" in df.columns: + df = df.drop(columns=["geometry"]) df.to_excel(writer, sheet_name=short_sheet_name, index=False) for column in df: @@ -1142,7 +1182,6 @@ def build_excel(self): col_idx = df.columns.get_loc(column) if column_length <= 50: - writer.sheets[short_sheet_name].set_column( col_idx, col_idx, column_length ) @@ -1153,7 +1192,7 @@ def build_excel(self): writer.save() - def build_sqlite(self): + def build_sqlite(self, is_geodata: bool = False): """ Create a composite sqlite file for all resources with metadata as a seperate table. @@ -1176,7 +1215,10 @@ def build_sqlite(self): for slug, resource in self.resources().items(): if slug not in allowed_resource_slugs: continue - sheets[slug] = resource.get_df() + df = resource.get_df() + if is_geodata and "geometry" in df.columns: + df = df.drop(columns=["geometry"]) + sheets[slug] = df meta_df = resource.get_metadata_df() meta_df["resource"] = slug metadata.append(meta_df) @@ -1192,7 +1234,7 @@ def build_sqlite(self): df.to_sql(name, con, index=False) con.close() - def build_composite_json(self): + def build_composite_json(self, is_geodata: bool = False): """ This builds a composite json file that inlines the data as json. It can have less resources than the total, and some modifiers on the data. @@ -1211,7 +1253,7 @@ def build_composite_json(self): ] datapackage["resources"] = [ - x.get_resource(inline_data=True) + x.get_resource(inline_data=True, is_geodata=is_geodata) for x in self.resources().values() if x.slug in allowed_resource_slugs ] @@ -1236,7 +1278,6 @@ def convert_to_array_from_comma(value: t) -> list[t]: # for instance splitting comma seperated fields to arrays for resource_slug, modify_maps in composite_options["modify"].items(): for column, modify_type in modify_maps.items(): - # split specified columns to arrays and update the schema if modify_type == "comma-to-array": for resource in datapackage["resources"]: @@ -1271,9 +1312,10 @@ def build_composites(self): """ Create composite files for the datapackage """ - self.build_excel() - self.build_sqlite() - self.build_composite_json() + is_geodata = self.is_geodata() + self.build_excel(is_geodata) + self.build_sqlite(is_geodata) + self.build_composite_json(is_geodata) def build_markdown(self): """ @@ -1282,7 +1324,6 @@ def build_markdown(self): ... def print_status(self): - resources = list(self.resources().values()) df = pd.DataFrame( diff --git a/src/data_common/db/duck.py b/src/data_common/db/duck.py index d4dfbfb..6121705 100644 --- a/src/data_common/db/duck.py +++ b/src/data_common/db/duck.py @@ -1,14 +1,23 @@ -import inspect from functools import lru_cache from pathlib import Path -from typing import Any, Literal, Callable - +from typing import Any, Literal, Callable, Protocol, runtime_checkable, Union import duckdb import jinja2 import pandas as pd import toml +@runtime_checkable +class DuckView(Protocol): + query: str + + +@runtime_checkable +class DuckMacro(Protocol): + args: list[str] + macro: str + + @lru_cache def get_settings(toml_file: str = "pyproject.toml") -> dict: """ @@ -122,17 +131,57 @@ def __truediv__(self, other: str) -> "DuckUrl": return DuckUrl(f"{url}/{other}") +SourceType = Path | DuckUrl | pd.DataFrame + + +@runtime_checkable +class SourceView(Protocol): + @property + def source(self) -> SourceType: + ... + + class DuckQuery: def __init__(self): self.ddb = duckdb.connect(":memory:") self.https: bool = False + self.variables = {} + self._last_query: DuckResponse | None = None + + def set_jinja_variable(self, name: str, value: Any) -> "DuckQuery": + """ + Set jinja variables that can then be used in queries + """ + self.variables[name] = value + return self + + @property + def last_query(self): + """ + Get query for last view registered + """ + if not self._last_query: + raise ValueError("No previous query to execute") + return self._last_query def activate_https(self) -> None: if self.https is False: self.ddb.execute("install httpfs; load httpfs") - def register(self, name: str, item: pd.DataFrame | DuckUrl | Path) -> None: + def as_source(self, item: SourceView) -> "DuckResponse": + """ + Decorator to convert something implementing SourceView to a DuckResponse + """ + name = item.__name__ # type: ignore + source = getattr(item, "source", None) + + if source is None: + raise ValueError("Class must have a source attribute") + self.register(name, source) + return self.view(name) + + def register(self, name: str, item: SourceType) -> None: if isinstance(item, DuckUrl): self.activate_https() self.ddb.execute( @@ -156,14 +205,38 @@ def add_view(self, name: str, query: str) -> "DuckQuery": self.ddb.execute(f"CREATE OR REPLACE VIEW {name} AS {query}") return self + def as_view(self, cls: DuckView) -> "DuckResponse": + """ + Decorator to convert something implementing DuckView to a DuckResponse + """ + + query = getattr(cls, "query", None) + + if query is None: + raise ValueError("Class must have a query method") + + store_as_view = getattr(cls, "store_as_view", None) # type: ignore + + if store_as_view is None: + store_as_view: str = cls.__name__ # type: ignore + + return self.query(query, store_as=store_as_view) + + def view(self, view_name: str): + """ """ + return self.query(f"SELECT * FROM {view_name}") + def query( - self, query: str | Path, store_as: str | None = None, **kwargs: Any + self, query: str | Path | DuckView, store_as: str | None = None, **kwargs: Any ) -> DuckResponse: """ Execute a query """ + if isinstance(query, DuckView): + return self.as_view(query) + + query_vars = self.variables | kwargs - # if the query is a path, read it in if isinstance(query, Path) or query.endswith(".sql"): path = Path(query) if not path.exists(): @@ -189,11 +262,11 @@ def process_kwarg(key: str, value: Any) -> Any: return value - if kwargs: + if query_vars: env = jinja2.Environment() template = env.from_string(query) - args = {k: process_kwarg(k, v) for k, v in kwargs.items()} + args = {k: process_kwarg(k, v) for k, v in query_vars.items()} rendered_query = template.render(**args) else: @@ -202,9 +275,36 @@ def process_kwarg(key: str, value: Any) -> Any: if store_as: self.ddb.execute(f"CREATE OR REPLACE VIEW {store_as} AS {rendered_query}") rendered_query = f"SELECT * FROM {store_as}" - return DuckResponse(self, rendered_query) + + response = DuckResponse(self, rendered_query) + + self._last_query = response + return response + + def as_macro(self, item: DuckMacro): + name = item.__name__ # type: ignore + + args = getattr(item, "args", None) + + if args is None: + raise ValueError("Macro must have an args attribute") + + macro = getattr(item, "macro", None) + + if macro is None: + raise ValueError("Macro must have a macro method") + + macro_query = f""" + CREATE OR REPLACE MACRO {name}({", ".join(args)}) AS + {macro} + """ + self.query(macro_query).run() + + return item def macro(self, func: Callable[..., str]) -> None: + # depricated: converts a function + # prefer 'as_macro' for clarity # get function name name = func.__name__ # get arguments diff --git a/src/data_common/helpers/parquet.py b/src/data_common/helpers/parquet.py new file mode 100644 index 0000000..92c12e9 --- /dev/null +++ b/src/data_common/helpers/parquet.py @@ -0,0 +1,104 @@ +from pathlib import Path +import pyarrow as pa +import pyarrow.parquet as pq +import pandas as pd +import geopandas as gpd +import math +from tqdm import tqdm +from geopandas.io.arrow import _arrow_to_geopandas + + +def write_split_parquet( + from_file: Path, + output_path: Path, + chunk_size: int = 1000, + compression: str = "GZIP", + silent: bool = False, +): + """ + Split a Parquet file into multiple Parquet files. + """ + # initialize output directory + if not output_path.exists(): + output_path.mkdir(parents=True) + + if output_path.exists() and not output_path.is_dir(): + raise ValueError("Output path is not a directory.") + + else: + for file in output_path.iterdir(): + file.unlink() + table = pa.parquet.read_table(from_file) + + # Calculate the total number of records + total_records = table.num_rows + + # Calculate the number of chunks needed + num_chunks = math.ceil(total_records / chunk_size) + + # Split the table into chunks and write to separate Parquet files + for chunk_idx in tqdm(list(range(num_chunks)), disable=silent): + start_idx = chunk_idx * chunk_size + end_idx = min((chunk_idx + 1) * chunk_size, total_records) + + # Slice the table to create a new chunk + chunk_table = table.slice(start_idx, end_idx - start_idx) + + # Write the chunk to a Parquet file + output_file = output_path / f"{chunk_idx}.parquet" + pq.write_table(chunk_table, output_file, compression=compression) + + +def read_parquet_directory_to_table(directory_path: Path) -> pa.Table: + """ + Read all Parquet files in a directory and combine them into a single PyArrow Table. + """ + parquet_files = [ + file for file in directory_path.iterdir() if file.suffix == ".parquet" + ] + if not parquet_files: + raise ValueError("No Parquet files found in the directory.") + + # Read Parquet files and combine them into a single DataFrame + tables = [] + for file in parquet_files: + table = pq.read_table(file) + tables.append(table) + + return pa.concat_tables(tables) + + +def read_parquet_directory(directory_path: Path) -> pd.DataFrame: + """ + Read all Parquet files in a directory and combine them into a single Pandas DataFrame. + """ + table = read_parquet_directory_to_table(directory_path) + return table.to_pandas() + + +def read_split_geoparquet(fromdir: Path) -> gpd.GeoDataFrame: + """ + Read all Parquet files in a directory and combine them into a single GeoPandas DataFrame. + """ + table = read_parquet_directory_to_table(fromdir) + # convert pyarrow table to geopandas dataframe + return _arrow_to_geopandas(table) + + +def open_geo_file(file_path: Path) -> gpd.GeoDataFrame: + """ + Open a GeoFile (GeoJSON, Shapefile, GeoPackage, etc.) and return a GeoDataFrame. + """ + + # if the file_path is a directory return a GeoDataFrame + if file_path.is_dir(): + return read_split_geoparquet(file_path) + # if the file_name is "*.parquet", get the parent directory and return a GeoDataFrame + elif file_path.name == "*.parquet": + return read_split_geoparquet(file_path.parent) + # if it's another parquet file, return that using the normal method + elif file_path.suffix == ".parquet": + return gpd.read_parquet(file_path) + # if it's a GeoJSON, Shapefile, GeoPackage, etc. return that using the normal method + else: + return gpd.read_file(file_path) diff --git a/src/data_common/helpers/typing.py b/src/data_common/helpers/typing.py new file mode 100644 index 0000000..85ae348 --- /dev/null +++ b/src/data_common/helpers/typing.py @@ -0,0 +1,119 @@ +from typing import ( + get_args, + Any, + Type, + TypeVar, + Callable, + Generic, + ParamSpec, + get_type_hints, +) + +from inspect import signature + +T = TypeVar("T") +P = ParamSpec("P") + + +class ValidationTest(Generic[T]): + root_type: Type[T] + test: Callable[[T], Any] + error: Callable[[T], Exception] + + def __init__( + self, + root_type: Type[T], + test: Callable[[T], Any], + error: Callable[[T], Exception], + ): + self.root_type = root_type + self.test = test + self.error = error + + def __call__(self, *args, **kwargs): + return self.test(*args, **kwargs) + + +def inspect_function(func): + sig = signature(func) + parameters = sig.parameters + args = [] + kwargs = {} + + for param_name, param in parameters.items(): + if param.default == param.empty: + args.append(param_name) + else: + kwargs[param_name] = param.default + + return args, kwargs + + +def merge_args_kwargs(func, *args, **kwargs): + expected_args, expected_kwargs = inspect_function(func) + + if len(args) > len(expected_args): + raise ValueError( + f"Function expects {len(expected_args)} positional arguments, but {len(args)} were provided." + ) + + merged_kwargs = expected_kwargs.copy() + + for i, arg in enumerate(args): + merged_kwargs[expected_args[i]] = arg + + merged_kwargs.update(kwargs) + + return merged_kwargs + + +def enforce_types(func: Callable[P, T]) -> Callable[P, T]: + """ + This lets us move some basic validation items into the type hint structure + """ + type_hints = get_type_hints(func, include_extras=True) + expected_args, expected_kwargs = inspect_function(func) + + def wrapper(*args: P.args, **kwargs: P.kwargs): + if len(args) > len(expected_args): + raise ValueError( + f"Function expects {len(expected_args)} positional arguments, but {len(args)} were provided." + ) + + merged_kwargs = expected_kwargs.copy() + + for i, arg in enumerate(args): + merged_kwargs[expected_args[i]] = arg + + merged_kwargs.update(kwargs) + + for arg, type_ in type_hints.items(): + if arg == "return": + continue + parameter_value = merged_kwargs[arg] + enforce_type(parameter_value, type_) + value = func(*args, **kwargs) + if "return" in type_hints: + enforce_type(value, type_hints["return"]) + return value + + return wrapper + + +def enforce_type(object: T, annotated_type: Type[T]) -> None: + meta_data = get_args(annotated_type) + + if not meta_data: + if not isinstance(object, annotated_type): + raise TypeError(f"Expected {annotated_type} but got {type(object)}") + + if meta_data: + type_ = meta_data[0] + + if not isinstance(object, type_): + raise TypeError(f"Expected {type_} but got {type(object)}") + tests = meta_data[1:] + + for test in tests: + if not test(object): + raise test.error(object) diff --git a/src/data_common/management/run_notebook.py b/src/data_common/management/run_notebook.py index 27058aa..0cb12eb 100644 --- a/src/data_common/management/run_notebook.py +++ b/src/data_common/management/run_notebook.py @@ -3,7 +3,7 @@ from pathlib import Path -def run_notebook(notebook_filename: Path): +def run_notebook(notebook_filename: Path, save: bool = True): """ Run a notebook as part of another process """ @@ -12,6 +12,8 @@ def run_notebook(notebook_filename: Path): nb = nbformat.read(f, as_version=4) ep = ExecutePreprocessor(timeout=600) ep.preprocess(nb, {"metadata": {"path": "notebooks/"}}) - with open(notebook_filename, "w", encoding="utf-8") as f: - nbformat.write(nb, f) + if save: + print(f"Saving notebook: {notebook_filename}") + with open(notebook_filename, "w", encoding="utf-8") as f: + nbformat.write(nb, f) print("Done") diff --git a/src/data_common/management/settings.py b/src/data_common/management/settings.py index 7ab85b0..41aa195 100644 --- a/src/data_common/management/settings.py +++ b/src/data_common/management/settings.py @@ -25,7 +25,11 @@ def get_settings( settings_file = Path(*top_level, toml_file) - data = toml.load(settings_file)["notebook"]["settings"] + try: + data = toml.load(settings_file)["tool"]["notebook"]["settings"] + except KeyError: + # backward compatibiiity for invalid toml + data = toml.load(settings_file)["notebook"]["settings"] env_data = {} if env_file and Path(*top_level, env_file).exists(): diff --git a/src/data_common/pandas/df_extensions/space.py b/src/data_common/pandas/df_extensions/space.py index 6df9673..d7042dd 100644 --- a/src/data_common/pandas/df_extensions/space.py +++ b/src/data_common/pandas/df_extensions/space.py @@ -125,14 +125,12 @@ def t(x): self.label_df = label_df def set_k(self, k: int) -> "Cluster": - new = copy.deepcopy(self) new.k = k return new def get_label_name(self, n, include_short=True) -> str: - short_label = n name = self.label_names.get(self.k, {}).get(n, short_label) if include_short: @@ -205,7 +203,6 @@ def map_from_anchor(self, anchor: pd.DataFrame | Path) -> dict[int, int]: return mapping.to_dict() def get_label_options(self) -> list: - return [self.get_label_name(x) for x in range(1, self.k + 1)] def get_cluster_label_ids(self) -> pd.Series: @@ -215,7 +212,6 @@ def get_cluster_label_ids(self) -> pd.Series: return labels def get_cluster_labels(self, include_short=True) -> ArrayLike: - labels = self.get_cluster_label_ids() def f(x): @@ -227,7 +223,6 @@ def f(x): label_array = get_cluster_labels def get_cluster_descs(self) -> ArrayLike: - labels = self.get_cluster_label_ids() labels = labels.apply(lambda x: self.get_label_desc(n=x)) return np.array(labels) @@ -331,7 +326,7 @@ def _get_clusters(self, k: int): """ fetch k means results for this cluster """ - km = KMeans(n_clusters=k, random_state=self.default_seed, n_init=10) + km = KMeans(n_clusters=k, random_state=self.default_seed, n_init=10) # type: ignore return km.fit(self.df) def get_clusters(self, k: int): @@ -622,7 +617,6 @@ def join_distance(df_label_dict: Dict[str, pd.DataFrame]) -> pd.DataFrame: """ def prepare(df, label): - return ( df.set_index(list(df.columns[:2])) .rename(columns={"distance": label}) diff --git a/src/data_common/resources/dataset_template/{{cookiecutter.slug}}/datapackage.yaml b/src/data_common/resources/dataset_template/{{cookiecutter.slug}}/datapackage.yaml index 94cce6d..89c9176 100644 --- a/src/data_common/resources/dataset_template/{{cookiecutter.slug}}/datapackage.yaml +++ b/src/data_common/resources/dataset_template/{{cookiecutter.slug}}/datapackage.yaml @@ -31,6 +31,9 @@ custom: formats: csv: true parquet: true + gpkg: false + geojson: false + is_geodata: false composite: xlsx: include: all