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report: new module for briefing reports
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,92 @@ | ||
| """ | ||
| Briefing report generator module | ||
| """ | ||
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| import datetime | ||
| from typing import Callable, Any | ||
| from pathlib import Path | ||
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| import chevron | ||
| import plotly.io | ||
| import plotly.graph_objects as go | ||
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| from .util import read_csv, store_s3, invalidate_cache | ||
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| PlotFunction = Callable[..., dict[str, Any] | go.Figure] | ||
| PlotData = tuple[str, PlotFunction, dict[str, Any]] | ||
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| def render(template: Path, variables: dict[str, Any]) -> str: | ||
| with template.open() as f: | ||
| return chevron.render(f, variables) | ||
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| def render_figure(fig, key: str) -> str: | ||
| return {key: plotly.io.to_html(fig, include_plotlyjs=False, full_html=False)} | ||
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| def make_report( | ||
| outbreak_name: str, | ||
| data_url: str, | ||
| plots: list[PlotData], | ||
| date_columns: list[str] = [], | ||
| output_bucket: str | None = None, | ||
| cloudfront_distribution: str | None = None, | ||
| ): | ||
| """Build epidemiological report | ||
| Parameters | ||
| ---------- | ||
| outbreak_name | ||
| Name of the outbreak | ||
| data_url | ||
| Data file for the outbreak, can be a S3 URL | ||
| plots | ||
| List of plot or table specifications for the outbreak, such as those | ||
| in :module:`olm.outbreaks` | ||
| date_columns | ||
| If specified, lists additional date columns to be passed to read_csv() | ||
| output_bucket | ||
| Output S3 bucket to write result to, in addition to local HTML output | ||
| to {outbreak_name}.html | ||
| cloudfront_distribution | ||
| If specified, invalidates the cache for the cloudfront distribution | ||
| without which changes are not made available | ||
| """ | ||
| assert " " not in outbreak_name, "Outbreak name should not have spaces" | ||
| date = datetime.datetime.today().date() | ||
| output_file = f"{outbreak_name}.html" | ||
| if not (template := Path(__file__).parent / "outbreaks" / output_file).exists(): | ||
| raise FileNotFoundError(f"Template for outbreak not found at: {template}") | ||
| var = {"published_date": str(date)} | ||
| df = read_csv(data_url, date_columns) | ||
| for plot in plots: | ||
| kwargs = {} if len(plot) == 2 else plot[2] | ||
| plot_type = plot[0].split("/")[0] | ||
| match plot_type: | ||
| case "data": | ||
| var.update(plot[1](df, **kwargs)) | ||
| case "table": | ||
| var[plot[0].removeprefix("table/")] = plot[1](df, **kwargs).to_html( | ||
| index=False | ||
| ) | ||
| case "figure": | ||
| var.update( | ||
| render_figure( | ||
| plot[1](df, **kwargs), plot[0].removeprefix("figure/") | ||
| ) | ||
| ) | ||
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| report_data = render(template, var) | ||
| Path(output_file).write_text(report_data) | ||
| print("wrote", output_file) | ||
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| if output_bucket: | ||
| store_s3( | ||
| report_data, | ||
| [f"{outbreak_name}/index.html", f"{outbreak_name}/{date}.html"], | ||
| bucket_name=output_bucket, | ||
| content_type="text/html", | ||
| ) | ||
| if cloudfront_distribution: | ||
| invalidate_cache(cloudfront_distribution) |
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