yaml config

outbreaks/includes/mpox-2024/2024-10-17_footnotes.md

@@ -0,0 +1,17 @@
+Footnotes for Africa CDC (ACDC) Epidemic Intelligence Weekly Report, 12 October
+2024 and WHO 2022-24 Mpox (Monkeypox) Outbreak: Global Trends Dashboard. Users
+should refer to
+[GitHub](https://github.com/globaldothealth/outbreak-data/issues?q=is%3Aissue+is%3Aopen+label%3A%22mpox+2024%22)
+to review all Open and Closed Issues.
+
+- **DRC**: G.h case counts, for suspected and confirmed cases, now align with
+  WHO’s dashboard data [starting with data as of 2024-10-13]. Africa CDC has not
+  reported suspected counts for two report cycles.
+- **Burundi**: G.h case counts, for suspected and confirmed cases, now align
+  with WHO’s dashboard data [starting with data as of 2024-10-13]. Africa CDC
+  case counts trail behind WHO counts.
+- **Uganda**: G.h will only provide confirmed case counts for Uganda moving
+  forward.
+- **Kenya**: location of death is not provided by source. G.h is unable to
+  capture this death in a linelist format. Deaths by country are provided in a
+  table format in our briefing report.

outbreaks/marburg.yml

@@ -0,0 +1,24 @@
+name: marburg
+id: GHL2023.D11.1D60.1
+description: Marburg 2023 Equatorial Guinea
+schema: https://raw.githubusercontent.com/globaldothealth/outbreak-schema/main/outbreak.schema.json
+plots:
+  data/get_counts:
+    date_col: Data_up_to
+  figure/epicurve:
+    title: Date of symptom onset
+    date_col: Date_onset_estimated
+    groupby_col: Case_status
+  figure/epicurve_location_status:
+    admin_column: Location_District
+  figure/age_gender:
+  figure/delay_distribution_consult:
+    col: Date_of_first_consult
+    title: Delay to consultation from onset
+    index: A
+    max_delay_days: 20
+  figure/delay_distribution_death:
+    col: Date_death
+    title: Delay to death from onset
+    index: B
+    max_delay_days: 20

outbreaks/mpox-2024.yml

@@ -0,0 +1,33 @@
+name: mpox-2024
+id: GHL2024.D11.1E71
+description: Mpox 2024
+url: https://mpox-2024.s3.eu-central-1.amazonaws.com/latest.csv
+schema: https://raw.githubusercontent.com/globaldothealth/outbreak-schema/main/GHL2024.D11.1E71.schema.json
+plots:
+  data/get_counts:
+    date_col: Date_entry
+  figure/age_gender:
+  table/clades/source_databutton:
+    link: https://worldhealthorg.shinyapps.io/mpx_global
+    button_text: Download MPXV clades
+    rename_columns:
+      country: Country
+      iso3: ISO3
+      clade_status: Clade status
+  table/aggregate/mpox_2024_aggregate:
+  data/get_countries_with_status:
+    country_col: Location_Admin0
+    statuses: [confirmed, suspected]
+  date/get_countries_with_anyof_statuses:
+    country_col: Location_Admin0
+    statuses: [confirmed, suspected]
+  figure/epicurve_source_report:
+    title: Date of report in primary source
+    date_col: Date_report_source_I
+    groupby_col: Case_status
+    values: [confirmed, suspected]
+  figure/epicurve_confirmed:
+    title: Date of case confirmation
+    date_col: Date_confirmation
+    groupby_col: Case_status
+    values: [confirmed]

src/olm/outbreaks/_footer.html → outbreaks/templates/_footer.html

@@ -7,8 +7,8 @@
 This report may be cited as:
 </p>
 <p class="citation-text">
-Global.health {{ description }} briefing report, published {{ published_date }},<br>
-retrieved from https://reports.global.health/{{ name }}/{{ published_date }}.html
+Global.health {{ description }} briefing report, published {{ published_date }}, retrieved from<br>
+https://reports.global.health/{{ name }}/{{ published_date }}.html
 </p>
 <p>If you cite this report, please also cite the relevant sources, which are
 mentioned in our <a href="https://github.com/globaldothealth/outbreak-data/wiki/{{ id }}">outbreak information page</a>.

src/olm/outbreaks/mpox-2024.html → outbreaks/templates/mpox-2024.html

@@ -54,3 +54,8 @@
     <figcaption><strong>Table 2</strong>: MPXV clade distribution, source:
         <a href="https://worldhealthorg.shinyapps.io/mpx_global/">WHO Mpox briefing report</a></figcaption>
 </figure>
+
+{{#footnotes}}
+<h2>Footnotes</h2>
+{{{ footnotes }}}
+{{/footnotes}}

pyproject.toml

@@ -14,6 +14,9 @@ dependencies = [
     "fastjsonschema>=2.20.0",
     "requests>=2.32.3",
     "pygsheets>=2.0.6",
+    "pyyaml>=6.0.2",
+    "mistune>=3.0.2",
+    "python-dotenv>=1.0.1",
 ]
 scripts = { olm = "olm:main" }
 

src/olm/__init__.py

@@ -4,11 +4,12 @@
 from pathlib import Path
 
 import requests
+from dotenv import load_dotenv
 
-from .report import make_report
-from .lint import lint
-from .outbreaks import OUTBREAKS
 from .util import msg_ok, msg_fail, bold_brackets
+from .outbreaks import OUTBREAKS, OUTBREAKS_PATH, Outbreak
+
+load_dotenv()
 
 USAGE = """[olm]: [O]ffice for [L]inelist [M]anagement
 
@@ -80,35 +81,32 @@ def main():
     match args.command:
         case "list":
             for outbreak in OUTBREAKS:
+                outbreak = Outbreak(OUTBREAKS_PATH / f"{outbreak}.yml")
                 print(
-                    f"\033[1m{outbreak:12s} \033[0m{OUTBREAKS[outbreak]['description']} [{OUTBREAKS[outbreak]['id']}]"
+                    f"\033[1m{outbreak:12s} \033[0m{outbreak.description} [{outbreak.id}]"
                 )
         case "get":
-            if "url" not in OUTBREAKS[args.outbreak]:
+            outbreak = Outbreak(OUTBREAKS_PATH / f"{args.outbreak}.yml")
+            if outbreak.url is None:
                 abort(f"no data URL found for {bold_outbreak}")
             output_file = f"{args.outbreak}.csv"
-            if (
-                res := requests.get(OUTBREAKS[args.outbreak]["url"])
-            ).status_code == 200:
+            if (res := requests.get(outbreak.url)).status_code == 200:
                 Path(output_file).write_text(res.text)
                 msg_ok("get", "wrote " + output_file)
         case "lint":
+            outbreak = Outbreak(OUTBREAKS_PATH / f"{args.outbreak}.yml", args.data)
             ignore_keys = args.ignore.split(",") if args.ignore is not None else []
-            if (
-                lint_result := lint(args.outbreak, args.data, args.schema, ignore_keys)
-            ).ok:
+            if (lint_result := outbreak.lint(ignore_keys)).ok:
                 msg_ok("lint", "succeeded for " + bold_outbreak)
             else:
                 msg_fail("lint", "failed for " + bold_outbreak)
                 print(lint_result)
                 sys.exit(2)
         case "report":
-            make_report(
-                args.outbreak,
-                args.data or OUTBREAKS[args.outbreak]["url"],
-                OUTBREAKS[args.outbreak],
-                output_bucket=args.bucket,
-                cloudfront_distribution=args.cloudfront,
+            outbreak = Outbreak(OUTBREAKS_PATH / f"{args.outbreak}.yml", args.data)
+            outbreak.make_report(
+                args.bucket,
+                args.cloudfront,
             )
             if args.open and (Path(args.outbreak + ".html")).exists():
                 webbrowser.open("file://" + str(Path.cwd() / (args.outbreak + ".html")))