chore: Run ruff format

manage.py

@@ -18,16 +18,16 @@ def parse(response):
 
 
 def warn(message):
-    click.secho(message, err=True, fg='yellow')
+    click.secho(message, err=True, fg="yellow")
 
 
 @contextmanager
 def csv_dump(filename, fieldnames):
     """
     Writes CSV headers to the given filename, and yields a ``csv.writer``.
     """
-    f = (basedir / 'codelists' / filename).open('w')
-    writer = csv.writer(f, lineterminator='\n')
+    f = (basedir / "codelists" / filename).open("w")
+    writer = csv.writer(f, lineterminator="\n")
     writer.writerow(fieldnames)
     try:
         yield writer
@@ -39,18 +39,21 @@ def csv_dump(filename, fieldnames):
 def edqm(email, password, url):
     with requests.Session() as session:
         # Get the CSRF token.
-        response = session.get('https://standardterms.edqm.eu/user/login')
+        response = session.get("https://standardterms.edqm.eu/user/login")
         response.raise_for_status()
 
         formkey = parse(response).xpath('//input[@name="_formkey"]/@value')[0]
 
         # https://stackoverflow.com/a/12385661/244258
-        response = session.post('https://standardterms.edqm.eu', files={
-            'email': (None, email),
-            'password': (None, password),
-            '_formkey': (None, formkey),
-            '_formname': (None, 'login'),
-        })
+        response = session.post(
+            "https://standardterms.edqm.eu",
+            files={
+                "email": (None, email),
+                "password": (None, password),
+                "_formkey": (None, formkey),
+                "_formname": (None, "login"),
+            },
+        )
         response.raise_for_status()
 
         # The "export" links do not include definitions, so we scrape the page.
@@ -59,64 +62,64 @@ def edqm(email, password, url):
 
         writer = csv.writer(sys.stdout)
         for status in parse(response).xpath('//span[starts-with(@id, "status_0_")]'):
-            if status.xpath('./span/text()')[0] != 'Current':
+            if status.xpath("./span/text()")[0] != "Current":
                 continue
 
             response = session.post(f"https://standardterms.edqm.eu/browse/get_details/{status.attrib['id'][9:]}/en")
             response.raise_for_status()
 
             document = parse(response)
-            keys = document.xpath('.//strong/text()')
+            keys = document.xpath(".//strong/text()")
             values = [value.strip() for value in document.xpath('.//span[@class="span6"]/text()')]
             properties = dict(zip(keys, values))
 
-            if properties['Domain'] != 'Veterinary only':
-                writer.writerow([properties['Term'], properties['Definition']])
+            if properties["Domain"] != "Veterinary only":
+                writer.writerow([properties["Term"], properties["Definition"]])
 
 
 def hl7(codelist):
-    response = requests.get(f'https://terminology.hl7.org/CodeSystem-v3-{codelist}.json')
+    response = requests.get(f"https://terminology.hl7.org/CodeSystem-v3-{codelist}.json")
     response.raise_for_status()
 
     data = response.json()
 
-    multi_value_properties = ('subsumedBy', 'synonymCode')
+    multi_value_properties = ("subsumedBy", "synonymCode")
     properties = set()
 
     # Transform the list of dicts into a dict.
-    for code in data['concept']:
-        code['properties'] = {}
+    for code in data["concept"]:
+        code["properties"] = {}
         for prop in multi_value_properties:
-            code['properties'][prop] = set()
-        for prop in code['property']:
-            properties.add(prop['code'])
+            code["properties"][prop] = set()
+        for prop in code["property"]:
+            properties.add(prop["code"])
             name, value = prop.values()
             if name in multi_value_properties:
-                code['properties'][name].add(value)
-            elif name in code['properties']:
+                code["properties"][name].add(value)
+            elif name in code["properties"]:
                 raise Exception(f"{name} set to {code['properties'][name]}, not {value}")
             else:
-                code['properties'][name] = value
+                code["properties"][name] = value
 
-    not_selectable = {code['code'] for code in data['concept'] if code['properties'].get('notSelectable')}
+    not_selectable = {code["code"] for code in data["concept"] if code["properties"].get("notSelectable")}
 
-    if codelist == 'RouteOfAdministration':
-        expected = {'internalId', 'notSelectable', 'status', 'subsumedBy', 'synonymCode'}
-    elif codelist == 'orderableDrugForm':
-        expected = {'internalId', 'notSelectable', 'status', 'subsumedBy'}
+    if codelist == "RouteOfAdministration":
+        expected = {"internalId", "notSelectable", "status", "subsumedBy", "synonymCode"}
+    elif codelist == "orderableDrugForm":
+        expected = {"internalId", "notSelectable", "status", "subsumedBy"}
     else:
         expected = set()
 
     difference = properties - expected
     if difference:
-        warn(f'{codelist}: unexpected new properties: {sorted(difference)}')
+        warn(f"{codelist}: unexpected new properties: {sorted(difference)}")
 
     codes = []
-    for code in data['concept']:
+    for code in data["concept"]:
         if (
-            not code['properties'].get('notSelectable')
-            and code['properties']['status'] == 'active'
-            and any(parent in not_selectable for parent in code['properties']['subsumedBy'])
+            not code["properties"].get("notSelectable")
+            and code["properties"]["status"] == "active"
+            and any(parent in not_selectable for parent in code["properties"]["subsumedBy"])
         ):
             codes.append(code)
 
@@ -135,19 +138,19 @@ def update_container():
     """
     # Retain the descriptions from EDQM.
     descriptions = {}
-    with (basedir / 'codelists' / 'immediateContainer.csv').open() as f:
+    with (basedir / "codelists" / "immediateContainer.csv").open() as f:
         reader = csv.DictReader(f)
         for row in reader:
-            descriptions[row['Code']] = row['Description']
+            descriptions[row["Code"]] = row["Description"]
 
     # https://terminology.hl7.org/CodeSystem/medicationknowledge-package-type/
-    response = requests.get('https://terminology.hl7.org/CodeSystem-medicationknowledge-package-type.json')
+    response = requests.get("https://terminology.hl7.org/CodeSystem-medicationknowledge-package-type.json")
     response.raise_for_status()
 
     data = response.json()
 
-    with csv_dump('immediateContainer.csv', ['Code', 'Title', 'Description']) as writer:
-        writer.writerows([[code['code'], code['display'], descriptions[code['code']]] for code in data['concept']])
+    with csv_dump("immediateContainer.csv", ["Code", "Title", "Description"]) as writer:
+        writer.writerows([[code["code"], code["display"], descriptions[code["code"]]] for code in data["concept"]])
 
 
 @cli.command()
@@ -156,7 +159,7 @@ def update_administration_route():
     Update schema/codelists/administrationRoute.csv.
     """
     # https://terminology.hl7.org/CodeSystem/v3-RouteOfAdministration/
-    codes, not_selectable = hl7('RouteOfAdministration')
+    codes, not_selectable = hl7("RouteOfAdministration")
 
     # "definition" is not used for Description, because it is the same as the "display", except for:
     #
@@ -165,15 +168,15 @@ def update_administration_route():
     # - "instillation, urethral", "Instillation, urethral" (lettercase change)
     # - "Topical application, vaginal", "Insertion, vaginal" (typographical error)
 
-    with csv_dump('administrationRoute.csv', ['Code', 'Title']) as writer:
+    with csv_dump("administrationRoute.csv", ["Code", "Title"]) as writer:
         for code in codes:
-            if code['properties']['synonymCode']:
+            if code["properties"]["synonymCode"]:
                 # Prefer IPINHL to its synonyms.
-                if code['code'] in ('ORINHL', 'RESPINHL'):
+                if code["code"] in ("ORINHL", "RESPINHL"):
                     continue
-                elif code['code'] != 'IPINHL':
-                    warn(f'RouteOfAdministration: unexpected synonymous code: {code}')
-            writer.writerow([code['code'], code['display'][0].upper() + code['display'][1:]])
+                elif code["code"] != "IPINHL":
+                    warn(f"RouteOfAdministration: unexpected synonymous code: {code}")
+            writer.writerow([code["code"], code["display"][0].upper() + code["display"][1:]])
 
 
 @cli.command()
@@ -182,13 +185,13 @@ def update_dosage_form():
     Update schema/codelists/dosageForm.csv from HL7.
     """
     # https://terminology.hl7.org/CodeSystem/v3-orderableDrugForm/
-    codes, not_selectable = hl7('orderableDrugForm')
+    codes, not_selectable = hl7("orderableDrugForm")
 
-    with csv_dump('dosageForm.csv', ['Code', 'Title', 'Description']) as writer:
+    with csv_dump("dosageForm.csv", ["Code", "Title", "Description"]) as writer:
         for code in codes:
-            if 'SPRY' in code['code'] and code['code'] != 'SPRY':
+            if "SPRY" in code["code"] and code["code"] != "SPRY":
                 continue
-            writer.writerow([code['code'], code['display'], code.get('definition')])
+            writer.writerow([code["code"], code["display"], code.get("definition")])
 
 
 @cli.command()
@@ -203,45 +206,45 @@ def update(ctx):
 
 
 @cli.command()
-@click.argument('email')
-@click.argument('password')
+@click.argument("email")
+@click.argument("password")
 def print_edqm_container(email, password):
-    edqm(email, password, 'https://standardterms.edqm.eu/browse/get_back_links/en/PAC_PAC/786')
+    edqm(email, password, "https://standardterms.edqm.eu/browse/get_back_links/en/PAC_PAC/786")
 
 
 @cli.command()
-@click.argument('email')
-@click.argument('password')
+@click.argument("email")
+@click.argument("password")
 def print_edqm_administration_route(email, password):
-    edqm(email, password, 'https://standardterms.edqm.eu/browse/get_concepts/ROA')
+    edqm(email, password, "https://standardterms.edqm.eu/browse/get_concepts/ROA")
 
 
 @cli.command()
 def download_inn_lists():
-    os.makedirs('inn', exist_ok=True)
+    os.makedirs("inn", exist_ok=True)
 
-    response = requests.get('https://www.who.int/teams/health-product-and-policy-standards/inn/inn-lists')
+    response = requests.get("https://www.who.int/teams/health-product-and-policy-standards/inn/inn-lists")
     response.raise_for_status()
 
     # Note: PDFs are scans before RL46 (September 2001) and PL86 (March 2002).
     document = parse(response)
-    base_url = 'https://cdn.who.int/media/docs/default-source/international-nonproprietary-names-(inn)/'
-    for column, prefix in (('PageContent_C021_Col00', 'pl'), ('PageContent_C021_Col01', 'rl')):
+    base_url = "https://cdn.who.int/media/docs/default-source/international-nonproprietary-names-(inn)/"
+    for column, prefix in (("PageContent_C021_Col00", "pl"), ("PageContent_C021_Col01", "rl")):
         for href in document.xpath(f'//div[@id="{column}"]//@href'):
             # Handle exceptions like:
             # https://www.who.int/publications/m/item/inn-proposed-list-57
             # https://www.who.int/publications/m/item/inn-pl-125-covid
-            suffix = re.search(r'\d+.*', href.lower()).group(0)
-            basename = f'{prefix}{suffix}.pdf'
-            filename = os.path.join('inn', basename)
+            suffix = re.search(r"\d+.*", href.lower()).group(0)
+            basename = f"{prefix}{suffix}.pdf"
+            filename = os.path.join("inn", basename)
             if not os.path.exists(filename):
-                click.echo(f'INFO - Downloading {basename}')
+                click.echo(f"INFO - Downloading {basename}")
                 response = requests.get(base_url + basename)
                 response.raise_for_status()
 
-                with open(filename, 'wb') as f:
+                with open(filename, "wb") as f:
                     f.write(response.content)
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     cli()