Support download of PMC oa_other

src/bluesearch/database/download.py

@@ -91,7 +91,7 @@ def generate_pmc_urls(
 
     Parameters
     ----------
-    component : {"author_manuscript", "oa_comm", "oa_noncomm"}
+    component : {"author_manuscript", "oa_comm", "oa_noncomm", "oa_other"}
         Part of the PMC to download.
     start_date
         Starting date to download the incremental files.
@@ -108,17 +108,20 @@ def generate_pmc_urls(
     ValueError
         If the chosen component does not exist on PMC.
     """
-    base_url = "https://ftp.ncbi.nlm.nih.gov/pub/pmc/"
-    if component in {"oa_comm", "oa_noncomm"}:
-        base_url += f"oa_bulk/{component}/xml/"
-    elif component == "author_manuscript":
-        base_url += "manuscript/xml/"
-    else:
+    avail_components = {"author_manuscript", "oa_comm", "oa_noncomm", "oa_other"}
+    if component not in avail_components:
         raise ValueError(
             f"Unexcepted component {component}. "
-            "Only {'author_manuscript', 'oa_comm', 'oa_noncomm'} are supported."
+            f"Only {avail_components} "
+            "are supported."
         )
 
+    base_url = "https://ftp.ncbi.nlm.nih.gov/pub/pmc/"
+    if component == "author_manuscript":
+        base_url += "manuscript/xml/"
+    else:
+        base_url += f"oa_bulk/{component}/xml/"
+
     days_list = get_daterange_list(start_date=start_date, end_date=end_date)
 
     url_list = []

src/bluesearch/entrypoint/database/download.py

@@ -143,7 +143,8 @@ def run(source: str, from_month: datetime, output_dir: Path, dry_run: bool) -> i
 
     if article_source == ArticleSource.PMC:
         url_dict = {}
-        for component in {"author_manuscript", "oa_comm", "oa_noncomm"}:
+        avail_components = ["author_manuscript", "oa_comm", "oa_noncomm", "oa_other"]
+        for component in avail_components:
             url_dict[component] = generate_pmc_urls(component, from_month)
 
         if dry_run:

tests/unit/database/test_download.py

@@ -74,6 +74,7 @@ def test_delta_wrong(self):
         ("author_manuscript", "https://ftp.ncbi.nlm.nih.gov/pub/pmc/manuscript/xml/"),
         ("oa_comm", "https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_bulk/oa_comm/xml/"),
         ("oa_noncomm", "https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_bulk/oa_noncomm/xml/"),
+        ("oa_other", "https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_bulk/oa_other/xml/"),
     ],
 )
 def test_generate_pmc_urls(monkeypatch, component, expected_url_start):

tests/unit/entrypoint/database/test_download.py

@@ -80,6 +80,7 @@ def fake_download_articles_func(url_list, output_dir):
         "author_manuscript",
         "oa_comm",
         "oa_noncomm",
+        "oa_other",
     }
     for sub_dir in pmc_path.iterdir():
         assert len(list(sub_dir.iterdir())) == 2