Request data URLs dynamically (#16)

- Request data URLs dynamically (8514e48cb751b21da108a41b6c3fc2e3326b9228)

open_access.py

@@ -15,7 +15,9 @@
 """PMC Open Access Subset."""
 
 import datetime
+from functools import lru_cache
 
+import fsspec
 import pandas as pd
 
 import datasets
@@ -52,28 +54,52 @@ _SUBSETS = {
     "non_commercial": "oa_noncomm",
     "other": "oa_other",
 }
-_BASELINE_DATE = "2023-02-09"
-_BASELINE_MAX_RANGE = 10
-_BASELINE_RANGES = {
-    "commercial": range(_BASELINE_MAX_RANGE),
-    "non_commercial": range(1, _BASELINE_MAX_RANGE),  # non-commercial PMC000xxxxxx baseline does not exist
-    "other": range(_BASELINE_MAX_RANGE),
-}
+
+
+@lru_cache(maxsize=None)
+def request_data_urls():
+    fs = fsspec.filesystem("https")
+    result = {}
+    for subset, subset_url in _SUBSETS.items():
+        urls = fs.ls(_URL.format(subset=subset_url), detail=False)
+        baseline_urls = [
+            url for url in urls for filename in url.split("/")[-1:] if filename.startswith(f"{subset_url}_txt.PMC")
+        ]
+        baseline_date = parse_date(baseline_urls[0])
+        baseline_file_list_urls = [url for url in baseline_urls if url.endswith(".csv")]
+        baseline_archive_urls = [url for url in baseline_urls if url.endswith(".tar.gz")]
+        incremental_urls = [
+            url for url in urls for filename in url.split("/")[-1:] if filename.startswith(f"{subset_url}_txt.incr.")
+        ]
+        incremental_file_list_urls = [url for url in incremental_urls if url.endswith(".csv")]
+        incremental_archive_urls = [url for url in incremental_urls if url.endswith(".tar.gz")]
+        result["baseline_date"] = baseline_date
+        result[subset] = {
+            "baseline_urls": list(zip(baseline_file_list_urls, baseline_archive_urls)),
+            "incremental_urls": list(zip(incremental_file_list_urls, incremental_archive_urls)),
+        }
+    return result
+
+
+def parse_date(url):
+    return url.split("/")[-1].split(".")[-3]
 
 
 class OpenAccessConfig(datasets.BuilderConfig):
     """BuilderConfig for the PMC Open Access Subset."""
 
-    def __init__(self, date=_BASELINE_DATE, subsets=None, **kwargs):
+    def __init__(self, date=None, subsets="all", **kwargs):
         """BuilderConfig for the PMC Open Access Subset.
 
         Args:
-            date (`str`, default _BASELINE_DATE) : Up to date, in ISO format. Pass 'latest' for latest date.
-            subsets (`str` or `list[str]`): List of subsets to load. Possible values are 'all' or any combination
+            date (`str`, default BASELINE_DATE) : Up to date, in ISO format. Pass 'latest' for latest date.
+            subsets (`str` or `list[str]`, default 'all'): List of subsets to load. Possible values are 'all' or any combination
                 of {'commercial', 'non_commercial', 'other'}.
             **kwargs: Keyword arguments forwarded to `BuilderConfig`.
         """
-        date = datetime.date.today().isoformat() if date=="latest" else date
+        if date is None:
+            date = request_data_urls()["baseline_date"]
+        date = datetime.date.today().isoformat() if date == "latest" else date
         subsets = [subsets] if isinstance(subsets, str) else subsets
         subsets_name = "+".join(subsets)
         name = f"{date}.{subsets_name}"
@@ -88,7 +114,7 @@ class OpenAccess(datasets.GeneratorBasedBuilder):
     VERSION = datasets.Version("1.0.0")
     BUILDER_CONFIG_CLASS = OpenAccessConfig
     BUILDER_CONFIGS = [OpenAccessConfig(subsets="all")] + [OpenAccessConfig(subsets=subset) for subset in _SUBSETS]
-    DEFAULT_CONFIG_NAME = f"{_BASELINE_DATE}.all"
+    DEFAULT_CONFIG_NAME = f"{request_data_urls()['baseline_date']}.all"
 
     def _info(self):
         return datasets.DatasetInfo(
@@ -111,27 +137,17 @@ class OpenAccess(datasets.GeneratorBasedBuilder):
         )
 
     def _split_generators(self, dl_manager):
-
+        urls = request_data_urls()
+        date = datetime.date.fromisoformat(self.config.date)
         paths = []
         for subset in self.config.subsets:
-            url = _URL.format(subset=_SUBSETS[subset])
-            basename = f"{_SUBSETS[subset]}_txt."
             # Baselines
-            baselines = [f"PMC00{i}xxxxxx.baseline.{_BASELINE_DATE}" for i in _BASELINE_RANGES[subset]]
-            baseline_urls = [
-                (f"{url}{basename}{baseline}.filelist.csv", f"{url}{basename}{baseline}.tar.gz")
-                for baseline in baselines
-            ]
+            baseline_urls = urls[subset]["baseline_urls"]
             # Incremental
-            date_delta = datetime.date.fromisoformat(self.config.date) - datetime.date.fromisoformat(_BASELINE_DATE)
-            incremental_dates = [
-                (datetime.date.fromisoformat(_BASELINE_DATE) + datetime.timedelta(days=i + 1)).isoformat()
-                for i in range(date_delta.days)
-            ]
-            incrementals = [f"incr.{date}" for date in incremental_dates]
             incremental_urls = [
-                (f"{url}{basename}{incremental}.filelist.csv", f"{url}{basename}{incremental}.tar.gz")
-                for incremental in incrementals
+                url_pair
+                for url_pair in urls[subset]["incremental_urls"]
+                if datetime.date.fromisoformat(parse_date(url_pair[0])) <= date
             ]
             paths += dl_manager.download(baseline_urls + incremental_urls)