Skip embargoed dandisets, start at nonzero dandiset

scrape_dandi/__init__.py

@@ -2,10 +2,15 @@ from pathlib import Path
 from tqdm import trange
 from datetime import datetime
 import sys
+from typing import Optional
 import click
 from dandi.consts import ZARR_EXTENSIONS, metadata_all_fields
-from dandi.dandiarchive import DandisetURL, _dandi_url_parser, parse_dandi_url
+from dandi.dandiarchive import DandisetURL, _dandi_url_parser, parse_dandi_url, ParsedDandiURL
 from dandi.cli.cmd_download import download
+from enum import StrEnum
+from dataclasses import dataclass
+import requests
+import argparse
 
 
 OUT_DIR = Path('/mnt/seedbank/p2p/dandi/')
@@ -18,6 +23,17 @@ DANDI_ID = 'DANDI:{:06d}'
 MAX_DANDISET = 683
 JOBS = 64
 
+class DownloadResultType(StrEnum):
+    SKIP = 'SKIP'
+    GET = 'GET'
+    ERROR = 'ERROR'
+
+@dataclass
+class DownloadResult:
+    id: str
+    type: DownloadResultType
+    err: Optional[Exception] = None
+
 
 def check_nwb(dandiset:int) -> bool:
     if dandiset == 108:
@@ -26,6 +42,8 @@ def check_nwb(dandiset:int) -> bool:
     id = DANDI_ID.format(dandiset)
     try:
         url = parse_dandi_url(id)
+        if not check_auth(url):
+            return False
         with url.navigate(strict=True) as (c, dandiset,assets):
             is_nwb = any([a.path.endswith('nwb') for a in assets])
             is_not_draft = dandiset.version.identifier != 'draft'
@@ -33,35 +51,77 @@ def check_nwb(dandiset:int) -> bool:
     except:
         return False
 
+def check_auth(url:ParsedDandiURL) -> bool:
+    with url.get_client() as client:
+        try:
+            dandiset = url.get_dandiset(client, lazy=False)
+        except requests.HTTPError as e:
+            if e.response.status_code == 401:
+                return False
+            else:
+                raise
+        return True
+
+def download_dandiset(i:int) -> DownloadResult:
+    id = DANDI_ID.format(i)
+    if not check_nwb(i) or i in SKIP_DANDISETS:
+        return DownloadResult(
+            id=id,
+            type=DownloadResultType.SKIP
+        )
+    id = DANDI_ID.format(i)
+    try:
+        download.main([
+
+            id,
+            '-o', str(OUT_DIR),
+            '--existing', 'refresh',
+            '--jobs', str(JOBS)
+        ], standalone_mode=False
+        )
+
+    except Exception as e:
+        return DownloadResult(
+            id=id,
+            type=DownloadResultType.ERROR,
+            err=e
+        )
+
+    return DownloadResult(
+        id=id,
+        type=DownloadResultType.GET
+    )
+        # continue
+
+def argparser() -> argparse.ArgumentParser:
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        '-s', '--start',
+        description="Dandiset ID (int) to start scraping (default 1)",
+        default=1,
+        type=int
+    )
+    return parser
 
 def main():
+    args = argparser().parse_args()
     
-    for i in trange(MAX_DANDISET):
+    for i in trange(args.start, MAX_DANDISET):
-        if not check_nwb(i) or i in SKIP_DANDISETS:
-            with open(LOG_TXT, 'a') as lfile:
-                lfile.write(f"{datetime.now().isoformat()} - {i:03d} - SKIP\n")
-            continue
-        id = DANDI_ID.format(i)
         try:
-            download.main([
+            res = download_dandiset(i)
-                
+            if res.type == DownloadResultType.SKIP:
-                    id,
+                with open(LOG_TXT, 'a') as lfile:
-                    '-o', str(OUT_DIR),
+                    lfile.write(f"{datetime.now().isoformat()} - {i:03d} - SKIP\n")
-                    '--existing', 'refresh',
+            elif res.type == DownloadResultType.ERROR:
-                    '--jobs', str(JOBS)
+                with open(LOG_TXT, 'a') as lfile:
-                 ], standalone_mode=False
+                    lfile.write(f"{datetime.now().isoformat()} - {i:03d} - ERROR\n")
-            )
+                    lfile.write(str(res.err))
-            print('\nafterdl')
+            elif res.type == DownloadResultType.GET:
-            with open(LOG_TXT, 'a') as lfile:
+                with open(LOG_TXT, 'a') as lfile:
-                lfile.write(f"{datetime.now().isoformat()} - {i:03d} - GET\n")
+                    lfile.write(f"{datetime.now().isoformat()} - {i:03d} - GET\n")
         except KeyboardInterrupt:
-            sys.exit(1)
+            break
-        except Exception as e:
+
-            print('\nexception')
-            with open(LOG_TXT, 'a') as lfile:
-                lfile.write(f"{datetime.now().isoformat()} - {i:03d} - ERROR\n")
-                lfile.write(str(e))
-            # continue