From 2ceeccd5e5158362548b868390e9d411f73cd9ff Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Tue, 5 Jan 2021 12:29:41 +0000
Subject: fetch: do a straight dump of the original record

---
 workflows/tools/pubseq-fetch-data.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

(limited to 'workflows')

diff --git a/workflows/tools/pubseq-fetch-data.py b/workflows/tools/pubseq-fetch-data.py
index c22d754..3f5e6cf 100755
--- a/workflows/tools/pubseq-fetch-data.py
+++ b/workflows/tools/pubseq-fetch-data.py
@@ -28,14 +28,13 @@ if (len(ids)==0):
     with open(args.ids) as f:
         ids = [ l.strip() for l in f.readlines() ]
 
-for id in ids[0:2]:
+for id in ids:
     print(id)
     r = requests.get(f"http://covid19.genenetwork.org/api/sample/{id}.json")
     if r:
         m_url = r.json()[0]['metadata']
         mr = requests.get(m_url)
-        meta = mr.json()
         with open(dir+"/"+id+".json","w") as outf:
-            json.dump(meta, outf, indent=4)
+            outf.write(mr.text)
     else:
         raise Exception(f"Can not find record for {id}")
-- 
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