From 17cd8caa85991784f205109f2b64b255726a0e80 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Tue, 5 Jan 2021 07:13:15 -0600
Subject: Fetching fixes

---
 workflows/tools/pubseq-fetch-data.py | 30 +++++++++++++++++-------------
 1 file changed, 17 insertions(+), 13 deletions(-)

(limited to 'workflows')

diff --git a/workflows/tools/pubseq-fetch-data.py b/workflows/tools/pubseq-fetch-data.py
index 23c4dea..2119fdf 100755
--- a/workflows/tools/pubseq-fetch-data.py
+++ b/workflows/tools/pubseq-fetch-data.py
@@ -31,16 +31,20 @@ if (len(ids)==0):
 
 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)
-        with open(dir+"/"+id+".json","w") as outf:
-            outf.write(mr.text)
-        if args.fasta:
-            fa_url = r.json()[0]['fasta']
-            fr = requests.get(fa_url)
-            with open(dir+"/"+id+".fa","w") as outf:
-                outf.write(fr.text)
-    else:
-        raise Exception(f"Can not find record for {id}")
+    jsonfn = dir+"/"+id+".json"
+    if not os.path.exists(jsonfn):
+        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)
+            with open(dir+"/"+id+".json","w") as outf:
+                outf.write(mr.text)
+            if args.fasta:
+                fastafn = dir+"/"+id+".fa"
+                if os.path.exists(fastafn): continue
+                fa_url = r.json()[0]['fasta']
+                fr = requests.get(fa_url)
+                with open(fastafn,"w") as outf:
+                    outf.write(fr.text)
+        else:
+            raise Exception(f"Can not find record for {id}")
-- 
cgit v1.2.3