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author | Pjotr Prins | 2021-01-05 07:13:15 -0600 |
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committer | Pjotr Prins | 2021-01-05 07:13:15 -0600 |
commit | 17cd8caa85991784f205109f2b64b255726a0e80 (patch) | |
tree | 7d49c4a404d4361ee4609e10ad3918498d0090a4 /workflows | |
parent | ced9613aa1c18c6a68056d1898b69865beac9ac2 (diff) | |
download | bh20-seq-resource-17cd8caa85991784f205109f2b64b255726a0e80.tar.gz bh20-seq-resource-17cd8caa85991784f205109f2b64b255726a0e80.tar.lz bh20-seq-resource-17cd8caa85991784f205109f2b64b255726a0e80.zip |
Fetching fixes
Diffstat (limited to 'workflows')
-rwxr-xr-x | workflows/tools/pubseq-fetch-data.py | 30 |
1 files changed, 17 insertions, 13 deletions
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}") |