From d1332738de33f6e5c50b8d444590f4add9663853 Mon Sep 17 00:00:00 2001 From: Peter Amstutz Date: Tue, 29 Jul 2014 16:48:13 -0400 Subject: [PATCH] Debug manifest format to see why api server is rejecting it --- crunch_scripts/split-fastq.py | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/crunch_scripts/split-fastq.py b/crunch_scripts/split-fastq.py index 55e7fccf2f..b51a33493e 100755 --- a/crunch_scripts/split-fastq.py +++ b/crunch_scripts/split-fastq.py @@ -17,6 +17,8 @@ def put_manifest(manifest_text, sources=[]): m = hashlib.new('md5') m.update(combined) + print combined + uuid = "{}+{}".format(m.hexdigest(), len(combined)) collection = arvados.api().collections().create( @@ -54,8 +56,8 @@ for s in inp.all_streams(): p[1]["reader"] = s.files()[result.group(1) + "_2.fastq" + result.group(2)] m0 = p[0]["reader"].as_manifest()[1:] m1 = p[1]["reader"].as_manifest()[1:] - manifest_text += "_" + str(piece) + m0 - manifest_text += "_" + str(piece) + m1 + manifest_text += "./_" + str(piece) + m0 + manifest_text += "./_" + str(piece) + m1 piece += 1 # No pairs found so just put each fastq file into a separate directory @@ -69,7 +71,7 @@ if manifest_text == "": p = [{}] p[0]["reader"] = s.files()[result.group(0)] m0 = p[0]["reader"].as_manifest()[1:] - manifest_text += "_" + str(piece) + m0 + manifest_text += "./_" + str(piece) + m0 piece += 1 print manifest_text -- 2.39.5