From dc7c0b9c75f6afd4a435ff0771e7d414baeae9da Mon Sep 17 00:00:00 2001
From: aknecht2 <aknecht2@unl.edu>
Date: Tue, 15 Mar 2016 11:12:06 -0500
Subject: [PATCH] Changed overwrite default to True. Adjusted download to the
correct md5 value.
---
chipathlon/jobs/scripts/download_fastq.py | 2 +-
chipathlon/utils.py | 2 +-
chipathlon/workflow.py | 2 +-
3 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/chipathlon/jobs/scripts/download_fastq.py b/chipathlon/jobs/scripts/download_fastq.py
index 556b14e..9b79b4b 100644
--- a/chipathlon/jobs/scripts/download_fastq.py
+++ b/chipathlon/jobs/scripts/download_fastq.py
@@ -7,7 +7,7 @@ parser.add_argument("-u", "--url", dest="url", required=True, help="Target url."
parser.add_argument("-p", "--path", dest="path", required=True, help="Local path to file.")
parser.add_argument("-t", "--url_type", dest="url_type", default="ftp://", help="Type of url to access.")
parser.add_argument("-r", "--retries", dest="retries", default=3, type=int, help="Number of retries.")
-parser.add_argument("-o", "--overwrite", dest="overwrite", default=False, action="store_true", help="Overwrite local file if exists.")
+parser.add_argument("-n", "--overwrite", dest="overwrite", default=True, action="store_false", help="Dont' overwrite local file if exists.")
parser.add_argument("-m", "--md5", dest="md5", help="Check md5 value against passed value.")
args = parser.parse_args()
diff --git a/chipathlon/utils.py b/chipathlon/utils.py
index a0a93b6..62152d3 100644
--- a/chipathlon/utils.py
+++ b/chipathlon/utils.py
@@ -13,7 +13,7 @@ def progress(current, end, length=20):
sys.stdout.flush()
-def downloadFile(url, localpath, urltype="ftp://", retries=3, overwrite=False, checkmd5=False, md5=None):
+def downloadFile(url, localpath, urltype="ftp://", retries=3, overwrite=True, checkmd5=False, md5=None):
success = False
if url[:7] == "http://":
urltype = ""
diff --git a/chipathlon/workflow.py b/chipathlon/workflow.py
index 6921c58..c6c534c 100644
--- a/chipathlon/workflow.py
+++ b/chipathlon/workflow.py
@@ -253,7 +253,7 @@ class Workflow(object):
self.files[output_name] = output_file
job = Job(self.executables["download_fastq.py"])
job.uses(output_file, link=Link.OUTPUT, transfer=True)
- job.addArguments("-u", f["url"], "-p", output_file, "-t http://", "-m", f["content_md5sum"])
+ job.addArguments("-u", f["url"], "-p", output_file, "-t http://", "-m", f["md5sum"])
self.jobs[output_name] = job
self.dax.addJob(job)
return
--
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