From 192ab3eaf0967a68c1761a1ff14ada13e507caba Mon Sep 17 00:00:00 2001
From: aknecht2 <aknecht2@unl.edu>
Date: Thu, 8 Jun 2017 12:16:33 -0500
Subject: [PATCH] Fixed issues with circular dependncy in utils / db.py
---
chipathlon/db.py | 15 ++++++++++++++-
chipathlon/utils.py | 17 -----------------
scripts/chip-job-download-gridfs | 16 ++++++++--------
3 files changed, 22 insertions(+), 26 deletions(-)
diff --git a/chipathlon/db.py b/chipathlon/db.py
index cbb25e7..4903f77 100644
--- a/chipathlon/db.py
+++ b/chipathlon/db.py
@@ -11,7 +11,20 @@ import chipathlon.conf
from pprint import pprint
import hashlib
from chipathlon.utils import progress
-
+import bson
+
+def download_from_gridfs(host, gridfs_id, local_path, username=None, password=None, retries=3, overwrite=True, checkmd5=False):
+ mdb = chipathlon.db.MongoDB(host, username, password)
+ if not os.path.isfile(local_path) or overwrite:
+ for i in range(0, retries):
+ print "Attempt #%s, downloading file with ID '%s' to '%s'" % (i + 1, gridfs_id, local_path)
+ if mdb.fetch_from_gridfs(bson.objectid.ObjectId(gridfs_id), localpath, checkmd5):
+ return True
+ else:
+ print "Download attempt #%s from GridFS failed, retrying..." % (i + 1)
+ else:
+ print "File already exists, skipping download.\n"
+ return False
class MongoDB(object):
"""
diff --git a/chipathlon/utils.py b/chipathlon/utils.py
index 33176ca..8341947 100644
--- a/chipathlon/utils.py
+++ b/chipathlon/utils.py
@@ -3,8 +3,6 @@ import hashlib
import urllib2
import os
import traceback
-import chipathlon.db
-import bson.objectid
def progress(current, end, length=20):
percent = float(current) / end
@@ -50,21 +48,6 @@ def downloadFile(url, localpath, urltype="http://", retries=3, overwrite=True, c
print "File already exists, skipping download.\n"
return
-def downloadFromGridFS(hostname, username, password, gridfs_id, localpath, retries=3, overwrite=True, checkmd5=False):
- success = False
- mdb = chipathlon.db.MongoDB(hostname, username, password)
- if not os.path.isfile(localpath) or overwrite:
- for i in range(0, retries):
- print "Attempt #%s, downloading file with ID '%s' to '%s'" % (i + 1, gridfs_id, localpath)
- if mdb.fetch_from_gridfs(bson.objectid.ObjectId(gridfs_id), localpath, checkmd5):
- success = True
- break
- else:
- print "Download attempt #%s from GridFS failed, retrying..." % (i + 1)
- else:
- print "File already exists, skipping download.\n"
- return success
-
# http://pythoncentral.io/how-to-check-if-a-string-is-a-number-in-python-including-unicode/
def is_number(s):
try:
diff --git a/scripts/chip-job-download-gridfs b/scripts/chip-job-download-gridfs
index 97e59f9..f10efb1 100755
--- a/scripts/chip-job-download-gridfs
+++ b/scripts/chip-job-download-gridfs
@@ -1,5 +1,5 @@
#!/usr/bin/env python
-import chipathlon.utils
+import chipathlon.db
import argparse
parser = argparse.ArgumentParser(description="Download target file from GridFS.")
@@ -9,17 +9,17 @@ parser.add_argument("-p", "--password", dest="password", help="Database password
parser.add_argument("-i", "--id", dest="gridfs_id", required=True, help="GridFS ID.")
parser.add_argument("-d", "--destination", dest="destination", required=True, help="Local path to file destination.")
parser.add_argument("-r", "--retries", dest="retries", default=3, type=int, help="Number of retries.")
-parser.add_argument("-n", "--overwrite", dest="overwrite", default=True, action="store_false", help="Don't overwrite local file if it exists.")
+parser.add_argument("-n", "--no-overwrite", dest="overwrite", default=True, action="store_false", help="Don't overwrite local file if it exists.")
parser.add_argument("-c", "--checkmd5", dest="checkmd5", action="store_true", help="Check md5 value of downloaded file against database value.")
args = parser.parse_args()
-chipathlon.utils.downloadFromGridFS(
+chipathlon.db.download_from_gridfs(
args.host,
- args.username,
- args.password,
args.gridfs_id,
args.destination,
- args.retries,
- args.overwrite,
- args.checkmd5
+ username=args.username,
+ password=args.password,
+ retries=args.retries,
+ overwrite=args.overwrite,
+ checkmd5=args.checkmd5
)
--
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