diff --git a/chipathlon/db.py b/chipathlon/db.py
index 8e3be4ebd3512bd2fb42affe9a621c861e373ab6..91b38c43cc2b3306eaa65003fa42f79fdbc78d2b 100644
--- a/chipathlon/db.py
+++ b/chipathlon/db.py
@@ -30,7 +30,7 @@ class MongoDB(object):
operations much easier.
"""
- def __init__(self, host, username, password, debug=False):
+ def __init__(self, host="localhost", username=None, password=None, debug=False):
self.debug = debug
self.host = host
self.username = username
@@ -38,12 +38,14 @@ class MongoDB(object):
self.client = MongoClient(host)
self.db = self.client.chipseq
self.cache = collections.defaultdict(dict)
- try:
- self.db.authenticate(username, password, mechanism="SCRAM-SHA-1")
- except:
- print("Could not authenticate to db %s!" % (host,))
- print traceback.format_exc()
- sys.exit(1)
+ self.cache = {}
+ if username and password:
+ try:
+ self.db.authenticate(username, password, mechanism="SCRAM-SHA-1")
+ except:
+ print("Could not authenticate to db %s!" % (host,))
+ print traceback.format_exc()
+ sys.exit(1)
self.gfs = gridfs.GridFS(self.db)
return
diff --git a/chipathlon/workflow.py b/chipathlon/workflow.py
index daa210eece1e9cb4278b8aa24c95491ba3ec440c..d29bf080b7d716a5b62587dc1a8cf29e2e4839b7 100644
--- a/chipathlon/workflow.py
+++ b/chipathlon/workflow.py
@@ -58,8 +58,9 @@ class Workflow(object):
"""
def __init__(self, job_home, run_file, param_file, config_file,
- properties_file, host, username, password, execute_site="local",
- output_site="local", save_db=True, rewrite=False, debug=False):
+ properties_file, execute_site="local", output_site="local",
+ host="localhost", username=None, password=None, save_db=True,
+ rewrite=False, debug=False):
# debug mode, print out additional information
self.debug = debug
# Job site information
@@ -405,4 +406,3 @@ class Workflow(object):
with open(os.path.join(self.base_path, "input/chipathlon.dax"), "w") as wh:
self.dax.writeXML(wh)
return
-����������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������������
diff --git a/scripts/chip-create-run b/scripts/chip-create-run
index 9236e5aa91b2d1895936a8bacf3c1705ac5a7319..bc1dec2cf3a5554f4e7980e349a38b33c08fc59e 100644
--- a/scripts/chip-create-run
+++ b/scripts/chip-create-run
@@ -6,9 +6,9 @@ import yaml
import pprint
parser = argparse.ArgumentParser(description="Create a run file from a list of experiment accessions.")
-parser.add_argument("-H", "--host", dest="host", required=True, help="Database host.")
-parser.add_argument("-u", "--username", dest="username", required=True, help="Database user.")
-parser.add_argument("-p", "--password", dest="password", required=True, help="Database user password.")
+parser.add_argument("-H", "--host", dest="host", default="localhost", help="Database host. (default: %(default)s)")
+parser.add_argument("-u", "--username", dest="username", help="Database username (if required).")
+parser.add_argument("-p", "--password", dest="password", help="Database password (if required).")
parser.add_argument("-n", "--name", dest="name", required=True, help="Name of the run file to create.")
parser.add_argument("-f", "--file_type", dest="file_type", default="fastq", help="Type of files to extract (fastq or bam).")
diff --git a/scripts/chip-gen b/scripts/chip-gen
index 000eb722cfa1219ec16b6ca154d2216e656c5894..c07a4eb77649f969499f7178a204eb4b99704179 100644
--- a/scripts/chip-gen
+++ b/scripts/chip-gen
@@ -3,9 +3,9 @@ from chipathlon.workflow import Workflow
import argparse
parser = argparse.ArgumentParser(description="Generates a workflow from a run, param & config file.")
-parser.add_argument("-H", "--host", dest="host", required=True, help="Database host.")
-parser.add_argument("-u", "--username", dest="username", required=True, help="Database user.")
-parser.add_argument("-p", "--password", dest="password", required=True, help="Database user password.")
+parser.add_argument("-H", "--host", dest="host", default="localhost", help="Database host. (default: %(default)s)")
+parser.add_argument("-u", "--username", dest="username", help="Database username (if required).")
+parser.add_argument("-p", "--password", dest="password", help="Database password (if required).")
parser.add_argument("-d", "--dir", dest="dir", required=True, help="Directory name to generate files in.")
parser.add_argument("--param", dest="param", required=True, help="Path to param file to load.")
parser.add_argument("--conf", dest="config", required=True, help="Path to config file to load.")
diff --git a/scripts/chip-job-download-gridfs b/scripts/chip-job-download-gridfs
index 46b6f9dc112db80477b209440a4bd57c753fc2f6..97e59f97c9739679b7567b37a4605fb6f91e1406 100755
--- a/scripts/chip-job-download-gridfs
+++ b/scripts/chip-job-download-gridfs
@@ -3,9 +3,9 @@ import chipathlon.utils
import argparse
parser = argparse.ArgumentParser(description="Download target file from GridFS.")
-parser.add_argument("-p", "--password", dest="password", required=True, help="Database user password.")
-parser.add_argument("-u", "--username", dest="username", required=True, help="Database user.")
-parser.add_argument("-H", "--host", dest="host", required=True, help="Database host.")
+parser.add_argument("-H", "--host", dest="host", default="localhost", help="Database host. (default: %(default)s)")
+parser.add_argument("-u", "--username", dest="username", help="Database username (if required).")
+parser.add_argument("-p", "--password", dest="password", help="Database password (if required).")
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.")
diff --git a/scripts/chip-job-save-result b/scripts/chip-job-save-result
index df2b8eacaaf02996f1212d5ca3e4bd56408813bd..8dbf27d5b1602490ded48121e86c0ae9b0dc590e 100755
--- a/scripts/chip-job-save-result
+++ b/scripts/chip-job-save-result
@@ -5,9 +5,9 @@ import yaml
import os
parser = argparse.ArgumentParser(description="Insert a bed file into the database.")
-parser.add_argument("-p", "--password", dest="password", required=True, help="Database user password.")
-parser.add_argument("-u", "--username", dest="username", required=True, help="Database user.")
-parser.add_argument("-d", "--host", dest="host", required=True, help="Database host.")
+parser.add_argument("-u", "--username", dest="username", help="Database username (if required).")
+parser.add_argument("-p", "--password", dest="password", help="Database password (if required).")
+parser.add_argument("-d", "--host", dest="host", default="localhost", help="Database host. (default: %(default)s)")
parser.add_argument("-f", "--file", dest="file", required=True, help="Path to result file.")
parser.add_argument("-m", "--meta", dest="meta", required=True, help="Path to meta yaml file.")
args = parser.parse_args()
diff --git a/scripts/chip-meta-download b/scripts/chip-meta-download
index f4e6fcbda3e4fb6ce8fe9398ae0dd40bf0ff6efd..7c1a674c70f8809ed6f3b1635b5fbede57247266 100644
--- a/scripts/chip-meta-download
+++ b/scripts/chip-meta-download
@@ -12,6 +12,7 @@ import datetime
parser = argparse.ArgumentParser(description="Download raw JSON for all experiments.")
parser.add_argument("-o", "--output-dir", dest="outputdir", default=os.getcwd(), help="Output directory. (default: %(default)s)")
+parser.add_argument("-q", "--quiet", action='store_true', help="Quiet mode. Do not print progress information. (default: false)")
args = parser.parse_args()
encode_baseurl = "https://www.encodeproject.org/experiments/"
@@ -39,7 +40,8 @@ for i, exp_id in enumerate(exp_ids):
r = requests.get(exp_url, params=json_arg)
with open(os.path.join(args.outputdir, "data", "%s.json" % (exp_id,)), "w") as wh:
wh.write(r.text)
-
- progress(i, total)
-progress(total, total)
+ if not args.quiet:
+ progress(i, total)
+if not args.quiet:
+ progress(total, total)
print
diff --git a/scripts/chip-meta-import b/scripts/chip-meta-import
index bd307c86eaa702443ac34480c6a20b9ab7898846..3ff18ee72a703fdf29bbbe912389ccd845256154 100644
--- a/scripts/chip-meta-import
+++ b/scripts/chip-meta-import
@@ -9,18 +9,20 @@ import os
import os.path
parser = argparse.ArgumentParser(description="Read per-experiment JSON files and create experiment and samples collections.")
-parser.add_argument("-H", "--host", dest="host", default="hcc-anvil-175-9.unl.edu", help="Database host. (default: %(default)s)")
-parser.add_argument("-u", "--username", dest="username", default="aknecht", required=True, help="Database user. (default: %(default)s)")
-parser.add_argument("-p", "--password", dest="password", required=True, help="Database user password.")
+parser.add_argument("-H", "--host", dest="host", default="localhost", help="Database host. (default: %(default)s)")
+parser.add_argument("-u", "--username", dest="username", help="Database username (if required).")
+parser.add_argument("-p", "--password", dest="password", help="Database password (if required).")
parser.add_argument("-i", "--input-dir", dest="inputdir", default=os.getcwd(), help="Directory containing per-experiment JSON files. (default: %(default)s)")
parser.add_argument("-d", "--drop", dest="drop", default=False, action="store_true", help="Drop data if it exists. (default: %(default)s)")
parser.add_argument("-s", "--samples", dest="samples", default=False, action="store_true", help="Only recreate the samples collection.")
+parser.add_argument("-q", "--quiet", action='store_true', help="Quiet mode. Do not print progress information. (default: false)")
args = parser.parse_args()
client = MongoClient(args.host)
db = client.chipseq
-db.authenticate(args.username, args.password, mechanism="SCRAM-SHA-1")
+if args.username:
+ db.authenticate(args.username, args.password, mechanism="SCRAM-SHA-1")
if args.drop:
if not args.samples:
@@ -30,7 +32,8 @@ if args.drop:
if not args.samples:
# Insert all experiment JSON files into DB
json_filelist = os.listdir(args.inputdir)
-
+ if not args.quiet:
+ print "Creating experiments collection..."
for i, json_file in enumerate(json_filelist):
if json_file.endswith("json"):
exp_file_contents = open(os.path.join(args.inputdir, json_file)).read()
@@ -42,7 +45,8 @@ if not args.samples:
db.experiments.insert_one(exp_json_data)
except Exception:
pass
- progress(i, len(json_filelist))
+ if not args.quiet:
+ progress(i, len(json_filelist))
organism = {
"mm": "mouse",
@@ -59,6 +63,8 @@ cursor = db.experiments.find({
total = cursor.count()
# Create the samples collection using the 'files' value from each experiment
+if not args.quiet:
+ print "\nCreating samples collection..."
for i, document in enumerate(cursor):
for f in document["files"]:
doc = {}
@@ -84,8 +90,8 @@ for i, document in enumerate(cursor):
db.samples.update_one({'_id': result.inserted_id}, {"$set": f})
except Exception:
pass
- progress(i, total)
+ if not args.quiet:
+ progress(i, total)
-progress(total, total)
print
cursor.close()