Added examples. Created base db class with authentication>

chipathlon/db.py

 from pymongo import MongoClient
+import gridfs
+import sys
+import traceback
 
-def setup
+class MongoDB(object):
+
+    def __init__(self, host, username, password):
+        self.client = MongoClient(args.host)
+        self.db = client.chipseq
+        try:
+            self.db.authenticate(args.username, args.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
+
+    def load_bed(self, collection, result_id, bed_file, attributes = {}):
+
+        return
+
+    

examples/gridfs_example.py

+from pymongo import MongoClient
+import argparse
+from pprint import pprint
+import gridfs
+
+parser = argparse.ArgumentParser(description = "Perform a join between the experiment and sample collections.")
+parser.add_argument("--password", dest="password", required=True, help="Database user password.")
+parser.add_argument("--username", dest="username", default="aknecht", required=True, help="Database user.")
+parser.add_argument("--host", dest="host", default="hcc-anvil-241-41.unl.edu", required=True, help="Database host.")
+args = parser.parse_args()
+
+# Everything in a db named chipseq
+# Set up connection and authenticate
+
+client = MongoClient(args.host)
+db = client.chipseq
+db.authenticate(args.username, args.password, mechanism="SCRAM-SHA-1")
+
+gfs = gridfs.GridFS(db)
+
+# Put a file
+with open("join_example.py", "r") as rh:
+    gfs.put(rh, filename = "foo", attribute1 = "asdf", attribute2 = "asdf")
+
+# Find files
+cursor = gfs.find({
+    "filename": "foo",
+    "attribute1": "asdf"
+})
+
+for document in cursor:
+    print document.read()

examples/join_example.py

+from pymongo import MongoClient
+import argparse
+from pprint import pprint
+
+parser = argparse.ArgumentParser(description = "Perform a join between the experiment and sample collections.")
+parser.add_argument("--password", dest="password", required=True, help="Database user password.")
+parser.add_argument("--username", dest="username", default="aknecht", required=True, help="Database user.")
+parser.add_argument("--host", dest="host", default="hcc-anvil-241-41.unl.edu", required=True, help="Database host.")
+args = parser.parse_args()
+
+# Everything in a db named chipseq
+# Set up connection and authenticate
+
+client = MongoClient(args.host)
+db = client.chipseq
+db.authenticate(args.username, args.password, mechanism="SCRAM-SHA-1")
+
+cursor = db.experiments.aggregate([
+    {
+        "$lookup": {
+            "from": "samples",
+            "localField": "_id",
+            "foreignField": "experiment_id",
+            "as": "samples"
+        }
+    }
+    ## Potentially more aggregation steps here.
+])
+
+for document in cursor:
+    if len(document["samples"]) > 0:
+        pprint(document)
+        break