From 549e7cd01734a2ee6655de6da643aaa4cb410aa3 Mon Sep 17 00:00:00 2001
From: aknecht2 <aknecht2@unl.edu>
Date: Mon, 29 Feb 2016 16:11:00 -0600
Subject: [PATCH] Added new tests. Added all sample verification.
---
chipathlon/db.py | 27 +++++++++++++++++++++++++++
chipathlon/tester.py | 17 +++++++++++++++--
2 files changed, 42 insertions(+), 2 deletions(-)
diff --git a/chipathlon/db.py b/chipathlon/db.py
index 2eeef6e..8846474 100644
--- a/chipathlon/db.py
+++ b/chipathlon/db.py
@@ -22,6 +22,33 @@ class MongoDB(object):
return
+ def check_valid_samples(self):
+ cursor = self.db.experiments.aggregate([
+ {
+ "$match": {
+ "target": {"$exists": True},
+ "revoked_files.0": {"$exists": False},
+ "assembly.0": {"$exists": True},
+ "assembly.1": {"$exists": False}
+ }
+ },
+ {
+ "$lookup": {
+ "from": "samples",
+ "localField": "_id",
+ "foreignField": "experiment_id",
+ "as": "samples"
+ }
+ }
+ ])
+ total = 0
+ has_samples = 0
+ for document in cursor:
+ total += 1
+ if len(document["samples"]) > 0:
+ has_samples += 1
+ return (has_samples, total)
+
def get_samples(self, experiment_id):
valid = True
msg = ""
diff --git a/chipathlon/tester.py b/chipathlon/tester.py
index ad96938..389cac6 100644
--- a/chipathlon/tester.py
+++ b/chipathlon/tester.py
@@ -75,12 +75,23 @@ def exp_files_test_3():
print_test("Exp_Files_Test_3", not valid and msg == "Experiment with id 'ENCSR329RIP' does not have all required metadata (assembly, target, no revoked_files).")
return
-# Test8, multiple control experiments, no possible control_inputs
+# Test8, multiple control experiments
def exp_files_test_4():
valid, msg, data = mdb.get_samples("ENCSR000CWZ")
print_test("Exp_Files_Test_4", valid and msg == "Succesfully retrieved input files for experiment with id 'ENCSR000CWZ'." and len(data["control"]) == 4 and len(data["experiment"]) == 2)
return
+# Test9, multiple control experiments, no possible control_inputs
+def exp_files_test_5():
+ valid, msg, data = mdb.get_samples("ENCSR000DKB")
+ print_test("Exp_Files_Test_5", not valid and msg == "Experiment with id 'ENCSR000DKB' has '0' possible control inputs, and '3' possible experiment inputs.")
+ return
+
+def valid_samples():
+ has_samples, total = mdb.check_valid_samples()
+ print_test("Verify_All_Samples", has_samples == total)
+ return
+
tests = [
@@ -91,7 +102,9 @@ tests = [
exp_files_test_1,
exp_files_test_2,
exp_files_test_3,
- exp_files_test_4
+ exp_files_test_4,
+ exp_files_test_5,
+ valid_samples
]
for test in tests:
test()
--
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