Integration tests

README.md

@@ -24,3 +24,10 @@ cd app && python main.py
 docker build -t imuse-server .
 docker run -d -v $(pwd)/obj:/obj -p 80:80 imuse-server
 ```
+
+### Integration Tests
+To run the integration tests, start the service at localhost on port 8000 (see instructions above), then run the following:
+```
+python -m unittest discover -s test
+```
+Alternatively, you could change the `API_BASE` variable in `test/constants_for_tests.py` and run the tests against any running instance of the app.

requirements_dev.txt

@@ -0,0 +1 @@
+requests==2.19.1

test/constants_for_tests.py

@@ -0,0 +1 @@
+API_BASE = 'http://localhost:8000'

test/test_clustering.py

@@ -0,0 +1,31 @@
+import requests
+import json
+import unittest
+
+from constants_for_tests import *
+
+class TestClustering(unittest.TestCase):
+
+    def test_clustering(self):
+        url = API_BASE + '/clustering'
+        payload = {
+            "sources":["ICGC-BRCA-EU"],
+            "signatures":[
+                "COSMIC 1",
+                "COSMIC 2",
+                "COSMIC 3",
+                "COSMIC 5",
+                "COSMIC 6",
+                "COSMIC 8",
+                "COSMIC 13",
+                "COSMIC 17",
+                "COSMIC 18",
+                "COSMIC 20",
+                "COSMIC 26",
+                "COSMIC 30"
+            ]
+        }
+        r = requests.post(url, data=json.dumps(payload))
+        r.raise_for_status()
+        res = r.json()
+        self.assertEqual({'name', 'children'}, set(res.keys()))

test/test_data_listing.py

@@ -0,0 +1,27 @@
+import requests
+import unittest
+
+from constants_for_tests import *
+
+class TestDataListing(unittest.TestCase):
+
+    def test_data_listing(self):
+        url = API_BASE + '/data-listing'
+        r = requests.post(url)
+        r.raise_for_status()
+        res = r.json()
+        self.assertEqual(['sources', 'sigs', 'sig_presets'], list(res.keys()))
+        self.assertIn("ICGC-BRCA-EU", list(res['sources'].keys()))
+        brca_obj = {
+            "name": "Breast ER+ and HER2- Cancer - EU/UK",
+            "num_donors": 569,
+            "source": "ICGC",
+            "has_clinical": True,
+            "has_ssm": True,
+            "has_counts": True
+        }
+        self.assertEqual(brca_obj, res['sources']['ICGC-BRCA-EU'])
+        self.assertEqual({'name', 'description', 'index', 'publication'}, set(res['sigs'][0].keys()))
+        self.assertEqual({'group', 'id', 'cancer-types'}, set(res['sig_presets'][0].keys()))
+        self.assertEqual({'name', 'id', 'signatures'}, set(res['sig_presets'][0]['cancer-types'][0].keys()))
+

test/test_exposures.py

@@ -0,0 +1,52 @@
+import requests
+import json
+import unittest
+
+from constants_for_tests import *
+
+class TestExposures(unittest.TestCase):
+
+    def test_exposures(self):
+        url = API_BASE + '/exposures'
+        payload = {
+            "sources": ["ICGC-BRCA-EU"],
+            "signatures": [
+                "COSMIC 1",
+                "COSMIC 2",
+                "COSMIC 3",
+                "COSMIC 4",
+                "COSMIC 5",
+                "COSMIC 6",
+                "COSMIC 7",
+                "COSMIC 8",
+                "COSMIC 9",
+                "COSMIC 10",
+                "COSMIC 11",
+                "COSMIC 12",
+                "COSMIC 13",
+                "COSMIC 14",
+                "COSMIC 15",
+                "COSMIC 16",
+                "COSMIC 17",
+                "COSMIC 18",
+                "COSMIC 19",
+                "COSMIC 20",
+                "COSMIC 21",
+                "COSMIC 22",
+                "COSMIC 23",
+                "COSMIC 24",
+                "COSMIC 25",
+                "COSMIC 26",
+                "COSMIC 27",
+                "COSMIC 28",
+                "COSMIC 29",
+                "COSMIC 30",
+                "5* A"
+            ]
+        }
+        r = requests.post(url, data=json.dumps(payload))
+        r.raise_for_status()
+        res = r.json()
+        self.assertEqual(569, len(res))
+        self.assertEqual({'donor_id', 'proj_id', 'exposures', 'clinical'}, set(res[0].keys()))
+        self.assertEqual(31, len(res[0]['exposures']))

test/test_exposures_single_donor.py

@@ -0,0 +1,54 @@
+import requests
+import json
+import unittest
+
+from constants_for_tests import *
+
+class TestExposuresSingleDonor(unittest.TestCase):
+
+    def test_exposures_single_donor(self):
+        url = API_BASE + '/exposures-single-donor'
+        payload = {
+            "donor_id": "DO220823", 
+            "proj_id": "ICGC-BRCA-EU", 
+            "sources":["PCAWG-BRCA-EU"],
+            "signatures":[
+                "COSMIC 1",
+                "COSMIC 2",
+                "COSMIC 3",
+                "COSMIC 4",
+                "COSMIC 5",
+                "COSMIC 6",
+                "COSMIC 7",
+                "COSMIC 8",
+                "COSMIC 9",
+                "COSMIC 10",
+                "COSMIC 11",
+                "COSMIC 12",
+                "COSMIC 13",
+                "COSMIC 14",
+                "COSMIC 15",
+                "COSMIC 16",
+                "COSMIC 17",
+                "COSMIC 18",
+                "COSMIC 19",
+                "COSMIC 20",
+                "COSMIC 21",
+                "COSMIC 22",
+                "COSMIC 23",
+                "COSMIC 24",
+                "COSMIC 25",
+                "COSMIC 26",
+                "COSMIC 27",
+                "COSMIC 28",
+                "COSMIC 29",
+                "COSMIC 30",
+                "5* A"
+            ]
+        }
+        r = requests.post(url, data=json.dumps(payload))
+        r.raise_for_status()
+        res = r.json()
+        self.assertEqual(1, len(res))
+        self.assertEqual({'donor_id', 'proj_id', 'exposures', 'clinical'}, set(res[0].keys()))
+        self.assertEqual(31, len(res[0]['exposures']))

test/test_kataegis.py

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+import requests
+import json
+import unittest
+
+from constants_for_tests import *
+
+class TestKataegis(unittest.TestCase):
+
+    def test_kataegis(self):
+        url = API_BASE + '/kataegis'
+
+        payload = {
+            "sources":[
+                "ICGC-BRCA-EU"
+            ]
+        }
+        r = requests.post(url, data=json.dumps(payload))
+        r.raise_for_status()
+        res = r.json()
+        self.assertEqual(569, len(res.keys()))
+        self.assertEqual(4, len(res['DO217786']['kataegis']['1']))

test/test_rainfall.py

@@ -0,0 +1,24 @@
+import requests
+import json
+import csv
+import unittest
+
+from constants_for_tests import *
+
+class TestRainfall(unittest.TestCase):
+
+    def test_rainfall(self):
+        url = API_BASE + '/kataegis-rainfall'
+
+        payload = {
+            "proj_id": "ICGC-BRCA-EU",
+            "donor_id": "DO217786"
+        }
+        r = requests.post(url, data=json.dumps(payload))
+        r.raise_for_status()
+        decoded_content = r.content.decode('utf-8')
+
+        res = list(csv.reader(decoded_content.splitlines(), delimiter=','))
+        self.assertEqual({'chr', 'pos', 'cat', 'cat_index', 'mut_dist', 'kataegis'}, set(res[0]))
+
+        self.assertEqual(3107, len(res))

test/test_samples_with_signatures.py

@@ -0,0 +1,55 @@
+import requests
+import json
+import unittest
+
+from constants_for_tests import *
+
+class TestSamplesWithSignatures(unittest.TestCase):
+
+    def test_samples_with_signatures(self):
+        url = API_BASE + '/samples-with-signatures'
+
+        payload = {
+            "sources":["ICGC-BRCA-EU"],
+            "signatures":[
+                "COSMIC 1",
+                "COSMIC 2",
+                "COSMIC 3",
+                "COSMIC 4",
+                "COSMIC 5",
+                "COSMIC 6",
+                "COSMIC 7",
+                "COSMIC 8",
+                "COSMIC 9",
+                "COSMIC 10",
+                "COSMIC 11",
+                "COSMIC 12",
+                "COSMIC 13",
+                "COSMIC 14",
+                "COSMIC 15",
+                "COSMIC 16",
+                "COSMIC 17",
+                "COSMIC 18",
+                "COSMIC 19",
+                "COSMIC 20",
+                "COSMIC 21",
+                "COSMIC 22",
+                "COSMIC 23",
+                "COSMIC 24",
+                "COSMIC 25",
+                "COSMIC 26",
+                "COSMIC 27",
+                "COSMIC 28",
+                "COSMIC 29",
+                "COSMIC 30",
+                "5* A"
+            ]
+        }
+        r = requests.post(url, data=json.dumps(payload))
+        r.raise_for_status()
+        res = r.json()
+
+        self.assertEqual({'signatures', 'projects'}, set(res.keys()))
+        self.assertEqual(31, len(list(res['signatures'].keys())))
+        self.assertEqual(569, res['projects']['ICGC-BRCA-EU'])
+

test/test_signature.py

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+import requests
+import json
+import unittest
+
+from constants_for_tests import *
+
+class TestSignature(unittest.TestCase):
+
+    def test_signature(self):
+        url = API_BASE + '/signature'
+
+        payload = {
+            "signature": "COSMIC 1"
+        }
+        r = requests.post(url, data=json.dumps(payload))
+        r.raise_for_status()
+        res = r.json()
+
+        self.assertEqual({'data', 'meta'}, set(res.keys()))
+        self.assertEqual(96, len(res['data']))
+        self.assertEqual(["A[C>A]A", 0.011098326], res['data'][0])
+
+        self.assertEqual({'name', 'description', 'index', 'publication'}, set(res['meta'].keys()))
+
+    def test_another_signature(self):
+        url = API_BASE + '/signature'
+
+        payload = {
+            "signature": "COSMIC 2"
+        }
+        r = requests.post(url, data=json.dumps(payload))
+        r.raise_for_status()
+        res = r.json()
+
+        self.assertEqual(["A[C>A]A", 0.0006827080000000001], res['data'][0])