Tests

src/efs_distributed/measurements/measurementManager.py

@@ -2,7 +2,6 @@
 from aiocache.serializers import JsonSerializer
 import pandas as pd
 from .measurementClass import DbMeasurement, FileMeasurement, ComputedMeasurement
-from efs_trackhub import TrackHub
 from efs_parser import GtfParsedFile, TbxFile, BigBed
 import ujson
 import requests
@@ -267,7 +266,7 @@ def import_files(self, fileSource, fileHandler=None, genome=None):
             json_string = f.read()
 
         records = ujson.loads(json_string)
-        self.import_records(records, fileHandler=fileHandler, genome=genome)
+        return self.import_records(records, fileHandler=fileHandler, genome=genome)
 
     def import_records(self, records, fileHandler=None, genome=None):
         """Import measurements from a list of records (usually from a decoded json string)

tests/test_distributed.py

@@ -0,0 +1,63 @@
+import pytest
+import os
+from efs_distributed.handler import FileHandlerProcess
+from efs_distributed.measurements import MeasurementManager
+from distributed import Client
+import asyncio
+import sys
+records = [{
+                   'url': 'https://egg2.wustl.edu/roadmap/data/byFileType/signal/consolidated/macs2signal/foldChange/E079-H3K27me3.fc.signal.bigwig',
+                   'file_type': 'bigwig', 'datatype': 'bp', 'name': 'E079-H3K27me3', 'id': 'E079-H3K27me3',
+                   'genome': 'hg19', 'annotation': {'group': 'digestive', 'tissue': 'Esophagus', 'marker': 'H3K27me3'}},
+               {
+                   'url': 'https://egg2.wustl.edu/roadmap/data/byFileType/signal/consolidated/macs2signal/foldChange/E106-H3K27me3.fc.signal.bigwig',
+                   'file_type': 'bigwig', 'datatype': 'bp', 'name': 'E106-H3K27me3', 'id': 'E106-H3K27me3',
+                   'genome': 'hg19',
+                   'annotation': {'group': 'digestive', 'tissue': 'Sigmoid Colon', 'marker': 'H3K27me3'}}]
+mMgr = MeasurementManager()
+fms = mMgr.import_records(records, genome="hg19")
+
+res = asyncio.run(fms[0].get_data("chr1", 1000000, 1002000, bins=100))
+df = res[0]
+def test_columns():
+    columns = df.columns.tolist()
+    assert columns==['start', 'end', 'E079-H3K27me3']
+
+def test_range():
+    start = 1000000
+    end = 1002000
+    for _, row in df.iterrows():
+        assert (row['start'] <= end or row['end'] >= start)
+
+
+def test_get_bytes():
+    mMgr = MeasurementManager()
+    fms = mMgr.import_records(records, genome="hg19")
+    res , err = asyncio.run(fms[0].get_byteRanges("chr1", 1000000, 1002000, bins=100))
+    df = res
+    size = sys.getsizeof(df)
+    assert size == 10727
+
+def test_bin_rows():
+    mMgr = MeasurementManager()
+    fms = mMgr.import_records(records, genome="hg19")
+    res = asyncio.run(fms[0].get_data("chr1", 1000000, 1002000, bins=100))
+    df = res[0]
+    rows = len(df)
+    assert rows == 100
+
+def test_bin_rows_from_file():
+    mMgr = MeasurementManager()
+    fms = mMgr.import_files("test_json.json", genome="hg19")
+    res = asyncio.run(fms[0].get_data("chr1", 1000000, 1002000, bins=100))
+    df = res[0]
+    rows = len(df)
+    assert rows == 100
+
+def test_mean():
+    mMgr = MeasurementManager()
+    fms = mMgr.import_records(records, genome="hg19")
+    res = asyncio.run(fms[0].get_data("chr1", 1000000, 1002000, bins=100))
+    df = res[0]
+    mean = df['E079-H3K27me3'].mean()
+    assert mean == 1.6159404346346855

tests/test_json.json

@@ -0,0 +1 @@
+[{"url": "https://egg2.wustl.edu/roadmap/data/byFileType/signal/consolidated/macs2signal/foldChange/E079-H3K27me3.fc.signal.bigwig", "file_type": "bigwig", "datatype": "bp", "name": "E079-H3K27me3", "id": "E079-H3K27me3", "genome": "hg19", "annotation": {"group": "digestive", "tissue": "Esophagus", "marker": "H3K27me3"}}, {"url": "https://egg2.wustl.edu/roadmap/data/byFileType/signal/consolidated/macs2signal/foldChange/E106-H3K27me3.fc.signal.bigwig", "file_type": "bigwig", "datatype": "bp", "name": "E106-H3K27me3", "id": "E106-H3K27me3", "genome": "hg19", "annotation": {"group": "digestive", "tissue": "Sigmoid Colon", "marker": "H3K27me3"}}]