Updated tests

tests/conftest.py

@@ -0,0 +1,55 @@
+import pytest
+
+@pytest.fixture(scope="module",
+    params=[
+        (
+            'tests/data/Version1/images/',
+            'tests/data/Version1/images/Index.idx.xml',
+            'tests/data/Version1/config_v1.yml', 
+            'tests/data/Version1/load_data_version1.csv',
+            {
+                "488 long": "OrigRNA",
+                "Alexa 488": "OrigER",
+                "Alexa 568": "OrigAGP",
+                "Alexa 647": "OrigMito",
+                "HOECHST 33342": "OrigDNA",
+                "Brightfield": "OrigBrightfield"
+                },
+        ),
+        (
+            'tests/data/Version5/images/',
+            'tests/data/Version5/images/Index.idx.xml',
+            'tests/data/Version5/config_v5.yml', 
+            'tests/data/Version5/load_data_version5.csv',
+             {
+                "Brightfield high": "OrigBrightfield",
+                "Alexa 568": "OrigAGP",
+                "Alexa 647": "OrigMito",
+                "Alexa 488": "OrigER",
+                "488 650": "OrigRNA",
+                "Digital Phase Contrast": "OrigDPC"
+            },
+        ),
+        (
+            'tests/data/Version7/images/',
+            'tests/data/Version7/images/Index.xml',
+            'tests/data/Version7/config_v7.yml', 
+            'tests/data/Version7/load_data_version7.csv',
+                {
+                    "HOECHST 33342": "OrigDNA",
+                    "Alexa 568": "OrigAGP",
+                    "Alexa 647": "OrigMito",
+                    "Alexa 488": "OrigER",
+                    "Alexa 488 Em 650": "OrigRNA",
+                    "Brightfield": "OrigBrightfield",
+                    "405ex, 570-630-em)": "OrigActin"
+                },
+        ),
+    ],  
+    ids=["v1", "v5", "v7"],)
+def test_files(request):
+    index_directory, index_file, config_file, output_file, expected_channels = request.param
+    test_dict = {'index_directory':index_directory,'index_file':index_file,
+                 'config_file':config_file,'output_file':output_file,
+                 'expected_channels':expected_channels}
+    return test_dict

tests/test___main__.py

@@ -3,15 +3,14 @@
 import src.pe2loaddata.__main__
 
 
-def test_with_file():
+def test_with_file(test_files):
     runner = click.testing.CliRunner()
 
     command = src.pe2loaddata.__main__.main
-
     result = runner.invoke(command, [
-        "tests/data/config.yml",
+        test_files["config_file"],
         "--index-file",
-        "tests/data/images/Index.idx.xml",
+        test_files["index_file"],
         "test.csv"
 
     ])
@@ -20,23 +19,23 @@ def test_with_file():
 
     os.remove("test.csv")
 
-def test_with_directory():
+def test_with_directory(test_files):
     runner = click.testing.CliRunner()
 
     command = src.pe2loaddata.__main__.main
 
     result = runner.invoke(command, [
-        "tests/data/config.yml",
+        test_files["config_file"],
         "--index-directory",
-        "tests/data/images/",
+        test_files["index_directory"],
         "test.csv"
     ])
     assert result.exit_code == 0
 
     os.remove("test.csv")
 
-def test_with_import():
+def test_with_import(test_files):
     assert not os.path.exists("test.csv")
-    src.pe2loaddata.__main__.headless("tests/data/config.yml","test.csv",index_file="tests/data/images/Index.idx.xml",index_directory=os.curdir)
+    src.pe2loaddata.__main__.headless(test_files["config_file"],"test.csv",index_file=test_files["index_file"],index_directory=test_files["index_directory"])
     assert os.path.exists("test.csv")
     os.remove("test.csv")

tests/test_append_illum_cols.py

@@ -45,21 +45,14 @@ def test_check_dir_arg():
     except ArgumentTypeError:
         assert True
 
-def test_load_config():
-    pathname = "./tests/data/config.yml"
+def test_load_config(test_files):
+    pathname = test_files["config_file"]
 
     assert os.path.exists(pathname)
 
     channels = load_config(pathname)
 
-    expected_channels = {
-            "488 long": "OrigRNA",
-            "Alexa 488": "OrigER",
-            "Alexa 568": "OrigAGP",
-            "Alexa 647": "OrigMito",
-            "HOECHST 33342": "OrigDNA",
-            "Brightfield": "OrigBrightfield"
-    }
+    expected_channels = test_files["expected_channels"]
 
     assert channels == expected_channels
 
@@ -69,27 +62,18 @@ def test_parse_args():
     pass
 
 
-def test_main():
-    config_file = "./tests/data/config.yml"
-    input_csv = "./tests/data/load_data.csv"
-    illum_filetype = ".mat"
+def test_main(test_files):
+    config_file = test_files["config_file"]
+    input_csv = test_files["output_file"]
+    illum_filetype = ".npy"
     nrows = sum(1 for _ in open(input_csv)) - 1
 
-
-
-    expected_channels = {
-        "488 long": "OrigRNA",
-        "Alexa 488": "OrigER",
-        "Alexa 568": "OrigAGP",
-        "Alexa 647": "OrigMito",
-        "HOECHST 33342": "OrigDNA",
-        "Brightfield": "OrigBrightfield"
-    }
+    expected_channels = test_files["expected_channels"]
 
     assert os.path.exists(config_file)
     channels = load_config(config_file)
     illum_directory = "tests/data/illum/"
-    plate_id = "BR00100044"
+    plate_id = "BR00121482"
 
     assert nrows !=  {}
     assert channels == expected_channels
@@ -102,16 +86,16 @@ def test_main():
 
     os.remove('illum.csv')
 
-def test_write_csv():
-    config_file = "./tests/data/config.yml"
-    input_csv = "tests/data/load_data.csv"
-    illum_filetype = ".mat"
+def test_write_csv(test_files):
+    config_file = test_files["config_file"]
+    input_csv = test_files["output_file"]
+    illum_filetype = ".npy"
 
     nrows = sum(1 for _ in open(input_csv)) - 1
 
     channels = load_config(config_file)
     illum_directory = "tests/data/illum/"
-    plate_id = "BR00100044"
+    plate_id = "BR00121482"
 
     with open('illum.csv', 'w') as fd:
         writer = csv.writer(fd, lineterminator='\n')

tests/test_transformer.py

@@ -49,21 +49,14 @@ def test_parse_args():
     pass
 
 
-def test_load_config():
-    pathname = "./tests/data/config.yml"
+def test_load_config(test_files):
+    pathname = test_files["config_file"]
 
     assert os.path.exists(pathname)
 
     channels, metadata = load_config(pathname)
 
-    expected_channels = {
-        "488 long": "OrigRNA",
-        "Alexa 488": "OrigER",
-        "Alexa 568": "OrigAGP",
-        "Alexa 647": "OrigMito",
-        "HOECHST 33342": "OrigDNA",
-        "Brightfield": "OrigBrightfield"
-    }
+    expected_channels = test_files["expected_channels"]
 
     expected_metadata = {
         "AbsPositionZ": "AbsPositionZ",
@@ -95,16 +88,16 @@ def test_load_config():
     assert metadata == expected_metadata
 
 
-def test_write_csv():
-    config_file = "./tests/data/config.yml"
+def test_write_csv(test_files):
+    config_file = test_files["config_file"]
 
     assert os.path.exists(config_file)
 
     channels, metadata = load_config(config_file)
 
     channels = dict([(str(k).replace(" ", ""), v) for (k, v) in channels.items()])
 
-    index_file = "./tests/data/images/Index.idx.xml"
+    index_file = test_files["index_file"]
 
     handler = Handler()
 
@@ -117,7 +110,7 @@ def test_write_csv():
 
     paths = {}
 
-    index_directory = "./tests/data/images"
+    index_directory = test_files["index_directory"]
 
     for filename in os.listdir(index_directory):
         paths[filename] = index_directory
@@ -126,5 +119,20 @@ def test_write_csv():
         writer = csv.writer(fd, lineterminator='\n')
 
         write_csv(writer, images, plates, wells, maps, channels, metadata, paths)
+
+    gt = []
+    created = []
+
+    with open(test_files["output_file"]) as csvfile:
+        reader = csv.DictReader(csvfile)
+        for row in reader:
+            gt.append(row)
+
+    with open("example.csv") as csvfile:
+        reader = csv.DictReader(csvfile)
+        for row in reader:
+            created.append(row)
+
+    assert gt == created
 
     os.remove("example.csv")