chore: adding snapshot tests (#117)

Co-authored-by: Manuel Holtgrewe <manuel.holtgrewe@bih-charite.de>

requirements/test.txt

@@ -18,3 +18,5 @@ flake8 >=3.5.0
 isort
 
 pyright
+
+syrupy

tests/__snapshots__/test_apps.ambr

@@ -0,0 +1,65 @@
+# serializer version: 1
+# name: test_isatab2isatab
+  list([
+    '''
+      Investigation with only one study contains metadata:
+      	ID:	i_minimal
+      	Title:	Minimal Investigation
+      	Path:	i_minimal.txt
+      	Submission Date:	
+      	Public Release Date:	None
+      	Prefer recording metadata in the study section.
+    ''',
+    '''
+      Assay without platform:
+      Path:	a_minimal.txt
+      Measurement Type:	exome sequencing assay
+      Technology Type:	nucleotide sequencing
+      Technology Platform:	
+    ''',
+    'No reference headers available for section INVESTIGATION PUBLICATIONS. Applying default order.',
+    'No reference headers available for section INVESTIGATION CONTACTS. Applying default order.',
+    'No reference headers available for section STUDY DESIGN DESCRIPTORS. Applying default order.',
+    'No reference headers available for section STUDY PUBLICATIONS. Applying default order.',
+    'No reference headers available for section STUDY FACTORS. Applying default order.',
+    'No reference headers available for section STUDY CONTACTS. Applying default order.',
+  ])
+# ---
+# name: test_isatab2isatab_input_is_output
+  '<Result IsaException("Can\'t output ISA-tab files to same directory as as input: /home/runner/work/altamisa/tests/data/i_minimal == /home/runner/work/altamisa/tests/data/i_minimal")>'
+# ---
+# name: test_isatab_validate
+  list([
+    'Incomplete ontology source; found: , Incomplete 1, 1, Incomplete 1, ()',
+    'Incomplete ontology source; found: Incomplete 2, , 2, Incomplete 2, ()',
+    'Ontology source name including whitespace(s); found: Incomplete 2, , 2, Incomplete 2, ()',
+    'Incomplete ontology source; found: Incomplete 3, Incomplete 3, , Incomplete 3, ()',
+    'Ontology source name including whitespace(s); found: Incomplete 3, Incomplete 3, , Incomplete 3, ()',
+    'Incomplete ontology source; found: Incomplete 4, Incomplete 4, 4, , ()',
+    'Ontology source name including whitespace(s); found: Incomplete 4, Incomplete 4, 4, , ()',
+    '''
+      Investigation with only one study contains metadata:
+      	ID:	i_warnings
+      	Title:	Investigation with Warnings
+      	Path:	i_warnings.txt
+      	Submission Date:	
+      	Public Release Date:	None
+      	Prefer recording metadata in the study section.
+    ''',
+    'Invalid mail address: invalid_mail',
+    'Invalid phone/fax number: CALL-ME',
+    'Invalid phone/fax number: FAX-ME',
+    'Invalid pubmed_id string: not-pubmed',
+    'Invalid doi string: not-a-doi',
+    '''
+      Assay without platform:
+      Path:	a_warnings.txt
+      Measurement Type:	exome sequencing assay
+      Technology Type:	nucleotide sequencing
+      Technology Platform:	
+    ''',
+    'Assay path used more than once: a_warnings.txt',
+    "Found samples in assay 'a_warnings.txt' but not in parent study 's_warnings.txt':\\n0815-N2",
+    "Found samples in assay 'a_warnings.txt' but not in parent study 's_warnings.txt':\\n0815-N2",
+  ])
+# ---

tests/test_apps.py

@@ -4,6 +4,7 @@
 import os.path
 
 import pytest
+from syrupy.assertion import SnapshotAssertion
 from typer.testing import CliRunner
 
 from altamisa.apps import isatab2dot, isatab2isatab, isatab_validate
@@ -12,18 +13,18 @@
 runner = CliRunner()
 
 
-def test_isatab_validate():
+def test_isatab_validate(snapshot: SnapshotAssertion):
     i_file = os.path.join(os.path.dirname(__file__), "data", "i_warnings", "i_warnings.txt")
     argv = ["--input-investigation-file", i_file, "--show-duplicate-warnings"]
 
     with pytest.warns(IsaWarning) as record:
         result = runner.invoke(isatab_validate.app, argv)
         assert result.exit_code == 0
 
-    assert 17 == len(record)
+    assert snapshot == [str(r.message) for r in record]
 
 
-def test_isatab2isatab(tmpdir):
+def test_isatab2isatab(tmpdir, snapshot: SnapshotAssertion):
     i_file = os.path.join(os.path.dirname(__file__), "data", "i_minimal", "i_minimal.txt")
     argv = [
         "--input-investigation-file",
@@ -38,10 +39,10 @@ def test_isatab2isatab(tmpdir):
         result = runner.invoke(isatab2isatab.app, argv)
         assert result.exit_code == 0
 
-    assert 8 == len(record)
+    assert snapshot == [str(r.message) for r in record]
 
 
-def test_isatab2isatab_input_is_output(tmpdir):
+def test_isatab2isatab_input_is_output(tmpdir, snapshot: SnapshotAssertion):
     i_file = os.path.join(os.path.dirname(__file__), "data", "i_minimal", "i_minimal.txt")
     argv = [
         "--input-investigation-file",
@@ -54,7 +55,9 @@ def test_isatab2isatab_input_is_output(tmpdir):
 
     result = runner.invoke(isatab2isatab.app, argv)
     assert result.exit_code == 1
-    assert "Can't output ISA-tab files to same directory as as input" in str(result)
+    assert snapshot == str(result).replace(
+        os.path.dirname(__file__), "/home/runner/work/altamisa/tests"
+    )
 
 
 def test_isatab2dot(tmpdir):