added snapshot warning checks

tests/__snapshots__/test_parse_study.ambr

@@ -0,0 +1,86 @@
+# serializer version: 1
+# name: test_study_reader_minimal_study
+  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:	
+    ''',
+  ])
+# ---
+# name: test_study_reader_minimal_study_iostring
+  list([
+    '''
+      Investigation with only one study contains metadata:
+      	ID:	i_minimal
+      	Title:	Minimal Investigation
+      	Path:	<no file>
+      	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:	
+    ''',
+  ])
+# ---
+# name: test_study_reader_minimal_study_iostring2
+  list([
+    '''
+      Investigation with only one study contains metadata:
+      	ID:	i_minimal
+      	Title:	Minimal Investigation
+      	Path:	<no file>
+      	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:	
+    ''',
+  ])
+# ---
+# name: test_study_reader_small_study
+  list([
+    '''
+      Investigation with only one study contains metadata:
+      	ID:	i_small
+      	Title:	Small Investigation
+      	Path:	i_small.txt
+      	Submission Date:	
+      	Public Release Date:	None
+      	Prefer recording metadata in the study section.
+    ''',
+    '''
+      Assay without platform:
+      Path:	a_small.txt
+      Measurement Type:	exome sequencing assay
+      Technology Type:	nucleotide sequencing
+      Technology Platform:	
+    ''',
+  ])
+# ---
+# name: test_study_reader_small_study.1
+  list([
+    "Found annotated material/file without name: Material(type='Sample Name', unique_name='S1-Empty Sample Name-13-5', name='', extract_label=None, characteristics=(Characteristics(name='status', value=['1'], unit=None),), comments=(), factor_values=(FactorValue(name='treatment', value=[''], unit=None),), material_type=None, headers=['Sample Name', 'Characteristics[status]', 'Factor Value[treatment]'])",
+  ])
+# ---

tests/test_parse_study.py

@@ -7,6 +7,8 @@
 import os
 
 import pytest
+from syrupy.assertion import SnapshotAssertion
+from typing import Iterator, TextIO
 
 from altamisa.constants import table_headers
 from altamisa.exceptions import IsaWarning
@@ -69,7 +71,7 @@ def test_study_row_reader_minimal_study(minimal_investigation_file, minimal_stud
     assert expected == first_row[2]
 
 
-def test_study_reader_minimal_study(minimal_investigation_file, minimal_study_file):
+def test_study_reader_minimal_study(minimal_investigation_file, minimal_study_file, snapshot: SnapshotAssertion):
     """Use ``StudyReader`` to read in minimal study file.
 
     Using the ``StudyReader`` instead of the ``StudyRowReader`` gives us
@@ -81,7 +83,7 @@ def test_study_reader_minimal_study(minimal_investigation_file, minimal_study_fi
         InvestigationValidator(investigation).validate()
 
     # Check warnings
-    assert 2 == len(record)
+    assert snapshot == [str(r.message) for r in record]
 
     # Create new row reader and check read headers
     reader = StudyReader.from_stream("S1", minimal_study_file)
@@ -318,15 +320,15 @@ def test_study_row_reader_small_study(small_investigation_file, small_study_file
     assert expected == third_row[2]
 
 
-def test_study_reader_small_study(small_investigation_file, small_study_file):
+def test_study_reader_small_study(small_investigation_file, small_study_file, snapshot: SnapshotAssertion):
     """Use ``StudyReader`` to read in small study file."""
     # Load investigation (tested elsewhere)
     with pytest.warns(IsaWarning) as record:
         investigation = InvestigationReader.from_stream(small_investigation_file).read()
         InvestigationValidator(investigation).validate()
 
     # Check warnings
-    assert 2 == len(record)
+    assert snapshot == [str(r.message) for r in record]
 
     # Create new row reader and check read headers
     reader = StudyReader.from_stream("S1", small_study_file)
@@ -337,7 +339,7 @@ def test_study_reader_small_study(small_investigation_file, small_study_file):
     with pytest.warns(IsaWarning) as record:
         StudyValidator(investigation, investigation.studies[0], study).validate()
     # Check warnings
-    assert 1 == len(record)
+    assert snapshot == [str(r.message) for r in record]
 
     # Check results
     assert os.path.normpath(str(study.file)).endswith(os.path.normpath("data/i_small/s_small.txt"))
@@ -559,15 +561,15 @@ def test_study_reader_small_study(small_investigation_file, small_study_file):
     assert expected == study.arcs
 
 
-def test_study_reader_minimal_study_iostring(minimal_investigation_file, minimal_study_file):
+def test_study_reader_minimal_study_iostring(minimal_investigation_file, minimal_study_file, snapshot: SnapshotAssertion):
     # Load investigation (tested elsewhere)
     stringio = io.StringIO(minimal_investigation_file.read())
     investigation = InvestigationReader.from_stream(stringio).read()
     with pytest.warns(IsaWarning) as record:
         InvestigationValidator(investigation).validate()
 
     # Check warnings
-    assert 2 == len(record)
+    assert snapshot == [str(r.message) for r in record]
 
     # Create new study reader and read from StringIO with original filename indicated
     stringio = io.StringIO(minimal_study_file.read())
@@ -588,15 +590,15 @@ def test_study_reader_minimal_study_iostring(minimal_investigation_file, minimal
     assert 2 == len(study.arcs)
 
 
-def test_study_reader_minimal_study_iostring2(minimal_investigation_file, minimal_study_file):
+def test_study_reader_minimal_study_iostring2(minimal_investigation_file, minimal_study_file, snapshot: SnapshotAssertion):
     # Load investigation (tested elsewhere)
     stringio = io.StringIO(minimal_investigation_file.read())
     investigation = InvestigationReader.from_stream(stringio).read()
     with pytest.warns(IsaWarning) as record:
         InvestigationValidator(investigation).validate()
 
     # Check warnings
-    assert 2 == len(record)
+    assert snapshot == [str(r.message) for r in record]
 
     # Create new study reader and read from StringIO with no filename indicated
     stringio = io.StringIO(minimal_study_file.read())