all tests pass

server/tests/unit/services/test_assembly.py

@@ -10,7 +10,6 @@
 def test_init_from_id_wrong_version(Session, setup, data_path):
     with Session() as session, session.begin():
         session.add_all(setup)
-    # excinfo.value contains msg
     with pytest.raises(AssemblyVersionError) as exc:
         service = AssemblyService.from_id(Session(), assembly_id=3)
     assert (

server/tests/unit/services/test_data_importer.py

@@ -84,10 +84,19 @@ def _get_data_with_header(fmt):
 
 
 @pytest.mark.parametrize(
-    "fmt",
-    [("minimum"), ("chrom"), ("strand"), ("maximum"), ("association")],
+    "fmt,msg",
+    [
+        ("minimum", "Value start: -1 out of range."),
+        (
+            "chrom",
+            "Unrecognized chrom: A. Ignore this warningfor scaffolds and contigs, otherwise this could be due to misformatting!",
+        ),
+        ("strand", "Unrecognized strand: ."),
+        ("maximum", "Value score: 200 out of range."),
+        ("association", "Unrecognized name: m5C."),
+    ],
 )
-def test_importer_parse_record_fail(fmt, Session, EUF_specs):
+def test_importer_parse_record_fail(fmt, msg, Session, EUF_specs):
     format, version, specs = EUF_specs
     expected_record = _get_record(fmt)
     importer = EUFDataImporter(
@@ -98,8 +107,10 @@ def test_importer_parse_record_fail(fmt, Session, EUF_specs):
         seqids=["1"],
         specs_ver=version,
     )
-    with pytest.raises(ValueError) as excinfo:
+    with pytest.raises(ValueError) as exc:
         importer.parse_record(expected_record)
+    assert str(exc.value) == msg
+    assert exc.type == ValueError
 
 
 def test_importer_parse_record(Session, EUF_specs):
@@ -237,8 +248,12 @@ def parse_record(record):
             return record
 
     importer = TestBaseImporter()
-    with pytest.raises(Exception) as excinfo:
+    with pytest.raises(Exception) as exc:
         importer._validate_columns()
+    assert (
+        str(exc.value)
+        == "Column name chromStart doesn't match any of the ORM mapped attribute names for Data. This can be caused by a file header with wrong column names, or a change in model declaration. Aborting transaction!"
+    )
 
 
 def test_base_importer_comment_fail(Session):
@@ -257,5 +272,7 @@ def __init__(self):
         def parse_record(record):
             return record
 
-    with pytest.raises(ValueError) as excinfo:
+    with pytest.raises(ValueError) as exc:
         importer = TestBaseImporter()
+    assert str(exc.value) == "Maximum length of 1 expected, got 2 for comment."
+    assert exc.type == ValueError

server/tests/unit/services/test_header_importer.py

@@ -91,13 +91,39 @@ def _get_header(EUF_specs, fmt=None):
     return StringIO(string)
 
 
+@pytest.mark.parametrize(
+    "fmt,error,msg",
+    [
+        (
+            "version",
+            SpecsError,
+            "Unknown or outdated version bedRModv0.0.",
+        ),  # wrong version
+        ("EOF", EOFError, "filen"),  # empty
+    ],
+)
+def test_importer_read_version_fail(fmt, error, msg, Session, EUF_specs):
+    format, version, specs = EUF_specs
+    handle = _get_header(EUF_specs, fmt)
+    importer = EUFHeaderImporter(
+        Session(),
+        filen="filen",
+        handle=handle,
+        smid="ABCDEFGH",
+        eufid="123456789ABC",
+        title="Title",
+    )
+    with pytest.raises(error) as exc:
+        importer._read_version()
+    assert str(exc.value) == msg
+    assert exc.type == error
+
+
 @pytest.mark.parametrize(
     "fmt",
     [
         (None),  # expected version
         ("string"),  # wrong format but right version
-        ("version"),  # wrong version
-        ("EOF"),  # empty
     ],
 )
 def test_importer_read_version(fmt, Session, EUF_specs):
@@ -111,26 +137,42 @@ def test_importer_read_version(fmt, Session, EUF_specs):
         eufid="123456789ABC",
         title="Title",
     )
-    if fmt == "version":
-        with pytest.raises(SpecsError) as excinfo:
-            importer._read_version()
-    elif fmt == "EOF":
-        with pytest.raises(EOFError) as excinfo:
-            importer._read_version()
-    else:
-        importer._read_version()
-        assert version == importer._specs_ver
-        assert len(specs["headers"]) == importer._num_cols
-        # ignore fileformat
-        assert specs["required"][1:] == importer._required
+    importer._read_version()
+    assert version == importer._specs_ver
+    assert len(specs["headers"]) == importer._num_cols
+    # ignore fileformat
+    assert specs["required"][1:] == importer._required
+
+
+@pytest.mark.parametrize(
+    "fmt,msg",
+    [
+        ("misformatted", "#organism=."),
+        ("missing", "#annotation_version=."),
+    ],
+)
+def test_importer_parse_lines_fail(fmt, msg, Session, EUF_specs):
+    handle = _get_header(EUF_specs, fmt)
+    importer = EUFHeaderImporter(
+        Session(),
+        filen="filen",
+        handle=handle,
+        smid="ABCDEFGH",
+        eufid="123456789ABC",
+        title="Title",
+    )
+    importer._lino = 1
+    importer._read_version()
+    with pytest.raises(SpecsError) as exc:
+        importer._parse_lines()
+    assert str(exc.value) == f"Missing or misformatted header: {msg}"
+    assert exc.type == SpecsError
 
 
 @pytest.mark.parametrize(
     "fmt",
     [
         ("full"),
-        ("misformatted"),
-        ("missing"),
         ("longer"),
         ("disordered"),
     ],
@@ -147,23 +189,19 @@ def test_importer_parse_lines(fmt, Session, EUF_specs):
     )
     importer._lino = 1
     importer._read_version()
-    if fmt in ["full", "longer", "disordered"]:
-        importer._parse_lines()
-        assert importer._lino == importer._num_cols
-        assert importer.taxid == 9606
-        assert importer.assembly == "GRCh38"
-        assert importer._header["id"] == "123456789ABC"
-        assert importer._header["project_id"] == "ABCDEFGH"
-        assert importer._header["title"] == "Title"
-        assert importer._header["modification_type"] == "RNA"
-        assert importer._header["sequencing_platform"] == "Sequencing platform"
-        assert importer._header["basecalling"] is None
-        assert importer._header["bioinformatics_workflow"] == "Workflow"
-        assert importer._header["experiment"] == "Description of experiment."
-        assert importer._header["external_source"] is None
-    else:
-        with pytest.raises(SpecsError) as excinfo:
-            importer._parse_lines()
+    importer._parse_lines()
+    assert importer._lino == importer._num_cols
+    assert importer.taxid == 9606
+    assert importer.assembly == "GRCh38"
+    assert importer._header["id"] == "123456789ABC"
+    assert importer._header["project_id"] == "ABCDEFGH"
+    assert importer._header["title"] == "Title"
+    assert importer._header["modification_type"] == "RNA"
+    assert importer._header["sequencing_platform"] == "Sequencing platform"
+    assert importer._header["basecalling"] is None
+    assert importer._header["bioinformatics_workflow"] == "Workflow"
+    assert importer._header["experiment"] == "Description of experiment."
+    assert importer._header["external_source"] is None
 
 
 @pytest.mark.parametrize(
@@ -188,8 +226,13 @@ def test_importer_validate_columns(fmt, Session, EUF_specs):
     if fmt == "columns_extra":
         importer._validate_columns()
     else:
-        with pytest.raises(SpecsError) as excinfo:
+        with pytest.raises(SpecsError) as exc:
             importer._validate_columns()
+        assert (
+            str(exc.value)
+            == "Column count (header) doesn't match required count at row 2 for bedRModv1.7."
+        )
+        assert exc.type == SpecsError
 
 
 def test_importer(Session, EUF_specs):

server/tests/unit/services/test_project.py

@@ -139,8 +139,10 @@ def test_project_validate_keys_error(
         metadata_fmt=metadata_fmt,
         missing_key=missing_key,
     )
-    with pytest.raises(KeyError):
+    with pytest.raises(KeyError) as exc:
         ProjectService(Session(), project)._validate_keys()
+    assert str(exc.value) == f"'Keys not found: {missing_key}.'"
+    assert exc.type == KeyError
 
 
 def test_project_add_selection(Session, setup, project_template, data_path):
@@ -216,9 +218,12 @@ def test_project_validate_existing_entry(
         missing_key=missing_key,
     )
 
-    # excinfo.value contains msg
-    with pytest.raises(DuplicateProjectError) as excinfo:
+    with pytest.raises(DuplicateProjectError) as exc:
         ProjectService(Session(), project)._validate_entry()
+    assert (
+        str(exc.value)
+        == f"At least one similar record exists with SMID = {smid} and title = Title. Aborting transaction!"
+    )
 
 
 def test_project_validate_entry(Session, project_template, data_path):