addapt to ruamel changes in tabs reporting

Author: mr-c

schema_salad/codegen.py

@@ -13,15 +13,14 @@
 )
 from urllib.parse import urlsplit
 
-
 from . import schema
 from .codegen_base import CodeGenBase
 from .exceptions import SchemaSaladException
 from .java_codegen import JavaCodeGen
 from .python_codegen import PythonCodeGen
-from .typescript_codegen import TypeScriptCodeGen
 from .ref_resolver import Loader
 from .schema import shortname
+from .typescript_codegen import TypeScriptCodeGen
 from .utils import aslist
 
 FIELD_SORT_ORDER = ["id", "class", "name"]

schema_salad/ref_resolver.py

@@ -91,9 +91,10 @@ def to_validation_exception(e: MarkedYAMLError) -> ValidationException:
 
     if e.context:
         parent = ValidationException(e.context)
-        mark = e.context_mark
-        parent.file = re.sub(fname_regex, "", mark.name)
-        parent.start = (mark.line + 1, mark.column + 1)
+        context_mark = e.context_mark
+        if context_mark:
+            parent.file = re.sub(fname_regex, "", context_mark.name)
+            parent.start = (context_mark.line + 1, context_mark.column + 1)
         parent.end = None
         parent.children = [exc]
         return parent

schema_salad/tests/test_cwl11.py

@@ -14,6 +14,7 @@
 from _pytest.tmpdir import TempPathFactory
 
 from schema_salad.avro.schema import Names, SchemaParseException
+from schema_salad.exceptions import ValidationException
 from schema_salad.ref_resolver import Loader
 from schema_salad.schema import load_and_validate, load_schema
 
@@ -64,3 +65,13 @@ def test_outputBinding(cwl_v1_2_schema: SchemaType) -> None:
         cwl_v1_2_schema, src="test_real_cwl/bio-cwl-tools/bamtools_stats.cwl"
     )
     print(f"the res:{res}")
+
+
+def test_yaml_tab_error(cwl_v1_2_schema: SchemaType) -> None:
+    """Tabs in the file."""
+    with pytest.raises(
+        ValidationException,
+        match=r".+found\s+character\s+'\\t'\s+that\s+cannot\s+start\s+any\s+token$",
+    ):
+        res = load_cwl(cwl_v1_2_schema, src="test_real_cwl/tabs_rna_seq_workflow.cwl")
+        print(res)

schema_salad/tests/test_real_cwl/tabs_rna_seq_workflow.cwl

@@ -0,0 +1,56 @@
+cwlVersion: v1.2
+class: Workflow
+
+inputs:
+        rna_reads_human: File
+	ref_genome: Directory
+        annotations: File
+
+steps:
+ quality_control:
+ run: bio-cwl-tools/fastqc/fastqc_2.cwl
+ in:
+ reads_file: rna_reads_human
+ out: [html_file]
+
+mapping_reads:
+ requirements:
+ ResourceRequirement:
+ ramMin: 9000
+ run: bio-cwl-tools/STAR/STAR-Align.cwl
+ in:
+ RunThreadN: {default: 4}
+ GenomeDir: ref_genome
+ ForwardReads: rna_reads_human
+ OutSAMtype: {default: BAM}
+ SortedByCoordinate: {default: true}
+ OutSAMunmapped: {default: Within}
+ out: [alignment]
+
+index_alignment:
+ run: bio-cwl-tools/samtools/samtools_index.cwl
+ in:
+ bam_sorted: mapping_reads/alignment
+ out: [bam_sorted_indexed]
+
+count_reads:
+ requirements:
+ ResourceRequirement:
+ ramMin: 500
+ run: bio-cwl-tools/subread/featureCounts.cwl
+ in:
+ mapped_reads: index_alignment/bam_sorted_indexed
+ annotations: annotations
+ out: [featurecounts]
+
+outputs:
+qc_html:
+ type: File
+ outputSource: quality_control/html_file
+ bam_sorted_indexed:
+ type: File
+ outputSource: index_alignment/bam_sorted_indexed
+ featurecounts:
+ type: File
+ outputSource: count_reads/featurecounts
+

schema_salad/typescript_codegen.py

@@ -17,11 +17,11 @@
 
 import pkg_resources
 
-from . import schema, _logger
+from . import _logger, schema
 from .codegen_base import CodeGenBase, TypeDef
 from .exceptions import SchemaException
-from .schema import shortname
 from .java_codegen import _ensure_directory_and_write, _safe_makedirs
+from .schema import shortname
 
 
 def doc_to_doc_string(doc: Optional[str], indent_level: int = 0) -> str:

typeshed/typing.pyi

@@ -402,6 +402,7 @@ class ItemsView(
     def __iter__(self) -> Iterator[Tuple[_KT_co, _VT_co]]: ...
     if sys.version_info >= (3, 8):
         def __reversed__(self) -> Iterator[Tuple[_KT_co, _VT_co]]: ...
+
     def __or__(self, o: Iterable[_T]) -> Set[Union[Tuple[_KT_co, _VT_co], _T]]: ...
     def __ror__(self, o: Iterable[_T]) -> Set[Union[Tuple[_KT_co, _VT_co], _T]]: ...
     def __sub__(self, o: Iterable[Any]) -> Set[Tuple[_KT_co, _VT_co]]: ...
@@ -417,6 +418,7 @@ class KeysView(MappingView, AbstractSet[_KT_co], Generic[_KT_co]):
     def __iter__(self) -> Iterator[_KT_co]: ...
     if sys.version_info >= (3, 8):
         def __reversed__(self) -> Iterator[_KT_co]: ...
+
     def __or__(self, o: Iterable[_T]) -> Set[Union[_KT_co, _T]]: ...
     def __ror__(self, o: Iterable[_T]) -> Set[Union[_KT_co, _T]]: ...
     def __sub__(self, o: Iterable[Any]) -> Set[_KT_co]: ...
@@ -691,6 +693,7 @@ class NamedTuple(Tuple[Any, ...]):
         def _asdict(self) -> Dict[str, Any]: ...
     else:
         def _asdict(self) -> collections.OrderedDict[str, Any]: ...
+
     def _replace(self: _T, **kwargs: Any) -> _T: ...
 
 # Internal mypy fallback type for all typed dicts (does not exist at runtime)
@@ -714,6 +717,7 @@ def type_check_only(func_or_cls: _C) -> _C: ...
 
 if sys.version_info >= (3, 7):
     from types import CodeType
+
     class ForwardRef:
         __forward_arg__: str
         __forward_code__: CodeType