[med-svn] [Git][python-team/packages/python-schema-salad][upstream] New upstream version 8.2.20220204150214
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Sun Apr 10 16:53:38 BST 2022
Michael R. Crusoe pushed to branch upstream at Debian Python Team / packages / python-schema-salad
Commits:
1554e80c by Michael R. Crusoe at 2022-04-10T17:05:17+02:00
New upstream version 8.2.20220204150214
- - - - -
23 changed files:
- PKG-INFO
- README.rst
- mypy-requirements.txt
- requirements.txt
- schema_salad.egg-info/PKG-INFO
- schema_salad.egg-info/SOURCES.txt
- schema_salad.egg-info/requires.txt
- schema_salad/codegen.py
- schema_salad/java/main_utils/LoadingOptions.java
- schema_salad/java/pom.xml
- schema_salad/java_codegen.py
- schema_salad/ref_resolver.py
- schema_salad/schema.py
- + schema_salad/tests/class_field_test.yml
- schema_salad/tests/test_cwl11.py
- + schema_salad/tests/test_real_cwl/tabs_rna_seq_workflow.cwl
- schema_salad/tests/test_typescript_codegen.py
- schema_salad/typescript/package.json
- schema_salad/typescript/tsconfig.json
- schema_salad/typescript_codegen.py
- setup.cfg
- setup.py
- typeshed/typing.pyi
Changes:
=====================================
PKG-INFO
=====================================
@@ -1,6 +1,6 @@
Metadata-Version: 2.1
Name: schema-salad
-Version: 8.2.20220103095339
+Version: 8.2.20220204150214
Summary: Schema Annotations for Linked Avro Data (SALAD)
Home-page: https://github.com/common-workflow-language/schema_salad
Author: Common workflow language working group
@@ -32,7 +32,7 @@ Description: |Linux Build Status| |Code coverage| |Documentation Status| |CII Be
between document and record oriented data modeling and the Semantic
Web.
- The Schema Salad library is Python 3.6+ only.
+ The Schema Salad library is Python 3.7+ only.
Installation
------------
=====================================
README.rst
=====================================
@@ -23,7 +23,7 @@ generation, and transformation to RDF_. Salad provides a bridge
between document and record oriented data modeling and the Semantic
Web.
-The Schema Salad library is Python 3.6+ only.
+The Schema Salad library is Python 3.7+ only.
Installation
------------
=====================================
mypy-requirements.txt
=====================================
@@ -1,5 +1,4 @@
-mypy==0.921
+mypy==0.931
black>=19.10b0
types-pkg_resources
types-requests
-types-dataclasses;python_version < "3.7"
=====================================
requirements.txt
=====================================
@@ -1,7 +1,5 @@
ruamel.yaml>= 0.12.4, != 0.16.6, < 0.18
-rdflib>= 4.2.2, < 6.0.0;python_version<='3.6'
rdflib>= 4.2.2, < 7.0.0
-rdflib-jsonld>=0.4.0, <= 0.6.1;python_version<='3.6'
mistune>=0.8.1,<0.9
CacheControl==0.12.10
lockfile==0.12.2 # needed for CacheControl's FileCache
=====================================
schema_salad.egg-info/PKG-INFO
=====================================
@@ -1,6 +1,6 @@
Metadata-Version: 2.1
Name: schema-salad
-Version: 8.2.20220103095339
+Version: 8.2.20220204150214
Summary: Schema Annotations for Linked Avro Data (SALAD)
Home-page: https://github.com/common-workflow-language/schema_salad
Author: Common workflow language working group
@@ -32,7 +32,7 @@ Description: |Linux Build Status| |Code coverage| |Documentation Status| |CII Be
between document and record oriented data modeling and the Semantic
Web.
- The Schema Salad library is Python 3.6+ only.
+ The Schema Salad library is Python 3.7+ only.
Installation
------------
=====================================
schema_salad.egg-info/SOURCES.txt
=====================================
@@ -116,6 +116,7 @@ schema_salad/tests/Process.yml
schema_salad/tests/__init__.py
schema_salad/tests/bad_schema.yml
schema_salad/tests/bad_schema2.yml
+schema_salad/tests/class_field_test.yml
schema_salad/tests/cwl-pre.yml
schema_salad/tests/formattest2.cwl
schema_salad/tests/frag.yml
@@ -159,6 +160,7 @@ schema_salad/tests/foreign/foreign_prop4.cwl
schema_salad/tests/foreign/foreign_prop5.cwl
schema_salad/tests/foreign/foreign_prop6.cwl
schema_salad/tests/foreign/foreign_prop7.cwl
+schema_salad/tests/test_real_cwl/tabs_rna_seq_workflow.cwl
schema_salad/tests/test_real_cwl/ICGC-TCGA-PanCancer/PreprocessedFilesType.yaml
schema_salad/tests/test_real_cwl/ICGC-TCGA-PanCancer/preprocess_util.js
schema_salad/tests/test_real_cwl/ICGC-TCGA-PanCancer/preprocess_vcf.cwl
=====================================
schema_salad.egg-info/requires.txt
=====================================
@@ -6,10 +6,6 @@ mistune<0.9,>=0.8.1
CacheControl<0.13,>=0.11.7
lockfile>=0.9
-[:python_version <= "3.6"]
-rdflib<6.0.0,>=4.2.2
-rdflib-jsonld<=0.6.1,>=0.3.0
-
[docs]
sphinx>=2.2
sphinx-rtd-theme
=====================================
schema_salad/codegen.py
=====================================
@@ -13,15 +13,14 @@ from typing import (
)
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/java/main_utils/LoadingOptions.java
=====================================
@@ -94,7 +94,7 @@ public class LoadingOptions {
final ArrayList<String> sp = new ArrayList(Arrays.asList(splitbase.fragment.split("/")));
int n = scopedRef;
while (n > 0 && sp.size() > 0) {
- sp.remove(0);
+ sp.remove(sp.size()-1);
n -= 1;
}
sp.add(url);
=====================================
schema_salad/java/pom.xml
=====================================
@@ -8,7 +8,7 @@
<description><![CDATA[${project_description}]]></description>
<version>${version}</version>
<properties>
- <commonslang.version>3.7</commonslang.version>
+ <commonslang.version>3.12.0</commonslang.version>
<project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
<project.reporting.outputEncoding>UTF-8</project.reporting.outputEncoding>
<maven.compiler.source>8</maven.compiler.source>
@@ -31,7 +31,7 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-compiler-plugin</artifactId>
- <version>3.8.0</version>
+ <version>3.8.1</version>
<configuration>
<release>11</release>
<showDeprecation>true</showDeprecation>
@@ -53,18 +53,19 @@
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-surefire-plugin</artifactId>
- <version>2.21.0</version>
+ <version>2.22.2</version>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-javadoc-plugin</artifactId>
- <version>3.1.1</version>
+ <version>3.3.1</version>
<configuration>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-jar-plugin</artifactId>
+ <version>3.2.0</version>
<configuration>
<archive>
<manifestFile>src/main/resources/META-INF/MANIFEST.MF</manifestFile>
@@ -111,12 +112,22 @@
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
- <version>4.13.1</version>
+ <version>4.13.2</version>
</dependency>
<dependency>
<groupId>org.snakeyaml</groupId>
<artifactId>snakeyaml-engine</artifactId>
- <version>2.2.1</version>
+ <version>2.3</version>
+ </dependency>
+ <dependency>
+ <groupId>com.fasterxml.jackson.core</groupId>
+ <artifactId>jackson-databind</artifactId>
+ <version>2.12.6</version>
+ </dependency>
+ <dependency>
+ <groupId>com.fasterxml.jackson.dataformat</groupId>
+ <artifactId>jackson-dataformat-yaml</artifactId>
+ <version>2.10.4</version>
</dependency>
</dependencies>
<profiles>
=====================================
schema_salad/java_codegen.py
=====================================
@@ -446,11 +446,16 @@ public class {cls}Impl extends SavableImpl implements {cls} {{
"https://w3id.org/cwl/salad#array",
):
i = self.type_loader(type_declaration["items"])
+ instance_type = (
+ "java.util.List<String>"
+ if i.instance_type == "String"
+ else "java.util.List<Object>"
+ )
return self.declare_type(
TypeDef(
# special doesn't work out with subclassing, gotta be more clever
# instance_type="List<{}>".format(i.instance_type),
- instance_type="java.util.List<Object>",
+ instance_type=instance_type,
name=f"array_of_{i.name}",
init=f"new ArrayLoader({i.name})",
loader_type="Loader<java.util.List<{}>>".format(
=====================================
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/schema.py
=====================================
@@ -562,7 +562,7 @@ def make_valid_avro(
if "symbols" in avro:
avro["symbols"] = [avro_field_name(sym) for sym in avro["symbols"]]
return avro
- if isinstance(items, MutableSequence):
+ if items and isinstance(items, MutableSequence):
ret = []
for i in items:
ret.append(
=====================================
schema_salad/tests/class_field_test.yml
=====================================
@@ -0,0 +1,29 @@
+$base: "https://example.com/classFieldTest#"
+
+$namespaces:
+ classFieldTest: "https://example.com/classFieldTest#"
+
+$graph:
+- name: ClassFieldString
+ type: record
+ documentRoot: true
+ fields:
+ - name: "class"
+ jsonldPredicate:
+ "_id": "@type"
+ "_type": "@vocab"
+ type: string
+
+- name: ClassFieldEnum
+ type: record
+ documentRoot: true
+ fields:
+ - name: class
+ jsonldPredicate:
+ "_id": "@type"
+ "_type": "@vocab"
+ type:
+ type: enum
+ name: ClassFieldEnum_class
+ symbols:
+ - classFieldTest:ClassFieldEnum
\ No newline at end of file
=====================================
schema_salad/tests/test_cwl11.py
=====================================
@@ -14,6 +14,7 @@ import requests
from _pytest.tmpdir import TempPathFactory
from schema_salad.avro.schema import Names, SchemaParseException
+from schema_salad.exceptions import ValidationException
from schema_salad.ref_resolver import Loader
from schema_salad.schema import load_and_validate, load_schema
@@ -64,3 +65,13 @@ def test_outputBinding(cwl_v1_2_schema: SchemaType) -> None:
cwl_v1_2_schema, src="test_real_cwl/bio-cwl-tools/bamtools_stats.cwl"
)
print(f"the res:{res}")
+
+
+def test_yaml_tab_error(cwl_v1_2_schema: SchemaType) -> None:
+ """Tabs in the file."""
+ with pytest.raises(
+ ValidationException,
+ match=r".+found\s+character\s+'\\t'\s+that\s+cannot\s+start\s+any\s+token$",
+ ):
+ 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/tests/test_typescript_codegen.py
=====================================
@@ -46,6 +46,35 @@ def test_meta_schema_gen(tmp_path: Path) -> None:
)
+def test_class_field(tmp_path: Path) -> None:
+ schema_path = get_data_uri("tests/class_field_test.yml")
+ assert schema_path
+ target_dir = tmp_path / "target"
+
+ target_dir.mkdir()
+ typescript_codegen(schema_path, target_dir)
+
+ package_json_path = target_dir / "package.json"
+ assert package_json_path.exists
+
+ tests_dir = target_dir / "src" / "test"
+ assert tests_dir.exists()
+
+ with open(target_dir / "src" / "ClassFieldString.ts") as f:
+ assert (
+ " constructor ({loadingOptions, extensionFields, class_ = 'ClassFieldString'} :"
+ + " {loadingOptions?: LoadingOptions} & Internal.ClassFieldStringProperties) {\n"
+ in f.read()
+ )
+ with open(target_dir / "src" / "ClassFieldEnum.ts") as f:
+ assert (
+ " constructor ({loadingOptions, extensionFields, class_ = "
+ + "Internal.ClassFieldEnum_class.CLASSFIELDENUM} :"
+ + " {loadingOptions?: LoadingOptions} & Internal.ClassFieldEnumProperties) {\n"
+ in f.read()
+ )
+
+
def get_data_uri(resource_path: str) -> str:
path = get_data(resource_path)
assert path
=====================================
schema_salad/typescript/package.json
=====================================
@@ -2,9 +2,12 @@
"name": "${project_name}",
"version": "${version}",
"description": "${project_description}",
- "main": "index.js",
+ "main": "dist/index.js",
+ "types": "dist/index.d.ts",
"scripts": {
- "test": "nyc --reporter=lcov mocha --require ts-node/register src/test/**/*.ts"
+ "build": "rimraf ./dist && tsc",
+ "test": "nyc --reporter=lcov mocha --require ts-node/register src/test/**/*.ts",
+ "doc": "rimraf ./docs && typedoc src/index.ts"
},
"license": "${license_name}",
"devDependencies": {
@@ -22,13 +25,18 @@
"nyc": "^15.1.0",
"sinon": "^12.0.1",
"ts-node": "^10.4.0",
+ "typedoc": "^0.22.10",
"typescript": "^4.4.4",
- "codecov.io": "^0.1.6"
+ "codecov.io": "^0.1.6",
+ "rimraf": "^3.0.2"
},
"dependencies": {
"js-yaml": "^4.1.0",
"node-fetch": "^2.6.6",
"uri-js": "^4.4.1",
"uuid": "^8.3.2"
- }
+ },
+ "files": [
+ "/dist"
+ ]
}
=====================================
schema_salad/typescript/tsconfig.json
=====================================
@@ -12,6 +12,7 @@
},
"include": ["./src/**/*"],
"exclude": [
- "node_modules"
+ "node_modules",
+ "./src/test"
]
}
\ No newline at end of file
=====================================
schema_salad/typescript_codegen.py
=====================================
@@ -17,11 +17,11 @@ from typing import (
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:
@@ -495,14 +495,22 @@ export enum {enum_name} {{
doc_str=doc_to_doc_string(doc, indent_level=1)
)
)
- f.write(
- " {safename}{optionalstring}: {type}\n".format(
- safename=safename,
- type=fieldtype.instance_type,
- optionalstring=optionalstring,
+ if fieldname == "class":
+ f.write(
+ " {safename}{optionalstring}: {type}\n".format(
+ safename=safename,
+ type=fieldtype.instance_type,
+ optionalstring="?",
+ )
+ )
+ else:
+ f.write(
+ " {safename}{optionalstring}: {type}\n".format(
+ safename=safename,
+ type=fieldtype.instance_type,
+ optionalstring=optionalstring,
+ )
)
- )
-
if self.current_class_is_abstract:
return
@@ -525,13 +533,22 @@ export enum {enum_name} {{
)
)
if fieldname == "class":
- self.current_constructor_signature.write(
- ", {safename} = {type}.{val}".format(
- safename=safename,
- type=fieldtype.instance_type,
- val=self.current_class.replace("-", "_").replace(".", "_").upper(),
+ if fieldtype.instance_type == "string":
+ self.current_constructor_signature.write(
+ ", {safename} = '{val}'".format(
+ safename=safename, val=self.current_class
+ )
+ )
+ else:
+ self.current_constructor_signature.write(
+ ", {safename} = {type}.{val}".format(
+ safename=safename,
+ type=fieldtype.instance_type,
+ val=self.current_class.replace("-", "_")
+ .replace(".", "_")
+ .upper(),
+ )
)
- )
else:
self.current_constructor_signature.write(
", {safename}".format(
@@ -720,13 +737,16 @@ export enum {enum_name} {{
)
def epilogue(self, root_loader: TypeDef) -> None:
+
"""Trigger to generate the epilouge code."""
pd = "This project contains TypeScript objects and utilities "
pd = pd + ' auto-generated by <a href=\\"https://github.com/'
pd = pd + 'common-workflow-language/schema_salad\\">Schema Salad</a>'
pd = pd + " for parsing documents corresponding to the "
pd = pd + str(self.base_uri) + " schema."
- generated_class_imports = ",\n ".join(self.record_types)
+
+ sorted_record_types = sorted(self.record_types)
+ generated_class_imports = ",\n ".join(sorted_record_types)
template_vars: MutableMapping[str, str] = dict(
project_name=self.package,
version="0.0.1-SNAPSHOT",
@@ -767,8 +787,9 @@ export enum {enum_name} {{
collected_type.name, collected_type.init
)
+ sorted_modules = sorted(self.modules)
internal_module_exports = "\n".join(
- f"export * from '../{f}'" for f in self.modules
+ f"export * from '../{f}'" for f in sorted_modules
)
example_tests = ""
=====================================
setup.cfg
=====================================
@@ -14,6 +14,6 @@ use_parentheses = True
line_length = 88
[egg_info]
-tag_build = .20220103095339
+tag_build = .20220204150214
tag_date = 0
=====================================
setup.py
=====================================
@@ -77,9 +77,7 @@ install_requires = [
"ruamel.yaml >= 0.12.4, != 0.16.6, < 0.18",
# once the minimum version for ruamel.yaml >= 0.15.99
# then please update the mypy targets in the Makefile
- "rdflib >= 4.2.2, < 6.0.0;python_version<='3.6'",
"rdflib >= 4.2.2, < 7.0.0",
- "rdflib-jsonld >= 0.3.0, <= 0.6.1;python_version<='3.6'",
"mistune >= 0.8.1, < 0.9",
"CacheControl >= 0.11.7, < 0.13",
"lockfile >= 0.9", # needed for CacheControl's FileCache
=====================================
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
View it on GitLab: https://salsa.debian.org/python-team/packages/python-schema-salad/-/commit/1554e80c2bf6c0452457117bdb3dbb8634c48b11
--
View it on GitLab: https://salsa.debian.org/python-team/packages/python-schema-salad/-/commit/1554e80c2bf6c0452457117bdb3dbb8634c48b11
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