From 469dbe8cf97d6de55351ab3f46026a46c982c2e3 Mon Sep 17 00:00:00 2001 From: Jan Range Date: Thu, 22 Feb 2024 12:36:36 +0100 Subject: [PATCH 1/6] add `namespaces` to codegen --- sdRDM/generator/classrender.py | 6 ++++++ sdRDM/generator/codegen.py | 31 +++++++++++++++++-------------- 2 files changed, 23 insertions(+), 14 deletions(-) diff --git a/sdRDM/generator/classrender.py b/sdRDM/generator/classrender.py index d5071f7..8ad1afa 100644 --- a/sdRDM/generator/classrender.py +++ b/sdRDM/generator/classrender.py @@ -14,6 +14,7 @@ def render_object( objects: List[Dict], enums: List[Dict], inherits: List[Dict], + namespaces: Dict, repo: Optional[str] = None, commit: Optional[str] = None, small_types: Dict = {}, @@ -31,6 +32,7 @@ def render_object( objects=all_objects, repo=repo, commit=commit, + namespaces=namespaces, ) for subtype in small_types.values() if subtype["origin"] == object["name"] @@ -46,6 +48,7 @@ def render_object( objects=all_objects, repo=repo, commit=commit, + namespaces=namespaces, ) methods_part = render_add_methods( @@ -84,6 +87,7 @@ def render_class( object: Dict, inherits: List[Dict], objects: List[Dict], + namespaces: Dict, repo: Optional[str] = None, commit: Optional[str] = None, ) -> str: @@ -101,6 +105,7 @@ def render_class( if filtered and len(filtered) == 1: inherit = filtered[0]["parent"] + return template.render( name=name, inherit=inherit, @@ -115,6 +120,7 @@ def render_class( ], repo=repo, commit=commit, + namespaces=namespaces, ) diff --git a/sdRDM/generator/codegen.py b/sdRDM/generator/codegen.py index 3bb230f..25a09b1 100644 --- a/sdRDM/generator/codegen.py +++ b/sdRDM/generator/codegen.py @@ -71,13 +71,14 @@ def generate_api_from_parser( # Write classes to the directory write_classes( - libpath, - parser.objects, - parser.enums, - parser.inherits, - use_formatter, - url, - commit, + libpath=libpath, + objects=parser.objects, + enums=parser.enums, + inherits=parser.inherits, + use_formatter=use_formatter, + repo=url, + commit=commit, + namespaces=parser.namespaces, ) # Write init files @@ -108,6 +109,7 @@ def write_classes( enums: List[Dict], inherits: List[Dict], use_formatter: bool, + namespaces: Dict, repo: Optional[str] = None, commit: Optional[str] = None, ) -> None: @@ -122,13 +124,14 @@ def write_classes( for object in objects: rendered = render_object( - object, - objects, - enums, - inherits, - repo, - commit, - small_types, + object=object, + objects=objects, + enums=enums, + inherits=inherits, + repo=repo, + commit=commit, + small_types=small_types, + namespaces=namespaces, ) path = os.path.join(libpath, "core", f"{object['name'].lower()}.py") save_rendered_to_file(rendered, path, use_formatter) From e3955bd58db9f3592eaef9f26d9f6a3d17a529bf Mon Sep 17 00:00:00 2001 From: Jan Range Date: Thu, 22 Feb 2024 12:36:55 +0100 Subject: [PATCH 2/6] `namespaces` addition to meta --- sdRDM/generator/templates/class_template.jinja2 | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/sdRDM/generator/templates/class_template.jinja2 b/sdRDM/generator/templates/class_template.jinja2 index 024c10f..f4c73ee 100644 --- a/sdRDM/generator/templates/class_template.jinja2 +++ b/sdRDM/generator/templates/class_template.jinja2 @@ -1,7 +1,15 @@ @forge_signature class {{name}}({% if inherit is not none %} {{inherit}} - {% else %}sdRDM.DataModel{% endif %}, {% if repo %}nsmap={"": "{{ repo }}@{{ commit }}#{{ name }}"},{% endif %}): + {% else %}sdRDM.DataModel{% endif %}, + {% if namespaces %} + nsmap = { + {% for key, value in namespaces.items() %} + "{{key}}": "{{value}}", + {% endfor %} + }, + {% endif %} + ): {% if docstring is not none %}"""{{ docstring }}"""{% endif %} From cfb8ae91f6d0ffce78001dbb39d08da8c0460868 Mon Sep 17 00:00:00 2001 From: Jan Range Date: Thu, 22 Feb 2024 12:37:09 +0100 Subject: [PATCH 3/6] extract and pass namespaces --- sdRDM/markdown/markdownparser.py | 37 +++++++++++++++++++++++++++++++- 1 file changed, 36 insertions(+), 1 deletion(-) diff --git a/sdRDM/markdown/markdownparser.py b/sdRDM/markdown/markdownparser.py index 2c22b0b..e472339 100644 --- a/sdRDM/markdown/markdownparser.py +++ b/sdRDM/markdown/markdownparser.py @@ -1,5 +1,7 @@ +from io import StringIO import re +import frontmatter from typing import List, Tuple, Dict, IO from markdown_it import MarkdownIt from markdown_it.token import Token @@ -17,6 +19,7 @@ class MarkdownParser(BaseModel): inherits: List = [] compositions: List = [] external_objects: Dict = {} + namespaces: Dict = {} @classmethod def parse(cls, handle: IO): @@ -24,7 +27,9 @@ def parse(cls, handle: IO): parser = cls() - doc = MarkdownIt().parse(cls.clean_html_tags(handle.readlines())) + content = parser.clean_html_tags(handle.readlines()) + doc = MarkdownIt().parse(parser._remove_header(content)) + parser.namespaces = parser._extract_namespaces(content) modules, enumerations = parser.get_objects_and_enumerations(doc) for module, model in modules.items(): @@ -62,6 +67,36 @@ def add_model(self, parser: "MarkdownParser"): self.compositions += parser.compositions self.external_objects.update(parser.external_objects) + @staticmethod + def _extract_namespaces(content: str): + """Extracts all namespaces from the model. + + Args: + content (str): The content of the model. + + Returns: + dict: A dictionary containing the extracted namespaces. + """ + + doc = frontmatter.load(StringIO(content)) + return doc.get("xmlns", {}) + + @staticmethod + def _remove_header(text: str): + """ + Removes the header from the given text. + + Args: + text (str): The text containing the header. + + Returns: + str: The text with the header removed. + """ + header = re.search(r"^---\n.*?\n---\n", text, re.DOTALL) + if header: + text = text.replace(header.group(), "") + return text.strip() + def _has_duplicate_object_names(self, parser): """Checks whether there are redundancies within the model""" From 6c93cbd3672746a437b8afab1ddc4b32ae5e8225 Mon Sep 17 00:00:00 2001 From: Jan Range Date: Thu, 22 Feb 2024 12:37:17 +0100 Subject: [PATCH 4/6] update tests for `namespaces` --- tests/end2end/test_creation.py | 17 ++++++++++++++++- tests/end2end/test_serialisation.py | 2 +- tests/fixtures/static/model_all.md | 7 +++++++ tests/fixtures/static/model_all_expected.xml | 4 ++-- 4 files changed, 26 insertions(+), 4 deletions(-) diff --git a/tests/end2end/test_creation.py b/tests/end2end/test_creation.py index ce48ad5..24aa247 100644 --- a/tests/end2end/test_creation.py +++ b/tests/end2end/test_creation.py @@ -5,7 +5,7 @@ @pytest.mark.e2e -def test_dataset_creation(model_all, model_all_dataset): +def test_dataset_creation(model_all): """Tests whether the data that is passed to the model is correctly parsed""" expected = { @@ -70,3 +70,18 @@ def test_dataset_creation(model_all, model_all_dataset): assert ( dataset.to_dict(mode="python") == expected ), "Dataset does not match expected values" + + +@pytest.mark.e2e +def test_ns_map(model_all): + """Tests whether the namespace map is correctly extracted from the model""" + + expected = { + "": "http://www.example.com/ns0", + "math": "http://www.example.com/math", + "chem": "http://www.example.com/chem", + } + + assert ( + model_all.Root.__xml_nsmap__ == expected + ), "Namespace map does not match expected values" diff --git a/tests/end2end/test_serialisation.py b/tests/end2end/test_serialisation.py index 13e38af..1d41c58 100644 --- a/tests/end2end/test_serialisation.py +++ b/tests/end2end/test_serialisation.py @@ -29,4 +29,4 @@ def test_xml_serialisation(model_all_dataset): expected = open("tests/fixtures/static/model_all_expected.xml").read() given = model_all_dataset.xml() - assert given == expected, "YAML serialisation does not match" + assert given.strip() == expected.strip(), "XML serialisation does not match" diff --git a/tests/fixtures/static/model_all.md b/tests/fixtures/static/model_all.md index 2d14ef8..c1ea5c1 100644 --- a/tests/fixtures/static/model_all.md +++ b/tests/fixtures/static/model_all.md @@ -1,3 +1,10 @@ +--- +xmlns: + "": "http://www.example.com/ns0" + "math": "http://www.example.com/math" + "chem": "http://www.example.com/chem" +--- + # Test This model tests all methods and types that are present within the sdRDM library. diff --git a/tests/fixtures/static/model_all_expected.xml b/tests/fixtures/static/model_all_expected.xml index c4cba59..d0105d9 100644 --- a/tests/fixtures/static/model_all_expected.xml +++ b/tests/fixtures/static/model_all_expected.xml @@ -1,5 +1,5 @@ - + string 1.5 1 @@ -27,4 +27,4 @@ 1 - + \ No newline at end of file From 58f2f56eb53f68e9aff1bb3367ecf08205f06cd9 Mon Sep 17 00:00:00 2001 From: Jan Range Date: Thu, 22 Feb 2024 12:40:37 +0100 Subject: [PATCH 5/6] update deps --- poetry.lock | 20 +++++++++++++++++++- pyproject.toml | 5 +++-- 2 files changed, 22 insertions(+), 3 deletions(-) diff --git a/poetry.lock b/poetry.lock index 46d8fa8..1dea40d 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1075,6 +1075,24 @@ files = [ [package.dependencies] six = ">=1.5" +[[package]] +name = "python-frontmatter" +version = "1.1.0" +description = "Parse and manage posts with YAML (or other) frontmatter" +optional = false +python-versions = "*" +files = [ + {file = "python-frontmatter-1.1.0.tar.gz", hash = "sha256:7118d2bd56af9149625745c58c9b51fb67e8d1294a0c76796dafdc72c36e5f6d"}, + {file = "python_frontmatter-1.1.0-py3-none-any.whl", hash = "sha256:335465556358d9d0e6c98bbeb69b1c969f2a4a21360587b9873bfc3b213407c1"}, +] + +[package.dependencies] +PyYAML = "*" + +[package.extras] +docs = ["sphinx"] +test = ["mypy", "pyaml", "pytest", "toml", "types-PyYAML", "types-toml"] + [[package]] name = "pytz" version = "2023.3.post1" @@ -1275,4 +1293,4 @@ tooling-extras = ["pyaml (>=23.7.0)", "pypandoc-binary (>=1.11)", "pytest (>=7.4 [metadata] lock-version = "2.0" python-versions = "^3.9" -content-hash = "16096ae3a2773221c000594c13a0ef9295936e7c17866604231eae9f74c35eca" +content-hash = "324cc254713d26134be35526046a643875e7e5e85084c0eab2f059796257f7a7" diff --git a/pyproject.toml b/pyproject.toml index 1447b2d..ef58861 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -9,8 +9,8 @@ packages = [{include = "sdRDM"}] [tool.poetry.dependencies] python = "^3.9" -pydantic = "2.5.3" -pydantic-xml = "^2.7.0" +pydantic = "^2.6.0" +pydantic-xml = "^2.9.0" numpy = "^1.26.3" pandas = "^2.1.4" jinja2 = "^3.1.3" @@ -30,6 +30,7 @@ astropy = "^6.0.0" markdown-it-py = "^3.0.0" rich = "^13.7.0" lxml = "^5.1.0" +python-frontmatter = "^1.1.0" [tool.poetry.group.dev.dependencies] coverage = "^7.4.0" From 721ed3da7fbd0552e378a9ba718bf99da0811cca Mon Sep 17 00:00:00 2001 From: Jan Range Date: Thu, 22 Feb 2024 12:49:53 +0100 Subject: [PATCH 6/6] update lock file --- poetry.lock | 688 +++++++++++++++++++++++++--------------------------- 1 file changed, 334 insertions(+), 354 deletions(-) diff --git a/poetry.lock b/poetry.lock index 1dea40d..720f5f8 100644 --- a/poetry.lock +++ b/poetry.lock @@ -79,13 +79,13 @@ test-all = ["astropy[test]", "coverage[toml]", "ipython (>=4.2)", "objgraph", "s [[package]] name = "astropy-iers-data" -version = "0.2024.1.8.0.30.55" +version = "0.2024.2.19.0.28.47" description = "IERS Earth Rotation and Leap Second tables for the astropy core package" optional = false python-versions = ">=3.8" files = [ - {file = "astropy-iers-data-0.2024.1.8.0.30.55.tar.gz", hash = "sha256:e0e57b67c0f69733eb57f24ad1647e5a1c6d26f7936a994e52da87deec75ffb0"}, - {file = "astropy_iers_data-0.2024.1.8.0.30.55-py3-none-any.whl", hash = "sha256:51d0f2206c8e09540f3bc6b3123fa6c6b5c41ce37088be6c43216425eea173ec"}, + {file = "astropy-iers-data-0.2024.2.19.0.28.47.tar.gz", hash = "sha256:29af64fc932fec656c1f75478d693aef4ba6364b8d32a5862d5d908fe8848248"}, + {file = "astropy_iers_data-0.2024.2.19.0.28.47-py3-none-any.whl", hash = "sha256:8ccf83b8e35b300fb77eeb189ed728ec6d8150c40f8788a42e542fdcf960fe49"}, ] [package.extras] @@ -109,13 +109,13 @@ tomli = {version = ">=2.0.1", markers = "python_version < \"3.11\""} [[package]] name = "bigtree" -version 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