semantic-transformers 0.1.0__tar.gz

semantic_transformers-0.1.0/LICENSE

@@ -0,0 +1,201 @@
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semantic_transformers-0.1.0/PKG-INFO

@@ -0,0 +1,189 @@
+Metadata-Version: 2.4
+Name: semantic-transformers
+Version: 0.1.0
+Summary: Machine-file extractors and transformers for semantic schema pipelines
+Author: Semantic Dataspace contributors
+License: MIT
+Project-URL: Homepage, https://github.com/Semantic-Dataspace/semantic-transformers
+Project-URL: Repository, https://github.com/Semantic-Dataspace/semantic-transformers
+Project-URL: Bug Tracker, https://github.com/Semantic-Dataspace/semantic-transformers/issues
+Keywords: materials science,ontology,linked data,rdf,etl,parsers
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pandas
+Requires-Dist: rdflib
+Requires-Dist: pyyaml
+Requires-Dist: jsonata-python
+Requires-Dist: jsonschema
+Provides-Extra: excel
+Requires-Dist: openpyxl; extra == "excel"
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: nbmake; extra == "dev"
+Dynamic: license-file
+
+# semantic-transformers
+
+A library and a curated collection of parsers that bridge raw instrument output
+files and the [semantic-schemas](../semantic-schemas/) knowledge graph pipeline.
+
+## What this repository contains
+
+```text
+semantic-transformers/
+  src/semantic_transformers/   Python library (Transformer, QuickMapper, …)
+  parsers/                     Machine-specific file parsers
+    <domain>/                  Mirrors the semantic-schemas folder structure
+      <specialisation>/
+        <machine>/             One folder per instrument model
+          <machine>_parser.py  Reads the instrument file
+          column_mapping.json  Maps column names to ontology class IRIs and units
+          README.md            Quick-start, schema compatibility, and known limitations
+  docs/                        Guides for users and contributors
+```
+
+## The two parts
+
+### 1. The library (`src/semantic_transformers/`)
+
+| Class | Role |
+|---|---|
+| `Parser` | Protocol to implement when adding support for a new instrument |
+| `ParseResult` | What every parser returns: simplified JSON + DataFrame |
+| `Transformer` | Runs parsing → JSONata transform → RDF graph |
+| `TransformResult` | What `Transformer.run()` returns: RDF graph + DataFrame |
+| `QuickMapper` | Turns any tabular file into RDF using a simple YAML mapping (no parser needed) |
+
+### 2. The parsers (`parsers/`)
+
+Each parser targets a specific instrument model. The folder path mirrors the
+`schemas/` tree in `semantic-schemas`:
+
+| Schema | Instrument | Parser path |
+|---|---|---|
+| `characterization/tensile-test/TTO` | Zwick/Roell (testXpert III) | `parsers/characterization/tensile-test/zwick/` |
+
+## Installation
+
+### Using pip (recommended)
+
+```bash
+# Install the transformers library
+pip install semantic-transformers
+
+# Optional: install optional dependencies
+pip install semantic-transformers[excel]  # for Excel file support
+pip install semantic-transformers[dev]    # for development and testing
+```
+
+### Development installation
+
+Both repositories are designed to be cloned as siblings under a shared folder:
+
+```bash
+mkdir semantic-dataspace && cd semantic-dataspace
+
+git clone https://github.com/Semantic-Dataspace/semantic-schemas
+git clone https://github.com/Semantic-Dataspace/semantic-transformers
+
+python3 -m venv .venv
+source .venv/bin/activate        # Windows: .venv\Scripts\activate
+
+pip install -e semantic-transformers/
+pip install jupyterlab            # only needed for the interactive notebooks
+```
+
+## Two ways to use this library
+
+### Option A: you have a supported instrument
+
+Use a ready-made parser and the matching schema notebook. For a Zwick/Roell
+tensile test:
+
+```bash
+jupyter lab semantic-schemas/schemas/characterization/tensile-test/TTO/docs/2_tensile_test_csv_workflow.ipynb
+```
+
+Edit **Step 0** (one line, point to your file) and run all cells. Done.
+
+### Option B: you have a tabular file with no existing parser
+
+Use `QuickMapper`. Provide a short YAML that names the columns and points each
+one at an ontology class IRI:
+
+```python
+from semantic_transformers import QuickMapper
+
+mapping = {
+    "label": "my experiment",
+    "columns": {
+        "Force": {
+            "iri":  "https://w3id.org/pmd/tto/StandardForce",
+            "unit": "http://qudt.org/vocab/unit/N",
+        },
+        "Extension": {
+            "iri": "https://w3id.org/pmd/tto/Extension",
+        },
+    },
+}
+
+result = QuickMapper(mapping).run("my_data.csv")
+print(result.graph.serialize(format="turtle"))
+print(result.dataframe.head())
+```
+
+Supported file formats: CSV, TSV, Excel (.xlsx), Parquet, JSON.
+See the [QuickMapper notebook](docs/3_quickstart-mapping.ipynb) for a guided walkthrough.
+
+## Development
+
+### Running the tests
+
+```bash
+python3 -m venv .venv
+source .venv/bin/activate
+pip install -e ".[dev]"
+pytest -v
+```
+
+### Refreshing notebook outputs (for documentation)
+
+Notebooks are committed with their output cells so that GitHub renders them as
+readable documentation.  After changing a parser or the library, re-execute all
+notebooks in-place to update the stored outputs before committing:
+
+```bash
+find docs -name "*.ipynb" ! -path "*/.ipynb_checkpoints/*" \
+  | xargs jupyter nbconvert \
+      --to notebook \
+      --execute \
+      --inplace \
+      --ExecutePreprocessor.timeout=300
+```
+
+Run this from the repository root.  Commit the resulting `*.ipynb` changes
+together with any code changes so that the rendered output on GitHub stays
+in sync.
+
+> **Tip.** To refresh a single notebook only, pass its path directly:
+>
+> ```bash
+> jupyter nbconvert --to notebook --execute --inplace \
+>     --ExecutePreprocessor.timeout=300 \
+>     docs/3_quickstart-mapping.ipynb
+> ```
+
+## Documentation
+
+- [Getting started](docs/1_getting-started.md): convert your first instrument file
+- [QuickMapper walkthrough](docs/3_quickstart-mapping.ipynb): turn any tabular file into RDF
+- [Adding a parser](docs/2_adding-a-parser.md): support a new instrument or handle file variants

semantic_transformers-0.1.0/README.md

@@ -0,0 +1,156 @@
+# semantic-transformers
+
+A library and a curated collection of parsers that bridge raw instrument output
+files and the [semantic-schemas](../semantic-schemas/) knowledge graph pipeline.
+
+## What this repository contains
+
+```text
+semantic-transformers/
+  src/semantic_transformers/   Python library (Transformer, QuickMapper, …)
+  parsers/                     Machine-specific file parsers
+    <domain>/                  Mirrors the semantic-schemas folder structure
+      <specialisation>/
+        <machine>/             One folder per instrument model
+          <machine>_parser.py  Reads the instrument file
+          column_mapping.json  Maps column names to ontology class IRIs and units
+          README.md            Quick-start, schema compatibility, and known limitations
+  docs/                        Guides for users and contributors
+```
+
+## The two parts
+
+### 1. The library (`src/semantic_transformers/`)
+
+| Class | Role |
+|---|---|
+| `Parser` | Protocol to implement when adding support for a new instrument |
+| `ParseResult` | What every parser returns: simplified JSON + DataFrame |
+| `Transformer` | Runs parsing → JSONata transform → RDF graph |
+| `TransformResult` | What `Transformer.run()` returns: RDF graph + DataFrame |
+| `QuickMapper` | Turns any tabular file into RDF using a simple YAML mapping (no parser needed) |
+
+### 2. The parsers (`parsers/`)
+
+Each parser targets a specific instrument model. The folder path mirrors the
+`schemas/` tree in `semantic-schemas`:
+
+| Schema | Instrument | Parser path |
+|---|---|---|
+| `characterization/tensile-test/TTO` | Zwick/Roell (testXpert III) | `parsers/characterization/tensile-test/zwick/` |
+
+## Installation
+
+### Using pip (recommended)
+
+```bash
+# Install the transformers library
+pip install semantic-transformers
+
+# Optional: install optional dependencies
+pip install semantic-transformers[excel]  # for Excel file support
+pip install semantic-transformers[dev]    # for development and testing
+```
+
+### Development installation
+
+Both repositories are designed to be cloned as siblings under a shared folder:
+
+```bash
+mkdir semantic-dataspace && cd semantic-dataspace
+
+git clone https://github.com/Semantic-Dataspace/semantic-schemas
+git clone https://github.com/Semantic-Dataspace/semantic-transformers
+
+python3 -m venv .venv
+source .venv/bin/activate        # Windows: .venv\Scripts\activate
+
+pip install -e semantic-transformers/
+pip install jupyterlab            # only needed for the interactive notebooks
+```
+
+## Two ways to use this library
+
+### Option A: you have a supported instrument
+
+Use a ready-made parser and the matching schema notebook. For a Zwick/Roell
+tensile test:
+
+```bash
+jupyter lab semantic-schemas/schemas/characterization/tensile-test/TTO/docs/2_tensile_test_csv_workflow.ipynb
+```
+
+Edit **Step 0** (one line, point to your file) and run all cells. Done.
+
+### Option B: you have a tabular file with no existing parser
+
+Use `QuickMapper`. Provide a short YAML that names the columns and points each
+one at an ontology class IRI:
+
+```python
+from semantic_transformers import QuickMapper
+
+mapping = {
+    "label": "my experiment",
+    "columns": {
+        "Force": {
+            "iri":  "https://w3id.org/pmd/tto/StandardForce",
+            "unit": "http://qudt.org/vocab/unit/N",
+        },
+        "Extension": {
+            "iri": "https://w3id.org/pmd/tto/Extension",
+        },
+    },
+}
+
+result = QuickMapper(mapping).run("my_data.csv")
+print(result.graph.serialize(format="turtle"))
+print(result.dataframe.head())
+```
+
+Supported file formats: CSV, TSV, Excel (.xlsx), Parquet, JSON.
+See the [QuickMapper notebook](docs/3_quickstart-mapping.ipynb) for a guided walkthrough.
+
+## Development
+
+### Running the tests
+
+```bash
+python3 -m venv .venv
+source .venv/bin/activate
+pip install -e ".[dev]"
+pytest -v
+```
+
+### Refreshing notebook outputs (for documentation)
+
+Notebooks are committed with their output cells so that GitHub renders them as
+readable documentation.  After changing a parser or the library, re-execute all
+notebooks in-place to update the stored outputs before committing:
+
+```bash
+find docs -name "*.ipynb" ! -path "*/.ipynb_checkpoints/*" \
+  | xargs jupyter nbconvert \
+      --to notebook \
+      --execute \
+      --inplace \
+      --ExecutePreprocessor.timeout=300
+```
+
+Run this from the repository root.  Commit the resulting `*.ipynb` changes
+together with any code changes so that the rendered output on GitHub stays
+in sync.
+
+> **Tip.** To refresh a single notebook only, pass its path directly:
+>
+> ```bash
+> jupyter nbconvert --to notebook --execute --inplace \
+>     --ExecutePreprocessor.timeout=300 \
+>     docs/3_quickstart-mapping.ipynb
+> ```
+
+## Documentation
+
+- [Getting started](docs/1_getting-started.md): convert your first instrument file
+- [QuickMapper walkthrough](docs/3_quickstart-mapping.ipynb): turn any tabular file into RDF
+- [Adding a parser](docs/2_adding-a-parser.md): support a new instrument or handle file variants

semantic_transformers-0.1.0/pyproject.toml

@@ -0,0 +1,57 @@
+[build-system]
+requires = ["setuptools>=68"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "semantic-transformers"
+version = "0.1.0"
+description = "Machine-file extractors and transformers for semantic schema pipelines"
+readme = "README.md"
+requires-python = ">=3.10"
+license = { text = "MIT" }
+authors = [
+    { name = "Semantic Dataspace contributors" },
+]
+keywords = [
+    "materials science",
+    "ontology",
+    "linked data",
+    "rdf",
+    "etl",
+    "parsers",
+]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "Topic :: Scientific/Engineering :: Information Analysis",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+]
+dependencies = [
+    "pandas",
+    "rdflib",
+    "pyyaml",
+    "jsonata-python",
+    "jsonschema",
+]
+
+[project.optional-dependencies]
+excel = ["openpyxl"]
+dev   = ["pytest", "nbmake"]
+
+[project.urls]
+Homepage = "https://github.com/Semantic-Dataspace/semantic-transformers"
+Repository = "https://github.com/Semantic-Dataspace/semantic-transformers"
+"Bug Tracker" = "https://github.com/Semantic-Dataspace/semantic-transformers/issues"
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.pytest.ini_options]
+testpaths = ["tests"]
+filterwarnings = [
+    "ignore::DeprecationWarning:rdflib.*",
+]

semantic_transformers-0.1.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

semantic_transformers-0.1.0/src/semantic_transformers/__init__.py

@@ -0,0 +1,23 @@
+"""
+semantic-transformers
+=====================
+Converters and machine-file parsers for semantic schema pipelines.
+
+Public API
+----------
+    ParseResult:     normalised parser output (simplified_json + DataFrame)
+    Parser:          protocol that all parsers must satisfy
+    Transformer:     runs parsing → JSONata transform → RDF
+    TransformResult: everything produced by Transformer.run()
+    QuickMapper:     turns any tabular file into RDF with a simple YAML mapping
+"""
+
+from .parser import Parser, ParseResult
+from .transformer import Transformer, TransformResult
+from .quick_mapper import QuickMapper
+
+__all__ = [
+    "Parser", "ParseResult",
+    "Transformer", "TransformResult",
+    "QuickMapper",
+]