diff --git a/Makefile b/Makefile
index b21a2c8..c88f588 100644
--- a/Makefile
+++ b/Makefile
@@ -96,13 +96,13 @@ $(DOCDIR):
gendoc: $(DOCDIR)
cp -pr $(SRC)/docs/* $(DOCDIR) ; \
- $(RUN) gen-doc -d $(DOCDIR) $(SOURCE_SCHEMA_PATH)
+ $(RUN) gen-doc -d $(DOCDIR) $(SOURCE_SCHEMA_PATH) --index-name datamodel
testdoc: gendoc serve
MKDOCS = $(RUN) mkdocs
mkd-%:
- $(MKDOCS) $*
+ $(MKDOCS) $* $(MKDOCS_ARGS)
PROJECT_FOLDERS = sqlschema shex shacl protobuf prefixmap owl jsonschema jsonld graphql excel
git-init-add: git-init git-add git-commit git-status
diff --git a/README.md b/README.md
index 0017d8d..b1ea7ff 100644
--- a/README.md
+++ b/README.md
@@ -1,5 +1,10 @@
# linkml-transformer
+[![Pyversions](https://img.shields.io/pypi/pyversions/linkml-transformer.svg)](https://pypi.python.org/pypi/linkml-transformer)
+![](https://github.com/linkml/linkml-transformer/workflows/Build/badge.svg)
+[![PyPi](https://img.shields.io/pypi/v/linkml-transformer.svg)](https://pypi.python.org/pypi/linkml-transformer)
+[![codecov](https://codecov.io/gh/linkml/linkml-transformer/branch/main/graph/badge.svg?token=WNQNG986UN)](https://codecov.io/gh/linkml/linkml-transformer)
+
LinkML Transformer is a framework for specifying and executing mappings between data models.
Features:
@@ -14,6 +19,10 @@ Features:
- Visualizations of mappings
- Mappings are reversible (provided all expressions used are reversible)
+For full documentation see:
+
+- [linkml.io/linkml-transformer/](https://linkml.io/linkml-transformer/)
+
Status:
The transformation data model is not yet fully stable, and may be subject to change.
@@ -21,325 +30,7 @@ Not all parts of the model are implemented in the reference Python framework.
## Quickstart
-* [Tutorial Notebook](notebooks/Tutorial.ipynb)
+* [Tutorial Notebook](src/docs/examples/Tutorial.ipynb)
* [Generated Docs](https://linkml.github.io/linkml-transformer/)
* [Compliance Suite](https://linkml.github.io/linkml-transformer/specification/compliance)
-## Basic idea
-
-Given an object that conforms to a LinkML schema,e.g.:
-
-```yaml
-given_name: Jane
-family_name: Doe
-height_in_cm: 172.0
-age_in_years: 33
-aliases: [Janey, Janie]
-```
-
-Define a mapping in YAML:
-
-```yaml
-class_derivations:
- Individual:
- populated_from: Person
- slot_derivations:
- name:
- expr: "{given_name} + ' ' + {family_name}"
- description: Concatenating given and family names
- note this is a bad assumption for names in general,
- this is just for demonstration
- height_in_meters:
- populated_from: height_in_cm
- unit_conversion:
- target_unit: m
- aliases:
- populated_from: aliases
- stringification:
- delimiter: '|'
-```
-
-Transform the data:
-
-```yaml
-name: Jane Doe
-height_in_meters: 1.72
-aliases: Janey|Janie
-```
-
-## Installation and usage
-
-Installation and command line usage:
-
-```bash
-pip[x] install linkml-transformer
-cd tests/input/examples/personinfo_basic
-linkml-tr map-data \
- -T transform/personinfo-to-agent.transform.yaml \
- -s source/personinfo.yaml \
- data/Container-001.yaml \
- -o output/Translated-001.yaml
-```
-
-The command line has subcommands for:
-
-- `map-data` - map data from a source schema to a target schema
-- `derive-schema` - derive a target schema from a source schema and a mapping
-- `invert` - reverses a mapping
-- `compile` - compiles a mapping to another framework
- - `markdown` - for generating static sites
- - `graphviz` - for generating visualizations
- - `python` - (partial)
- - forthcoming: `r2rml`, ...
-
-## Details
-
-This repo contains both:
-
-- A data model for a data model *transformation language*
-- A reference python implementation
-
-The transformation language is specified in terms of LinkML schemas.
-It is intended to be a *ployglot* transformation language, used for
-specifying how to map data models independent of underlying representation
-(TSVs, JSON/YAML, RDF, SQL Database, ...).
-
-Use cases include:
-
-- ETL and mapping from one data model to another
-- Database migrations (one version of a schema to another)
-- Creating "profiles"
-- Specifying mappings between different serializations of a model (e.g. OO to Relational)
-- Mapping between normalized/non-redundant forms and denormalized/query-optimized forms
-
-## Tutorials
-
-* [Tutorial Notebook](notebooks/Tutorial.ipynb) - for Python developers
-
-## Data Model
-
-The data model for transformations mirrors the data model for schemas:
-
-- A top level `TransformationSpecification` class contains:
- - Zero or more `ClassDerivation` objects, specifying how to map to a class, containing:
- - Zero or more `SlotDerivation` objects, specifying how to map to a slot, containing:
- - Zero or more `EnumDerivation` objects, specifying how to map permissible values.
-
-See the [generated docs](https://linkml.github.io/linkml-transformer/)
-
-## Conformance Suite
-
-The Transformers conformance suite contains a collection of tests for each feature of the language.
-
-See:
-
-* [Compliance Suite](https://linkml.github.io/linkml-transformer/specification/compliance)
-
-
-## Running the code
-
-```bash
-linkml-tr --help
-Usage: linkml-tr [OPTIONS] COMMAND [ARGS]...
-
- CLI for linkml-transformer.
-
-Options:
- -v, --verbose
- -q, --quiet TEXT
- --help Show this message and exit.
-
-Commands:
- derive-schema Derive a schema from a source schema and a mapping.
- map-data Map data in a source schema using a transformation.
-```
-
-### map-data
-
-Transforms (maps) data from a source schema to a target schema. This could range from a simple data dictionary mapping
-through to a complex mappings.
-
-```
-cd tests/input/examples/personinfo_basic
-linkml-tr map-data -T transform/personinfo-to-agent.transform.yaml -s source/personinfo.yaml data/Container-001.yaml
-```
-
-### derive-schema
-
-```
-cd tests/input/examples/personinfo_basic
-linkml-tr derive-schema -T transform/personinfo-to-agent.transform.yaml source/personinfo.yaml
-```
-
-
-## Examples
-
-See the tests folder for most up-to-date examples
-
-### Mapping between two similar data models
-
-Given a *source* object
-
-```yaml
-persons:
- - id: P:001
- name: fred bloggs
- primary_email: fred.bloggs@example.com
- age_in_years: 33
- has_familial_relationships:
- - type: SIBLING_OF
- related_to: P:002
- current_address:
- street: 1 oak street
- aliases:
- - a
- - b
- has_medical_history:
- - diagnosis:
- id: C:001
- name: c1
- - diagnosis:
- id: C:002
- - id: P:002
- name: Alison Wu
- has_familial_relationships:
- - type: SIBLING_OF
- related_to: P:001
- has_medical_history:
- - diagnosis:
- id: C:001
- name: c1 (renamed)
-organizations:
- - id: ROR:1
- name: Acme
-```
-
-and a corresponding schema, consider the case
-of mapping to a largely isomorphic schema, with some minor differences:
-
-- class names are changes (e.g Person to Agent)
-- age is represented as a string, e.g. "33 years"
-- some fields are denormalized
-
-The mapping may look like:
-
-```yaml
-id: my-mappings
-title: my mappings
-prefixes:
- foo: foo
-source_schema: s1
-target_schema: s2
-class_derivations:
- Container:
- populated_from: Container
- slot_derivations:
- agents:
- populated_from: persons
- Agent:
- populated_from: Person
- slot_derivations:
-
- ## implicitly same name in Agent
- id:
-
- label:
- populated_from: name
-
- age:
- expr: "str({age_in_years})+' years'"
-
- primary_email:
-
- gender:
-
- has_familial_relationships:
- populated_from: has_familial_relationships
-
- FamilialRelationship:
- populated_from: FamilialRelationship
- slot_derivations:
- type:
- related_to:
-```
-
-### Deriving Schemas
-
-Formally a mapping consists of a source schema `S`, a target schema `T`, and a mapping `M`.
-
-In practice, any of these can be *partially* specified and derived from the others.
-
-For example:
-
-- given `S`, and `T`, derive *isomorphic mappings* `M` based on shared URIs
-- given `S and `M`, derive `T` by applying M to the schema
-
-You can use the `derive-schema` command to derive a schema from a source schema and a mapping.
-This can also be thought of as "profiling" a schema (in the FHIR sense).
-
-See [tests/test_mapper/test_schema_mapper.py](tests/test_schema_mapper/test_schema_mapper.py) for examples
-
-### Measurements and units
-
-```yaml
-- id: P:001
- height:
- value: 172.0
- unit: cm
-```
-
-<==>
-
-```yaml
-- id: P:001
- height_in_cm: 172.0
-```
-
-<==>
-
-```yaml
-- id: P:001
- height: "172.0 cm"
-```
-
-## Not supported
-
-- Aggregation
-- ...
-
-## Why another framework?
-
-There are a number of excellent frameworks for performing mapping and data transformations.
-The LinkML Transformer framework was born out of a need for a framework that:
-
-- was not inherently tied to:
- - a particular serialization format (e.g. RDF, JSON, ...)
- - a particular programming language (e.g. Python, Java, ...)
- - a particular database system or database language (e.g. PostgreSQL or SQL or SPARQL)
- - not tied to a particular kind of transformation (e.g. ORM or Tables to RDF)
-- was a natural fit for the LinkML data modeling framework
-- was declarative and easy to perform machine reasoning over
-- is simple for simple use cases
-
-In its current state, this framework is less powerful and expressive than many other frameworks
-or methodologies for performing transformations. If you need to perform complex data transformations,
-you might be better off using an expressive query language like SPARQL or SQL, or even just coding
-transformations directly in a programming language or library like Python or Pandas (but note that
-even for the coding use case, the LinkML Transformer framework can be useful as a standard way
-of *documenting* transformations).
-
-Currently the main use case for this framework is *mostly isomorphic* transformations, with lightweight
-manipulations. These lend themselves well to a declarative framework. Uses cases that are a particularly good fit
-involve mapping between data-dictionary like standards, with large numbers of metadata elements, where these
-elements can often be mapped one-to-one, or with simple manipulations (e.g. unit conversions).
-
-The origins lie partly in the SSSOM standard, which is intended as an ultra-simple way of specifying
-precise mappings between *entities* (e.g. schema.org Person is the same as DBPedia person). We observed
-that many people wanted to extend the language to perform more complex mappings. To address this, we
-help a workshop at the Biocuration conference in Padua, Italy in 2022.
-
-- [Discussion](https://github.com/orgs/linkml/discussions/1829)
-- [SSSOM paper](https://academic.oup.com/database/article/doi/10.1093/database/baac035/6591806)
-- [SSSOM Update 2023](https://ceur-ws.org/Vol-3591/om2023_STpaper3.pdf)
-- [SSSOM Complex Mappings Workshop 2023](https://www.youtube.com/playlist?list=PLqu_J7ADQtKyX55F7RqZtaSS7TwGd3MoR)
-- [Mapping Data Structures: Challenges and Approaches](https://doi.org/10.5281/zenodo.10343505)
diff --git a/mkdocs.yml b/mkdocs.yml
index 2c610be..9db5a93 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -1,14 +1,21 @@
site_name: "LinkML-Transformer"
theme:
- name: material
+# name: material
+ name: windmill
features:
- content.tabs.link
plugins:
- search
- mermaid2
+ - mknotebooks:
+ execute: true # This will execute the notebooks when building the site
nav:
- Index: index.md
+ - Examples:
+ Tutorial: examples/Tutorial.ipynb
- Specification:
+ Data Model: datamodel.md
Compliance Suite: specification/compliance.md
-site_url: https://cmungall.github.io/linkml-transformer/
-repo_url: https://github.com/cmungall/linkml-transformer/
+ - FAQ: faq.md
+site_url: https://linkml.github.io/linkml-transformer/
+repo_url: https://github.com/linkml/linkml-transformer/
diff --git a/notebooks/Tutorial-SQLCompiler.ipynb b/notebooks/Tutorial-SQLCompiler.ipynb
new file mode 100644
index 0000000..dba5c4e
--- /dev/null
+++ b/notebooks/Tutorial-SQLCompiler.ipynb
@@ -0,0 +1,856 @@
+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "source": [
+ "# LinkML-Transformer tutorial: Compiling to SQL\n",
+ "\n",
+ "This tutorial walks through use of the SQL compiler"
+ ],
+ "metadata": {
+ "collapsed": false
+ },
+ "id": "df75d53a3e91e573"
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 3,
+ "outputs": [],
+ "source": [
+ "import yaml"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-03-22T15:31:47.717372Z",
+ "start_time": "2024-03-22T15:31:47.713457Z"
+ }
+ },
+ "id": "63a064b31f623bdd"
+ },
+ {
+ "cell_type": "markdown",
+ "source": [
+ "## Creating an example schema\n",
+ "\n",
+ "We will use a LinkML SchemaBuilder object to progressively build up a schema, adding\n",
+ "additional features as we go.\n",
+ "\n",
+ "We'll start with a simple `Person` schema, with a few single valued scalar slots:"
+ ],
+ "metadata": {
+ "collapsed": false
+ },
+ "id": "e2cbd6b8994905f6"
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 4,
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "name: test-schema\n",
+ "id: http://example.org/test-schema\n",
+ "imports:\n",
+ "- linkml:types\n",
+ "prefixes:\n",
+ " linkml: https://w3id.org/linkml/\n",
+ " test_schema: http://example.org/test-schema/\n",
+ "default_prefix: test_schema\n",
+ "default_range: string\n",
+ "slots:\n",
+ " family_name:\n",
+ " range: string\n",
+ " given_name:\n",
+ " range: string\n",
+ " age_in_years:\n",
+ " range: integer\n",
+ " height_in_cm:\n",
+ " range: float\n",
+ "classes:\n",
+ " Person:\n",
+ " slots:\n",
+ " - family_name\n",
+ " - given_name\n",
+ " - age_in_years\n",
+ " - height_in_cm\n"
+ ]
+ }
+ ],
+ "source": [
+ "from linkml.utils.schema_builder import SchemaBuilder\n",
+ "from linkml_runtime.linkml_model import SlotDefinition\n",
+ "\n",
+ "sb = SchemaBuilder()\n",
+ "sb.add_class(\"Person\", slots=[SlotDefinition(\"family_name\", range=\"string\"), \n",
+ " SlotDefinition(\"given_name\", range=\"string\"),\n",
+ " SlotDefinition(\"age_in_years\", range=\"integer\"),\n",
+ " SlotDefinition(\"height_in_cm\", range=\"float\"),\n",
+ " ])\n",
+ "sb.add_defaults()\n",
+ "print(yaml.dump(sb.as_dict(), sort_keys=False))"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-03-22T15:31:48.568091Z",
+ "start_time": "2024-03-22T15:31:48.546064Z"
+ }
+ },
+ "id": "ef2c60ef7fbcbe20"
+ },
+ {
+ "cell_type": "markdown",
+ "source": [
+ "## Creating a Transformer Session object\n",
+ "\n",
+ "We will use a `Session` object which conveniently wraps a number of different capabilities;\n",
+ "the first of these capabilities is to map (transform) data objects from one schema to another\n",
+ "(implicit) schema using a *transformer specification*).\n",
+ "\n",
+ "Our initial transformer specification will be a trivial isomorphic one that:\n",
+ "\n",
+ "- maps the `Person` class to an `Individual` class\n",
+ "- passes through `name` fields as-is\n",
+ "- renames measurement fields (`age_in_years` and `height_in_cm` to `age` and `height`)"
+ ],
+ "metadata": {
+ "collapsed": false
+ },
+ "id": "d4228629dd7e2ef2"
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 5,
+ "outputs": [],
+ "source": [
+ "from linkml_transformer.session import Session\n",
+ "\n",
+ "session = Session()\n",
+ "session.set_source_schema(sb.as_dict())"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-03-22T15:31:49.071324Z",
+ "start_time": "2024-03-22T15:31:49.057115Z"
+ }
+ },
+ "id": "a6257aa9e6ab021e"
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 6,
+ "outputs": [],
+ "source": [
+ "# Transformer specification (in YAML)\n",
+ "session.set_object_transformer(\"\"\"\n",
+ "class_derivations:\n",
+ " Individual:\n",
+ " populated_from: Person\n",
+ " slot_derivations:\n",
+ " family_name:\n",
+ " populated_from: family_name\n",
+ " given_name:\n",
+ " populated_from: given_name\n",
+ " age:\n",
+ " populated_from: age_in_years\n",
+ " height:\n",
+ " populated_from: height_in_cm\n",
+ "\"\"\")"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-03-22T15:31:49.541418Z",
+ "start_time": "2024-03-22T15:31:49.294760Z"
+ }
+ },
+ "id": "47b95e209790b423"
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 7,
+ "outputs": [],
+ "source": [
+ "from linkml_transformer.compiler.sql_compiler import SQLCompiler\n",
+ "\n",
+ "compiler = SQLCompiler()"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-03-22T15:31:49.951730Z",
+ "start_time": "2024-03-22T15:31:49.949246Z"
+ }
+ },
+ "id": "f1538dfa61775402"
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 9,
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "CREATE TABLE IF NOT EXISTS Individual (\n",
+ "family_name AS family_name\n",
+ "given_name AS given_name\n",
+ "age AS age_in_years\n",
+ "height AS height_in_cm\n",
+ ");\n"
+ ]
+ }
+ ],
+ "source": [
+ "compiled = compiler.compile(session.transformer_specification)\n",
+ "print(compiled.serialization)"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-03-22T15:32:08.957082Z",
+ "start_time": "2024-03-22T15:32:08.947948Z"
+ }
+ },
+ "id": "95b6adb322799f1f"
+ },
+ {
+ "cell_type": "markdown",
+ "source": [],
+ "metadata": {
+ "collapsed": false
+ },
+ "id": "8313d6acb588178e"
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 11,
+ "outputs": [],
+ "source": [
+ "import duckdb"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-03-22T17:13:13.511531Z",
+ "start_time": "2024-03-22T17:13:10.763461Z"
+ }
+ },
+ "id": "1c623cdc3c1cfbca"
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "outputs": [],
+ "source": [
+ "con = duckdb.connect(database=':memory:')\n"
+ ],
+ "metadata": {
+ "collapsed": false
+ },
+ "id": "564d2bd8387d7c77"
+ },
+ {
+ "cell_type": "markdown",
+ "source": [
+ "## Using Expressions\n",
+ "\n",
+ "In addition to renaming fields, we can derive field values via evaluation of function *expressions*.\n",
+ "\n",
+ "You are encouraged to follow the subset of Python defined by the LinkML expression language. This provides\n",
+ "both safety, and declarativity. However, if you need\n",
+ "to, you can include arbitrary Python code, provided you configure the session to allow this.\n",
+ "\n",
+ "We'll keep the original schema, and will provide a new Transformer specification, \n",
+ "giving an example of both string manipulation functions and arithmetic functions; the latter\n",
+ "perform unit conversions (later on we will see more flexible and declarative ways to perform unit conversions).\n",
+ "\n"
+ ],
+ "metadata": {
+ "collapsed": false
+ },
+ "id": "4562b534b6f23910"
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 10,
+ "outputs": [],
+ "source": [
+ "\n",
+ "session.set_object_transformer(\"\"\"\n",
+ "class_derivations:\n",
+ " Individual:\n",
+ " populated_from: Person\n",
+ " slot_derivations:\n",
+ " name:\n",
+ " expr: \"{given_name} + ' ' + {family_name}\"\n",
+ " description: Concatenating given and family names\n",
+ " note this is a bad assumption for names in general,\n",
+ " this is just for demonstration\n",
+ " age_in_months:\n",
+ " expr: age_in_years * 12\n",
+ " height_in_meters:\n",
+ " expr: height_in_cm / 100\n",
+ "\"\"\")\n"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-03-22T15:40:45.674315Z",
+ "start_time": "2024-03-22T15:40:45.634241Z"
+ }
+ },
+ "id": "789a7b6535ab410f"
+ },
+ {
+ "cell_type": "markdown",
+ "source": [
+ "Note that when we visualize this specification, dotted lines are shown indicating a relationship\n",
+ "between source and target that is different from direct copy:"
+ ],
+ "metadata": {
+ "collapsed": false
+ },
+ "id": "e02eaa2cde3172c8"
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 9,
+ "outputs": [
+ {
+ "data": {
+ "image/svg+xml": "\n\n\n\n\n",
+ "text/plain": ""
+ },
+ "execution_count": 9,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "session.graphviz()"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-01-17T22:30:03.283023Z",
+ "start_time": "2024-01-17T22:30:02.345894Z"
+ }
+ },
+ "id": "2a18ccb5d7dc469b"
+ },
+ {
+ "cell_type": "markdown",
+ "source": [
+ "Now we'll transform the same object as before, and see the results:"
+ ],
+ "metadata": {
+ "collapsed": false
+ },
+ "id": "f7019db8d391ab97"
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 10,
+ "outputs": [
+ {
+ "data": {
+ "text/plain": "{'name': 'Jane Doe', 'age_in_months': 504, 'height_in_meters': 1.8}"
+ },
+ "execution_count": 10,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "session.transform(obj)"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-01-17T22:30:03.283868Z",
+ "start_time": "2024-01-17T22:30:03.278695Z"
+ }
+ },
+ "id": "5e20e98e2b23751f"
+ },
+ {
+ "cell_type": "markdown",
+ "source": [
+ "As expected, we concatenated the name fields, and converted the age and height fields to different units.\n",
+ "\n",
+ "Let's take a look at the derived schema for this new transformation:"
+ ],
+ "metadata": {
+ "collapsed": false
+ },
+ "id": "ad9fd0f70178fd26"
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 11,
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "name: test-schema-derived\n",
+ "id: http://example.org/test-schema-derived\n",
+ "imports:\n",
+ "- linkml:types\n",
+ "prefixes:\n",
+ " linkml:\n",
+ " prefix_prefix: linkml\n",
+ " prefix_reference: https://w3id.org/linkml/\n",
+ " test_schema:\n",
+ " prefix_prefix: test_schema\n",
+ " prefix_reference: http://example.org/test-schema/\n",
+ "default_prefix: http://example.org/test-schema-derived/\n",
+ "default_range: string\n",
+ "classes:\n",
+ " Individual:\n",
+ " name: Individual\n",
+ " attributes:\n",
+ " name:\n",
+ " name: name\n",
+ " age_in_months:\n",
+ " name: age_in_months\n",
+ " height_in_meters:\n",
+ " name: height_in_meters\n"
+ ]
+ }
+ ],
+ "source": [
+ "print(yaml_dumper.dumps(session.target_schema()))"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-01-17T22:30:03.290589Z",
+ "start_time": "2024-01-17T22:30:03.286701Z"
+ }
+ },
+ "id": "7c1f7efef1836364"
+ },
+ {
+ "cell_type": "markdown",
+ "source": [
+ "Note that at this time, deriving ranges using expressions is not supported, so the two measurement fields\n",
+ "are erroneously typed as having the `default_range` of `string`. However, in principle, if you use the\n",
+ "linkml subset of Python it should be possible to infer the range of the derived field, and this may be added\n",
+ "in future versions. Currently the tool chain is at an early stage of development."
+ ],
+ "metadata": {
+ "collapsed": false
+ },
+ "id": "e87b7f45dc137a68"
+ },
+ {
+ "cell_type": "markdown",
+ "source": [
+ "## Unit conversions\n",
+ "\n",
+ "Next we will look at a different way of doing unit conversions. The LinkML specification allows\n",
+ "schemas to explicitly declare the units of slots, so let's modify our schema to do this, adding\n",
+ "a UCUM code for our `height_in_cm` slot:"
+ ],
+ "metadata": {
+ "collapsed": false
+ },
+ "id": "ff3d20924263ec15"
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 12,
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "name: test-schema\n",
+ "id: http://example.org/test-schema\n",
+ "imports:\n",
+ "- linkml:types\n",
+ "prefixes:\n",
+ " linkml: https://w3id.org/linkml/\n",
+ " test_schema: http://example.org/test-schema/\n",
+ "default_prefix: test_schema\n",
+ "default_range: string\n",
+ "slots:\n",
+ " family_name:\n",
+ " range: string\n",
+ " given_name:\n",
+ " range: string\n",
+ " age_in_years:\n",
+ " range: integer\n",
+ " height_in_cm:\n",
+ " range: float\n",
+ " unit:\n",
+ " ucum_code: cm\n",
+ "classes:\n",
+ " Person:\n",
+ " slots:\n",
+ " - family_name\n",
+ " - given_name\n",
+ " - age_in_years\n",
+ " - height_in_cm\n"
+ ]
+ }
+ ],
+ "source": [
+ "from linkml_runtime.linkml_model.units import UnitOfMeasure\n",
+ "sb.schema.slots['height_in_cm'].unit = UnitOfMeasure(ucum_code='cm')\n",
+ "session.set_source_schema(sb.as_dict())\n",
+ "print(yaml.dump(sb.as_dict(), sort_keys=False))"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-01-17T22:30:03.323328Z",
+ "start_time": "2024-01-17T22:30:03.300567Z"
+ }
+ },
+ "id": "65a5ce5d97e27f76"
+ },
+ {
+ "cell_type": "markdown",
+ "source": [
+ "## Adding target_unit to transformer specification\n",
+ "\n",
+ "We will create a new transformer specification, focusing on the `height_in_cm` field. We will\n",
+ "transform this into a `height_in_meters` field, and will use the `target_unit` field to specify\n",
+ "the target unit."
+ ],
+ "metadata": {
+ "collapsed": false
+ },
+ "id": "c5cf59ec9ac3148e"
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 13,
+ "outputs": [],
+ "source": [
+ "session.set_object_transformer(\"\"\"\n",
+ "class_derivations:\n",
+ " Individual:\n",
+ " populated_from: Person\n",
+ " slot_derivations:\n",
+ " name:\n",
+ " expr: \"{given_name} + ' ' + {family_name}\"\n",
+ " height_in_meters:\n",
+ " populated_from: height_in_cm\n",
+ " unit_conversion:\n",
+ " target_unit: m\n",
+ "\"\"\")"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-01-17T22:30:03.365363Z",
+ "start_time": "2024-01-17T22:30:03.321298Z"
+ }
+ },
+ "id": "bc99bad97970b1b7"
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 14,
+ "outputs": [
+ {
+ "data": {
+ "text/plain": "{'name': 'Jane Doe', 'height_in_meters': 1.8}"
+ },
+ "execution_count": 14,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "session.transform(obj)"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-01-17T22:30:03.622621Z",
+ "start_time": "2024-01-17T22:30:03.370531Z"
+ }
+ },
+ "id": "831b444d9c47e0ea"
+ },
+ {
+ "cell_type": "markdown",
+ "source": [
+ "## Units in derived schema\n",
+ "\n",
+ "Next we'll look at the derived target schema, and as expected we see that it has inferred\n",
+ "the target unit for the `height_in_meters` field:"
+ ],
+ "metadata": {
+ "collapsed": false
+ },
+ "id": "6f37087c6dfc30ef"
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 15,
+ "outputs": [
+ {
+ "name": "stdout",
+ "output_type": "stream",
+ "text": [
+ "name: test-schema-derived\n",
+ "id: http://example.org/test-schema-derived\n",
+ "imports:\n",
+ "- linkml:types\n",
+ "prefixes:\n",
+ " linkml:\n",
+ " prefix_prefix: linkml\n",
+ " prefix_reference: https://w3id.org/linkml/\n",
+ " test_schema:\n",
+ " prefix_prefix: test_schema\n",
+ " prefix_reference: http://example.org/test-schema/\n",
+ "default_prefix: http://example.org/test-schema-derived/\n",
+ "default_range: string\n",
+ "classes:\n",
+ " Individual:\n",
+ " name: Individual\n",
+ " attributes:\n",
+ " name:\n",
+ " name: name\n",
+ " height_in_meters:\n",
+ " name: height_in_meters\n",
+ " range: float\n",
+ " unit:\n",
+ " ucum_code: m\n"
+ ]
+ }
+ ],
+ "source": [
+ "print(yaml_dumper.dumps(session.target_schema()))\n"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-01-17T22:30:03.629604Z",
+ "start_time": "2024-01-17T22:30:03.624546Z"
+ }
+ },
+ "id": "b589e0e95550962d"
+ },
+ {
+ "cell_type": "markdown",
+ "source": [
+ "## Tabular serialization"
+ ],
+ "metadata": {
+ "collapsed": false
+ },
+ "id": "8f4c4cb125aade0b"
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 16,
+ "outputs": [],
+ "source": [
+ "slot = sb.add_slot(\"aliases\", multivalued=True, range=\"string\", replace_if_present=True)"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-01-17T22:30:03.630816Z",
+ "start_time": "2024-01-17T22:30:03.629262Z"
+ }
+ },
+ "id": "f492b27c0f0fbf88"
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 17,
+ "outputs": [],
+ "source": [
+ "sb.schema.classes['Person'].slots.append(slot.name)"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-01-17T22:30:03.661717Z",
+ "start_time": "2024-01-17T22:30:03.635358Z"
+ }
+ },
+ "id": "3ac3f93ab8561300"
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 18,
+ "outputs": [],
+ "source": [
+ "session.set_source_schema(sb.as_dict())"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-01-17T22:30:03.662631Z",
+ "start_time": "2024-01-17T22:30:03.646582Z"
+ }
+ },
+ "id": "84262d357323f76e"
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 19,
+ "outputs": [],
+ "source": [
+ "session.set_object_transformer(\"\"\"\n",
+ "class_derivations:\n",
+ " Individual:\n",
+ " populated_from: Person\n",
+ " slot_derivations:\n",
+ " family_name:\n",
+ " populated_from: family_name\n",
+ " given_name:\n",
+ " populated_from: given_name\n",
+ " age:\n",
+ " populated_from: age_in_years\n",
+ " height:\n",
+ " populated_from: height_in_cm\n",
+ " aliases:\n",
+ " populated_from: aliases\n",
+ " stringification:\n",
+ " delimiter: '|'\n",
+ "\"\"\") "
+ ],
+ "metadata": {
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-01-17T22:30:03.709283Z",
+ "start_time": "2024-01-17T22:30:03.667849Z"
+ }
+ },
+ "id": "2f282430f48e13c0"
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 20,
+ "outputs": [
+ {
+ "data": {
+ "text/plain": "{'family_name': 'Doe',\n 'given_name': 'Jane',\n 'age': 42,\n 'height': 180.0,\n 'aliases': 'Jane|Janie|Janey'}"
+ },
+ "execution_count": 20,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "obj = {\n",
+ " \"given_name\": \"Jane\",\n",
+ " \"family_name\": \"Doe\",\n",
+ " \"age_in_years\": 42,\n",
+ " \"height_in_cm\": 180.0,\n",
+ " \"aliases\": [\"Jane\", \"Janie\", \"Janey\"]\n",
+ " }\n",
+ "flattened = session.transform(obj)\n",
+ "flattened"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-01-17T22:30:03.739195Z",
+ "start_time": "2024-01-17T22:30:03.711288Z"
+ }
+ },
+ "id": "fdd23ae82909770e"
+ },
+ {
+ "cell_type": "markdown",
+ "source": [
+ "this can easily be serialized to a CSV/TSV"
+ ],
+ "metadata": {
+ "collapsed": false
+ },
+ "id": "c5174dcbf7dd0c43"
+ },
+ {
+ "cell_type": "markdown",
+ "source": [
+ "## Reverse transform\n",
+ "\n",
+ "If a transform does not contain one-way functions,\n",
+ "it can be *reversed*.\n",
+ "\n",
+ "In this case, reversing the transform allows us to map\n",
+ "from the tabular form back to the richer original representation."
+ ],
+ "metadata": {
+ "collapsed": false
+ },
+ "id": "fae8392b02526408"
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 21,
+ "outputs": [
+ {
+ "data": {
+ "text/plain": "{'family_name': 'Doe',\n 'given_name': 'Jane',\n 'age_in_years': 42,\n 'height_in_cm': 180.0,\n 'aliases': ['Jane', 'Janie', 'Janey']}"
+ },
+ "execution_count": 21,
+ "metadata": {},
+ "output_type": "execute_result"
+ }
+ ],
+ "source": [
+ "session.reverse_transform(flattened)"
+ ],
+ "metadata": {
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-01-17T22:30:03.781498Z",
+ "start_time": "2024-01-17T22:30:03.754420Z"
+ }
+ },
+ "id": "e8c1c3f98081d38"
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 21,
+ "outputs": [],
+ "source": [],
+ "metadata": {
+ "collapsed": false,
+ "ExecuteTime": {
+ "end_time": "2024-01-17T22:30:03.785065Z",
+ "start_time": "2024-01-17T22:30:03.782845Z"
+ }
+ },
+ "id": "ee14ace4b1c7d256"
+ }
+ ],
+ "metadata": {
+ "kernelspec": {
+ "display_name": "Python 3",
+ "language": "python",
+ "name": "python3"
+ },
+ "language_info": {
+ "codemirror_mode": {
+ "name": "ipython",
+ "version": 2
+ },
+ "file_extension": ".py",
+ "mimetype": "text/x-python",
+ "name": "python",
+ "nbconvert_exporter": "python",
+ "pygments_lexer": "ipython2",
+ "version": "2.7.6"
+ }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/poetry.lock b/poetry.lock
index 16c3dca..4d4c034 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -25,14 +25,14 @@ files = [
[[package]]
name = "anyio"
-version = "4.2.0"
+version = "4.3.0"
description = "High level compatibility layer for multiple asynchronous event loop implementations"
category = "dev"
optional = false
python-versions = ">=3.8"
files = [
- {file = "anyio-4.2.0-py3-none-any.whl", hash = "sha256:745843b39e829e108e518c489b31dc757de7d2131d53fac32bd8df268227bfee"},
- {file = "anyio-4.2.0.tar.gz", hash = "sha256:e1875bb4b4e2de1669f4bc7869b6d3f54231cdced71605e6e64c9be77e3be50f"},
+ {file = "anyio-4.3.0-py3-none-any.whl", hash = "sha256:048e05d0f6caeed70d731f3db756d35dcc1f35747c8c403364a8332c630441b8"},
+ {file = "anyio-4.3.0.tar.gz", hash = "sha256:f75253795a87df48568485fd18cdd2a3fa5c4f7c5be8e5e36637733fce06fed6"},
]
[package.dependencies]
@@ -48,14 +48,14 @@ trio = ["trio (>=0.23)"]
[[package]]
name = "appnope"
-version = "0.1.3"
+version = "0.1.4"
description = "Disable App Nap on macOS >= 10.9"
category = "dev"
optional = false
-python-versions = "*"
+python-versions = ">=3.6"
files = [
- {file = "appnope-0.1.3-py2.py3-none-any.whl", hash = "sha256:265a455292d0bd8a72453494fa24df5a11eb18373a60c7c0430889f22548605e"},
- {file = "appnope-0.1.3.tar.gz", hash = "sha256:02bd91c4de869fbb1e1c50aafc4098827a7a54ab2f39d9dcba6c9547ed920e24"},
+ {file = "appnope-0.1.4-py2.py3-none-any.whl", hash = "sha256:502575ee11cd7a28c0205f379b525beefebab9d161b7c964670864014ed7213c"},
+ {file = "appnope-0.1.4.tar.gz", hash = "sha256:1de3860566df9caf38f01f86f65e0e13e379af54f9e4bee1e66b48f2efffd1ee"},
]
[[package]]
@@ -139,14 +139,14 @@ test = ["dateparser (>=1.0.0,<2.0.0)", "pre-commit", "pytest", "pytest-cov", "py
[[package]]
name = "asteval"
-version = "0.9.31"
+version = "0.9.32"
description = "Safe, minimalistic evaluator of python expression using ast module"
category = "main"
optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
files = [
- {file = "asteval-0.9.31-py3-none-any.whl", hash = "sha256:2761750c184d97707c292b62df3b10e330a809a2201721acc435a2b89a114263"},
- {file = "asteval-0.9.31.tar.gz", hash = "sha256:a2da066b6696dba9835c5f7dec63e0ffb5bd2b4e3bb5f0b9a604aeafb17d833d"},
+ {file = "asteval-0.9.32-py3-none-any.whl", hash = "sha256:4d0da45a15f15eeb88bb53cf4c352591ccb00f00f81f74649fd7084519adc3fe"},
+ {file = "asteval-0.9.32.tar.gz", hash = "sha256:3bef25a973d378fda21c83a38c6292c4d0d94773f49f42073e69dbb19932bb74"},
]
[package.extras]
@@ -226,20 +226,23 @@ dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
[[package]]
name = "beautifulsoup4"
-version = "4.12.2"
+version = "4.12.3"
description = "Screen-scraping library"
category = "dev"
optional = false
python-versions = ">=3.6.0"
files = [
- {file = "beautifulsoup4-4.12.2-py3-none-any.whl", hash = "sha256:bd2520ca0d9d7d12694a53d44ac482d181b4ec1888909b035a3dbf40d0f57d4a"},
- {file = "beautifulsoup4-4.12.2.tar.gz", hash = "sha256:492bbc69dca35d12daac71c4db1bfff0c876c00ef4a2ffacce226d4638eb72da"},
+ {file = "beautifulsoup4-4.12.3-py3-none-any.whl", hash = "sha256:b80878c9f40111313e55da8ba20bdba06d8fa3969fc68304167741bbf9e082ed"},
+ {file = "beautifulsoup4-4.12.3.tar.gz", hash = "sha256:74e3d1928edc070d21748185c46e3fb33490f22f52a3addee9aee0f4f7781051"},
]
[package.dependencies]
soupsieve = ">1.2"
[package.extras]
+cchardet = ["cchardet"]
+chardet = ["chardet"]
+charset-normalizer = ["charset-normalizer"]
html5lib = ["html5lib"]
lxml = ["lxml"]
@@ -264,26 +267,26 @@ css = ["tinycss2 (>=1.1.0,<1.3)"]
[[package]]
name = "cachetools"
-version = "5.3.2"
+version = "5.3.3"
description = "Extensible memoizing collections and decorators"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.7"
files = [
- {file = "cachetools-5.3.2-py3-none-any.whl", hash = "sha256:861f35a13a451f94e301ce2bec7cac63e881232ccce7ed67fab9b5df4d3beaa1"},
- {file = "cachetools-5.3.2.tar.gz", hash = "sha256:086ee420196f7b2ab9ca2db2520aca326318b68fe5ba8bc4d49cca91add450f2"},
+ {file = "cachetools-5.3.3-py3-none-any.whl", hash = "sha256:0abad1021d3f8325b2fc1d2e9c8b9c9d57b04c3932657a72465447332c24d945"},
+ {file = "cachetools-5.3.3.tar.gz", hash = "sha256:ba29e2dfa0b8b556606f097407ed1aa62080ee108ab0dc5ec9d6a723a007d105"},
]
[[package]]
name = "certifi"
-version = "2023.11.17"
+version = "2024.2.2"
description = "Python package for providing Mozilla's CA Bundle."
category = "main"
optional = false
python-versions = ">=3.6"
files = [
- {file = "certifi-2023.11.17-py3-none-any.whl", hash = "sha256:e036ab49d5b79556f99cfc2d9320b34cfbe5be05c5871b51de9329f0603b0474"},
- {file = "certifi-2023.11.17.tar.gz", hash = "sha256:9b469f3a900bf28dc19b8cfbf8019bf47f7fdd1a65a1d4ffb98fc14166beb4d1"},
+ {file = "certifi-2024.2.2-py3-none-any.whl", hash = "sha256:dc383c07b76109f368f6106eee2b593b04a011ea4d55f652c6ca24a754d1cdd1"},
+ {file = "certifi-2024.2.2.tar.gz", hash = "sha256:0569859f95fc761b18b45ef421b1290a0f65f147e92a1e5eb3e635f9a5e4e66f"},
]
[[package]]
@@ -369,7 +372,7 @@ rdflib = ">=0.4.2"
name = "chardet"
version = "5.2.0"
description = "Universal encoding detector for Python 3"
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.7"
files = [
@@ -506,14 +509,14 @@ files = [
[[package]]
name = "comm"
-version = "0.2.1"
+version = "0.2.2"
description = "Jupyter Python Comm implementation, for usage in ipykernel, xeus-python etc."
category = "dev"
optional = false
python-versions = ">=3.8"
files = [
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version = "0.3.8"
description = "Distribution utilities"
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+
[[package]]
name = "editorconfig"
-version = "0.12.3"
+version = "0.12.4"
description = "EditorConfig File Locator and Interpreter for Python"
category = "dev"
optional = false
python-versions = "*"
files = [
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[[package]]
@@ -789,7 +852,7 @@ devel = ["colorama", "json-spec", "jsonschema", "pylint", "pytest", "pytest-benc
name = "filelock"
version = "3.13.1"
description = "A platform independent file lock."
-category = "main"
+category = "dev"
optional = false
python-versions = ">=3.8"
files = [
@@ -832,22 +895,55 @@ python-dateutil = ">=2.8.1"
[package.extras]
dev = ["flake8", "markdown", "twine", "wheel"]
+[[package]]
+name = "gitdb"
+version = "4.0.11"
+description = "Git Object Database"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+files = [
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+
+[package.dependencies]
+smmap = ">=3.0.1,<6"
+
+[[package]]
+name = "gitpython"
+version = "3.1.42"
+description = "GitPython is a Python library used to interact with Git repositories"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+files = [
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+[package.dependencies]
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+
+[package.extras]
+test = ["black", "coverage[toml]", "ddt (>=1.1.1,!=1.4.3)", "mock", "mypy", "pre-commit", "pytest (>=7.3.1)", "pytest-cov", "pytest-instafail", "pytest-mock", "pytest-sugar"]
+
[[package]]
name = "graphviz"
-version = "0.20.1"
+version = "0.20.3"
description = "Simple Python interface for Graphviz"
category = "dev"
optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
files = [
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dev = ["flake8", "pep8-naming", "tox (>=3)", "twine", "wheel"]
-docs = ["sphinx (>=5)", "sphinx-autodoc-typehints", "sphinx-rtd-theme"]
-test = ["coverage", "mock (>=4)", "pytest (>=7)", "pytest-cov", "pytest-mock (>=3)"]
+docs = ["sphinx (>=5,<7)", "sphinx-autodoc-typehints", "sphinx-rtd-theme"]
+test = ["coverage", "pytest (>=7,<8.1)", "pytest-cov", "pytest-mock (>=3)"]
[[package]]
name = "greenlet"
@@ -921,6 +1017,18 @@ files = [
docs = ["Sphinx", "furo"]
test = ["objgraph", "psutil"]
+[[package]]
+name = "h11"
+version = "0.14.0"
+description = "A pure-Python, bring-your-own-I/O implementation of HTTP/1.1"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+files = [
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+]
+
[[package]]
name = "hbreader"
version = "0.9.1"
@@ -933,6 +1041,53 @@ files = [
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]
+[[package]]
+name = "httpcore"
+version = "1.0.4"
+description = "A minimal low-level HTTP client."
+category = "dev"
+optional = false
+python-versions = ">=3.8"
+files = [
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+]
+
+[package.dependencies]
+certifi = "*"
+h11 = ">=0.13,<0.15"
+
+[package.extras]
+asyncio = ["anyio (>=4.0,<5.0)"]
+http2 = ["h2 (>=3,<5)"]
+socks = ["socksio (>=1.0.0,<2.0.0)"]
+trio = ["trio (>=0.22.0,<0.25.0)"]
+
+[[package]]
+name = "httpx"
+version = "0.27.0"
+description = "The next generation HTTP client."
+category = "dev"
+optional = false
+python-versions = ">=3.8"
+files = [
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+ {file = "httpx-0.27.0.tar.gz", hash = "sha256:a0cb88a46f32dc874e04ee956e4c2764aba2aa228f650b06788ba6bda2962ab5"},
+]
+
+[package.dependencies]
+anyio = "*"
+certifi = "*"
+httpcore = ">=1.0.0,<2.0.0"
+idna = "*"
+sniffio = "*"
+
+[package.extras]
+brotli = ["brotli", "brotlicffi"]
+cli = ["click (>=8.0.0,<9.0.0)", "pygments (>=2.0.0,<3.0.0)", "rich (>=10,<14)"]
+http2 = ["h2 (>=3,<5)"]
+socks = ["socksio (>=1.0.0,<2.0.0)"]
+
[[package]]
name = "idna"
version = "3.6"
@@ -947,23 +1102,23 @@ files = [
[[package]]
name = "importlib-metadata"
-version = "7.0.1"
+version = "7.1.0"
description = "Read metadata from Python packages"
category = "dev"
optional = false
python-versions = ">=3.8"
files = [
- {file = "importlib_metadata-7.0.1-py3-none-any.whl", hash = "sha256:4805911c3a4ec7c3966410053e9ec6a1fecd629117df5adee56dfc9432a1081e"},
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+ {file = "importlib_metadata-7.1.0.tar.gz", hash = "sha256:b78938b926ee8d5f020fc4772d487045805a55ddbad2ecf21c6d60938dc7fcd2"},
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[package.dependencies]
zipp = ">=0.5"
[package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
perf = ["ipython"]
-testing = ["flufl.flake8", "importlib-resources (>=1.3)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy (>=0.9.1)", "pytest-perf (>=0.9.2)", "pytest-ruff"]
+testing = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-perf (>=0.9.2)", "pytest-ruff (>=0.2.1)"]
[[package]]
name = "iniconfig"
@@ -979,14 +1134,14 @@ files = [
[[package]]
name = "ipykernel"
-version = "6.28.0"
+version = "6.29.3"
description = "IPython Kernel for Jupyter"
category = "dev"
optional = false
python-versions = ">=3.8"
files = [
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+ {file = "ipykernel-6.29.3.tar.gz", hash = "sha256:e14c250d1f9ea3989490225cc1a542781b095a18a19447fcf2b5eaf7d0ac5bd2"},
]
[package.dependencies]
@@ -1009,7 +1164,7 @@ cov = ["coverage[toml]", "curio", "matplotlib", "pytest-cov", "trio"]
docs = ["myst-parser", "pydata-sphinx-theme", "sphinx", "sphinx-autodoc-typehints", "sphinxcontrib-github-alt", "sphinxcontrib-spelling", "trio"]
pyqt5 = ["pyqt5"]
pyside6 = ["pyside6"]
-test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio", "pytest-cov", "pytest-timeout"]
+test = ["flaky", "ipyparallel", "pre-commit", "pytest (>=7.0)", "pytest-asyncio (>=0.23.5)", "pytest-cov", "pytest-timeout"]
[[package]]
name = "ipython"
@@ -1051,22 +1206,22 @@ test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.22)", "pa
[[package]]
name = "ipywidgets"
-version = "8.1.1"
+version = "8.1.2"
description = "Jupyter interactive widgets"
category = "dev"
optional = false
python-versions = ">=3.7"
files = [
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+ {file = "ipywidgets-8.1.2.tar.gz", hash = "sha256:d0b9b41e49bae926a866e613a39b0f0097745d2b9f1f3dd406641b4a57ec42c9"},
]
[package.dependencies]
comm = ">=0.1.3"
ipython = ">=6.1.0"
-jupyterlab-widgets = ">=3.0.9,<3.1.0"
+jupyterlab-widgets = ">=3.0.10,<3.1.0"
traitlets = ">=4.3.1"
-widgetsnbextension = ">=4.0.9,<4.1.0"
+widgetsnbextension = ">=4.0.10,<4.1.0"
[package.extras]
test = ["ipykernel", "jsonschema", "pytest (>=3.6.0)", "pytest-cov", "pytz"]
@@ -1123,14 +1278,14 @@ testing = ["Django", "attrs", "colorama", "docopt", "pytest (<7.0.0)"]
[[package]]
name = "jinja2"
-version = "3.1.2"
+version = "3.1.3"
description = "A very fast and expressive template engine."
category = "dev"
optional = false
python-versions = ">=3.7"
files = [
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]
[package.dependencies]
@@ -1141,13 +1296,13 @@ i18n = ["Babel (>=2.7)"]
[[package]]
name = "jsbeautifier"
-version = "1.14.11"
+version = "1.15.1"
description = "JavaScript unobfuscator and beautifier."
category = "dev"
optional = false
python-versions = "*"
files = [
- {file = "jsbeautifier-1.14.11.tar.gz", hash = "sha256:6b632581ea60dd1c133cd25a48ad187b4b91f526623c4b0fb5443ef805250505"},
+ {file = "jsbeautifier-1.15.1.tar.gz", hash = "sha256:ebd733b560704c602d744eafc839db60a1ee9326e30a2a80c4adb8718adc1b24"},
]
[package.dependencies]
@@ -1172,19 +1327,16 @@ pyyaml = "*"
[[package]]
name = "json5"
-version = "0.9.14"
+version = "0.9.24"
description = "A Python implementation of the JSON5 data format."
category = "dev"
optional = false
-python-versions = "*"
+python-versions = ">=3.8"
files = [
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+ {file = "json5-0.9.24-py3-none-any.whl", hash = "sha256:4ca101fd5c7cb47960c055ef8f4d0e31e15a7c6c48c3b6f1473fc83b6c462a13"},
+ {file = "json5-0.9.24.tar.gz", hash = "sha256:0c638399421da959a20952782800e5c1a78c14e08e1dc9738fa10d8ec14d58c8"},
]
-[package.extras]
-dev = ["hypothesis"]
-
[[package]]
name = "jsonasobj"
version = "1.3.1"
@@ -1229,14 +1381,14 @@ jsonpointer = ">=1.9"
[[package]]
name = "jsonpath-ng"
-version = "1.6.0"
+version = "1.6.1"
description = "A final implementation of JSONPath for Python that aims to be standard compliant, including arithmetic and binary comparison operators and providing clear AST for metaprogramming."
category = "dev"
optional = false
python-versions = "*"
files = [
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- {file = "jsonpath_ng-1.6.0-py3-none-any.whl", hash = "sha256:6fd04833412c4b3d9299edf369542f5e67095ca84efa17cbb7f06a34958adc9f"},
+ {file = "jsonpath-ng-1.6.1.tar.gz", hash = "sha256:086c37ba4917304850bd837aeab806670224d3f038fe2833ff593a672ef0a5fa"},
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]
[package.dependencies]
@@ -1256,14 +1408,14 @@ files = [
[[package]]
name = "jsonschema"
-version = "4.20.0"
+version = "4.21.1"
description = "An implementation of JSON Schema validation for Python"
category = "main"
optional = false
python-versions = ">=3.8"
files = [
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- {file = "jsonschema-4.20.0.tar.gz", hash = "sha256:4f614fd46d8d61258610998997743ec5492a648b33cf478c1ddc23ed4598a5fa"},
+ {file = "jsonschema-4.21.1-py3-none-any.whl", hash = "sha256:7996507afae316306f9e2290407761157c6f78002dcf7419acb99822143d1c6f"},
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@@ -1323,14 +1475,14 @@ qtconsole = "*"
[[package]]
name = "jupyter-client"
-version = "8.6.0"
+version = "8.6.1"
description = "Jupyter protocol implementation and client libraries"
category = "dev"
optional = false
python-versions = ">=3.8"
files = [
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@@ -1372,14 +1524,14 @@ test = ["flaky", "pexpect", "pytest"]
[[package]]
name = "jupyter-core"
-version = "5.7.1"
+version = "5.7.2"
description = "Jupyter core package. A base package on which Jupyter projects rely."
category = "dev"
optional = false
python-versions = ">=3.8"
files = [
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@@ -1389,18 +1541,18 @@ traitlets = ">=5.3"
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-test = ["ipykernel", "pre-commit", "pytest", "pytest-cov", "pytest-timeout"]
+test = ["ipykernel", "pre-commit", "pytest (<8)", "pytest-cov", "pytest-timeout"]
[[package]]
name = "jupyter-events"
-version = "0.9.0"
+version = "0.10.0"
description = "Jupyter Event System library"
category = "dev"
optional = false
python-versions = ">=3.8"
files = [
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@@ -1419,14 +1571,14 @@ test = ["click", "pre-commit", "pytest (>=7.0)", "pytest-asyncio (>=0.19.0)", "p
[[package]]
name = "jupyter-lsp"
-version = "2.2.1"
+version = "2.2.4"
description = "Multi-Language Server WebSocket proxy for Jupyter Notebook/Lab server"
category = "dev"
optional = false
python-versions = ">=3.8"
files = [
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@@ -1435,14 +1587,14 @@ jupyter-server = ">=1.1.2"
[[package]]
name = "jupyter-server"
-version = "2.12.2"
+version = "2.13.0"
description = "The backend—i.e. core services, APIs, and REST endpoints—to Jupyter web applications."
category = "dev"
optional = false
python-versions = ">=3.8"
files = [
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@@ -1468,18 +1620,18 @@ websocket-client = "*"
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[[package]]
name = "jupyter-server-terminals"
-version = "0.5.1"
+version = "0.5.3"
description = "A Jupyter Server Extension Providing Terminals."
category = "dev"
optional = false
python-versions = ">=3.8"
files = [
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@@ -1492,18 +1644,19 @@ test = ["jupyter-server (>=2.0.0)", "pytest (>=7.0)", "pytest-jupyter[server] (>
[[package]]
name = "jupyterlab"
-version = "4.0.10"
+version = "4.1.5"
description = "JupyterLab computational environment"
category = "dev"
optional = false
python-versions = ">=3.8"
files = [
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importlib-metadata = {version = ">=4.8.3", markers = "python_version < \"3.10\""}
ipykernel = "*"
jinja2 = ">=3.0.3"
@@ -1518,9 +1671,9 @@ tornado = ">=6.2.0"
traitlets = "*"
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[[package]]
@@ -1537,14 +1690,14 @@ files = [
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name = "jupyterlab-server"
-version = "2.25.2"
+version = "2.25.4"
description = "A set of server components for JupyterLab and JupyterLab like applications."
category = "dev"
optional = false
python-versions = ">=3.8"
files = [
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[[package]]
name = "jupyterlab-widgets"
-version = "3.0.9"
+version = "3.0.10"
description = "Jupyter interactive widgets for JupyterLab"
category = "dev"
optional = false
python-versions = ">=3.7"
files = [
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@@ -1594,14 +1747,14 @@ regex = ["regex"]
[[package]]
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+version = "1.7.6"
description = "Linked Open Data Modeling Language"
category = "dev"
optional = false
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+python-versions = "<4.0.0,>=3.8.1"
files = [
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jsonschema = {version = ">=4.0.0", extras = ["format"]}
linkml-dataops = "*"
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openpyxl = "*"
parse = "*"
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sqlalchemy = ">=1.4.31"
watchdog = ">=0.9.0"
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+tests = ["pyshacl (>=0.25.0,<0.26.0)"]
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version = "0.1.0"
@@ -1651,14 +1808,14 @@ linkml-runtime = ">=1.1.6"
[[package]]
name = "linkml-runtime"
-version = "1.6.3"
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description = "Runtime environment for LinkML, the Linked open data modeling language"
category = "main"
optional = false
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@@ -1697,72 +1854,72 @@ testing = ["coverage", "pyyaml"]
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[[package]]
name = "mkdocs-material"
-version = "9.5.3"
+version = "9.5.15"
description = "Documentation that simply works"
category = "dev"
optional = false
python-versions = ">=3.8"
files = [
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requests = ">=2.26,<3.0"
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[[package]]
@@ -1900,16 +2057,49 @@ pyyaml = "*"
requests = "*"
setuptools = ">=18.5"
+[[package]]
+name = "mkdocs-windmill"
+version = "1.0.5"
+description = "MkDocs theme focused on navigation and usability"
+category = "dev"
+optional = false
+python-versions = "*"
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+[package.dependencies]
+mkdocs = "*"
+
+[[package]]
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+description = "Plugin for mkdocs to generate markdown documents from jupyter notebooks."
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+
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name = "nbclient"
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+version = "0.10.0"
description = "A client library for executing notebooks. Formerly nbconvert's ExecutePreprocessor."
category = "dev"
optional = false
python-versions = ">=3.8.0"
files = [
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@@ -1921,18 +2111,18 @@ traitlets = ">=5.4"
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dev = ["pre-commit"]
docs = ["autodoc-traits", "mock", "moto", "myst-parser", "nbclient[test]", "sphinx (>=1.7)", "sphinx-book-theme", "sphinxcontrib-spelling"]
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[[package]]
name = "nbconvert"
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-description = "Converting Jupyter Notebooks"
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+description = "Converting Jupyter Notebooks (.ipynb files) to other formats. Output formats include asciidoc, html, latex, markdown, pdf, py, rst, script. nbconvert can be used both as a Python library (`import nbconvert`) or as a command line tool (invoked as `jupyter nbconvert ...`)."
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optional = false
python-versions = ">=3.8"
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qtpdf = ["nbconvert[qtpng]"]
qtpng = ["pyqtwebengine (>=5.15)"]
serve = ["tornado (>=6.1)"]
-test = ["flaky", "ipykernel", "ipywidgets (>=7.5)", "pytest"]
+test = ["flaky", "ipykernel", "ipywidgets (>=7.5)", "pytest (>=7)"]
webpdf = ["playwright"]
[[package]]
name = "nbformat"
-version = "5.9.2"
+version = "5.10.3"
description = "The Jupyter Notebook format"
category = "dev"
optional = false
python-versions = ">=3.8"
files = [
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@@ -1986,31 +2176,31 @@ test = ["pep440", "pre-commit", "pytest", "testpath"]
[[package]]
name = "nest-asyncio"
-version = "1.5.8"
+version = "1.6.0"
description = "Patch asyncio to allow nested event loops"
category = "dev"
optional = false
python-versions = ">=3.5"
files = [
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name = "notebook"
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description = "Jupyter Notebook - A web-based notebook environment for interactive computing"
category = "dev"
optional = false
python-versions = ">=3.8"
files = [
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jupyterlab-server = ">=2.22.1,<3"
notebook-shim = ">=0.2,<0.3"
tornado = ">=6.2.0"
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[[package]]
name = "notebook-shim"
-version = "0.2.3"
+version = "0.2.4"
description = "A shim layer for notebook traits and config"
category = "dev"
optional = false
python-versions = ">=3.7"
files = [
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@@ -2070,26 +2260,26 @@ dev = ["black", "mypy", "pytest"]
[[package]]
name = "overrides"
-version = "7.4.0"
+version = "7.7.0"
description = "A decorator to automatically detect mismatch when overriding a method."
category = "dev"
optional = false
python-versions = ">=3.6"
files = [
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[[package]]
name = "packaging"
-version = "23.2"
+version = "24.0"
description = "Core utilities for Python packages"
category = "main"
optional = false
python-versions = ">=3.7"
files = [
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@@ -2105,26 +2295,26 @@ files = [
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name = "pandocfilters"
-version = "1.5.0"
+version = "1.5.1"
description = "Utilities for writing pandoc filters in python"
category = "dev"
optional = false
python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
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name = "parse"
-version = "1.20.0"
+version = "1.20.1"
description = "parse() is the opposite of format()"
category = "dev"
optional = false
python-versions = "*"
files = [
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@@ -2199,30 +2389,30 @@ xarray = ["xarray"]
[[package]]
name = "platformdirs"
-version = "4.1.0"
+version = "4.2.0"
description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
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+category = "dev"
optional = false
python-versions = ">=3.8"
files = [
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[[package]]
name = "pluggy"
-version = "1.3.0"
+version = "1.4.0"
description = "plugin and hook calling mechanisms for python"
category = "main"
optional = false
python-versions = ">=3.8"
files = [
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python-versions = ">=3.8"
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+ {file = "watchdog-4.0.0-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:eed82cdf79cd7f0232e2fdc1ad05b06a5e102a43e331f7d041e5f0e0a34a51c4"},
+ {file = "watchdog-4.0.0-cp38-cp38-macosx_11_0_arm64.whl", hash = "sha256:ba30a896166f0fee83183cec913298151b73164160d965af2e93a20bbd2ab605"},
+ {file = "watchdog-4.0.0-cp39-cp39-macosx_10_9_universal2.whl", hash = "sha256:d18d7f18a47de6863cd480734613502904611730f8def45fc52a5d97503e5101"},
+ {file = "watchdog-4.0.0-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:2895bf0518361a9728773083908801a376743bcc37dfa252b801af8fd281b1ca"},
+ {file = "watchdog-4.0.0-cp39-cp39-macosx_11_0_arm64.whl", hash = "sha256:87e9df830022488e235dd601478c15ad73a0389628588ba0b028cb74eb72fed8"},
+ {file = "watchdog-4.0.0-pp310-pypy310_pp73-macosx_10_9_x86_64.whl", hash = "sha256:6e949a8a94186bced05b6508faa61b7adacc911115664ccb1923b9ad1f1ccf7b"},
+ {file = "watchdog-4.0.0-pp38-pypy38_pp73-macosx_10_9_x86_64.whl", hash = "sha256:6a4db54edea37d1058b08947c789a2354ee02972ed5d1e0dca9b0b820f4c7f92"},
+ {file = "watchdog-4.0.0-pp39-pypy39_pp73-macosx_10_9_x86_64.whl", hash = "sha256:d31481ccf4694a8416b681544c23bd271f5a123162ab603c7d7d2dd7dd901a07"},
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+ {file = "watchdog-4.0.0-py3-none-manylinux2014_armv7l.whl", hash = "sha256:6a9c71a0b02985b4b0b6d14b875a6c86ddea2fdbebd0c9a720a806a8bbffc69f"},
+ {file = "watchdog-4.0.0-py3-none-manylinux2014_i686.whl", hash = "sha256:557ba04c816d23ce98a06e70af6abaa0485f6d94994ec78a42b05d1c03dcbd50"},
+ {file = "watchdog-4.0.0-py3-none-manylinux2014_ppc64.whl", hash = "sha256:d0f9bd1fd919134d459d8abf954f63886745f4660ef66480b9d753a7c9d40927"},
+ {file = "watchdog-4.0.0-py3-none-manylinux2014_ppc64le.whl", hash = "sha256:f9b2fdca47dc855516b2d66eef3c39f2672cbf7e7a42e7e67ad2cbfcd6ba107d"},
+ {file = "watchdog-4.0.0-py3-none-manylinux2014_s390x.whl", hash = "sha256:73c7a935e62033bd5e8f0da33a4dcb763da2361921a69a5a95aaf6c93aa03a87"},
+ {file = "watchdog-4.0.0-py3-none-manylinux2014_x86_64.whl", hash = "sha256:6a80d5cae8c265842c7419c560b9961561556c4361b297b4c431903f8c33b269"},
+ {file = "watchdog-4.0.0-py3-none-win32.whl", hash = "sha256:8f9a542c979df62098ae9c58b19e03ad3df1c9d8c6895d96c0d51da17b243b1c"},
+ {file = "watchdog-4.0.0-py3-none-win_amd64.whl", hash = "sha256:f970663fa4f7e80401a7b0cbeec00fa801bf0287d93d48368fc3e6fa32716245"},
+ {file = "watchdog-4.0.0-py3-none-win_ia64.whl", hash = "sha256:9a03e16e55465177d416699331b0f3564138f1807ecc5f2de9d55d8f188d08c7"},
+ {file = "watchdog-4.0.0.tar.gz", hash = "sha256:e3e7065cbdabe6183ab82199d7a4f6b3ba0a438c5a512a68559846ccb76a78ec"},
]
[package.extras]
@@ -3968,14 +4161,14 @@ test = ["websockets"]
[[package]]
name = "widgetsnbextension"
-version = "4.0.9"
+version = "4.0.10"
description = "Jupyter interactive widgets for Jupyter Notebook"
category = "dev"
optional = false
python-versions = ">=3.7"
files = [
- {file = "widgetsnbextension-4.0.9-py3-none-any.whl", hash = "sha256:91452ca8445beb805792f206e560c1769284267a30ceb1cec9f5bcc887d15175"},
- {file = "widgetsnbextension-4.0.9.tar.gz", hash = "sha256:3c1f5e46dc1166dfd40a42d685e6a51396fd34ff878742a3e47c6f0cc4a2a385"},
+ {file = "widgetsnbextension-4.0.10-py3-none-any.whl", hash = "sha256:d37c3724ec32d8c48400a435ecfa7d3e259995201fbefa37163124a9fcb393cc"},
+ {file = "widgetsnbextension-4.0.10.tar.gz", hash = "sha256:64196c5ff3b9a9183a8e699a4227fb0b7002f252c814098e66c4d1cd0644688f"},
]
[[package]]
@@ -4060,21 +4253,21 @@ files = [
[[package]]
name = "zipp"
-version = "3.17.0"
+version = "3.18.1"
description = "Backport of pathlib-compatible object wrapper for zip files"
category = "dev"
optional = false
python-versions = ">=3.8"
files = [
- {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"},
- {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"},
+ {file = "zipp-3.18.1-py3-none-any.whl", hash = "sha256:206f5a15f2af3dbaee80769fb7dc6f249695e940acca08dfb2a4769fe61e538b"},
+ {file = "zipp-3.18.1.tar.gz", hash = "sha256:2884ed22e7d8961de1c9a05142eb69a247f120291bc0206a00a7642f09b5b715"},
]
[package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
[metadata]
lock-version = "2.0"
python-versions = "^3.9"
-content-hash = "aa8778026cd61fdf9b198224af216dafc02982e92682b2ecb63e3a85d1d0dcc4"
+content-hash = "4175279fa83ef62c842f590e323f31fd3080118d1323971402ba98c2d3439c6f"
diff --git a/pyproject.toml b/pyproject.toml
index 05e85f5..4b63f9e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -7,7 +7,7 @@ readme = "README.md"
[tool.poetry.dependencies]
python = "^3.9"
-linkml-runtime = ">=1.5.2"
+linkml-runtime = ">=1.7.2"
asteval = "^0.9.29"
deepdiff = "^6.7.1"
pydantic = "^2.5.3"
@@ -16,8 +16,11 @@ ucumvert = "^0.1.1"
[tool.poetry.dev-dependencies]
pytest = "^7.3.1"
pytest-cov = "^4.0.0"
-linkml = ">=1.5.0"
+linkml = ">=1.7.0"
mkdocs-mermaid2-plugin = "^0.6.0"
+mknotebooks = "^0.8.0"
+mkdocs-windmill = "*"
+tox = "*"
[tool.poetry.scripts]
linkml-tr = "linkml_transformer.cli.cli:main"
@@ -34,6 +37,10 @@ pint = "^0.23"
[tool.poetry.group.graphviz.dependencies]
graphviz = "^0.20.1"
+
+[tool.poetry.group.duckdb.dependencies]
+duckdb = "^0.10.1"
+
[build-system]
requires = ["poetry-core>=1.0.0"]
build-backend = "poetry.core.masonry.api"
diff --git a/src/docs/about.md b/src/docs/about.md
deleted file mode 100644
index 2269d5d..0000000
--- a/src/docs/about.md
+++ /dev/null
@@ -1 +0,0 @@
-# LinkML-Transformer
diff --git a/notebooks/Tutorial.ipynb b/src/docs/examples/Tutorial.ipynb
similarity index 92%
rename from notebooks/Tutorial.ipynb
rename to src/docs/examples/Tutorial.ipynb
index 73a00a9..456f5a1 100644
--- a/notebooks/Tutorial.ipynb
+++ b/src/docs/examples/Tutorial.ipynb
@@ -24,8 +24,8 @@
"metadata": {
"collapsed": false,
"ExecuteTime": {
- "end_time": "2024-01-17T22:29:59.302402Z",
- "start_time": "2024-01-17T22:29:58.965289Z"
+ "end_time": "2024-03-23T02:12:23.927439Z",
+ "start_time": "2024-03-23T02:12:23.819885Z"
}
},
"id": "63a064b31f623bdd"
@@ -97,8 +97,8 @@
"metadata": {
"collapsed": false,
"ExecuteTime": {
- "end_time": "2024-01-17T22:29:59.378265Z",
- "start_time": "2024-01-17T22:29:58.988218Z"
+ "end_time": "2024-03-23T02:12:24.139985Z",
+ "start_time": "2024-03-23T02:12:23.842320Z"
}
},
"id": "ef2c60ef7fbcbe20"
@@ -136,8 +136,8 @@
"metadata": {
"collapsed": false,
"ExecuteTime": {
- "end_time": "2024-01-17T22:30:01.239725Z",
- "start_time": "2024-01-17T22:29:59.312872Z"
+ "end_time": "2024-03-23T02:12:24.847826Z",
+ "start_time": "2024-03-23T02:12:24.138432Z"
}
},
"id": "a6257aa9e6ab021e"
@@ -166,8 +166,8 @@
"metadata": {
"collapsed": false,
"ExecuteTime": {
- "end_time": "2024-01-17T22:30:01.484509Z",
- "start_time": "2024-01-17T22:30:01.238874Z"
+ "end_time": "2024-03-23T02:12:25.094008Z",
+ "start_time": "2024-03-23T02:12:24.897951Z"
}
},
"id": "47b95e209790b423"
@@ -191,7 +191,7 @@
{
"data": {
"image/svg+xml": "\n\n\n\n\n",
- "text/plain": ""
+ "text/plain": ""
},
"execution_count": 5,
"metadata": {},
@@ -204,8 +204,8 @@
"metadata": {
"collapsed": false,
"ExecuteTime": {
- "end_time": "2024-01-17T22:30:02.244818Z",
- "start_time": "2024-01-17T22:30:01.486984Z"
+ "end_time": "2024-03-23T02:12:25.426050Z",
+ "start_time": "2024-03-23T02:12:25.096688Z"
}
},
"id": "1c623cdc3c1cfbca"
@@ -249,8 +249,8 @@
"metadata": {
"collapsed": false,
"ExecuteTime": {
- "end_time": "2024-01-17T22:30:02.251017Z",
- "start_time": "2024-01-17T22:30:02.241183Z"
+ "end_time": "2024-03-23T02:12:25.435969Z",
+ "start_time": "2024-03-23T02:12:25.431387Z"
}
},
"id": "9f4d1fc4ca97f80c"
@@ -331,13 +331,13 @@
"source": [
"from linkml_runtime.dumpers import yaml_dumper\n",
"\n",
- "print(yaml_dumper.dumps(session.target_schema()))"
+ "print(yaml_dumper.dumps(session.target_schema))"
],
"metadata": {
"collapsed": false,
"ExecuteTime": {
- "end_time": "2024-01-17T22:30:02.260147Z",
- "start_time": "2024-01-17T22:30:02.253561Z"
+ "end_time": "2024-03-23T02:12:25.442750Z",
+ "start_time": "2024-03-23T02:12:25.434388Z"
}
},
"id": "687912c18bf6752"
@@ -398,8 +398,8 @@
"metadata": {
"collapsed": false,
"ExecuteTime": {
- "end_time": "2024-01-17T22:30:02.326085Z",
- "start_time": "2024-01-17T22:30:02.258015Z"
+ "end_time": "2024-03-23T02:12:25.502675Z",
+ "start_time": "2024-03-23T02:12:25.460193Z"
}
},
"id": "789a7b6535ab410f"
@@ -422,7 +422,7 @@
{
"data": {
"image/svg+xml": "\n\n\n\n\n",
- "text/plain": ""
+ "text/plain": ""
},
"execution_count": 9,
"metadata": {},
@@ -435,8 +435,8 @@
"metadata": {
"collapsed": false,
"ExecuteTime": {
- "end_time": "2024-01-17T22:30:03.283023Z",
- "start_time": "2024-01-17T22:30:02.345894Z"
+ "end_time": "2024-03-23T02:12:25.810836Z",
+ "start_time": "2024-03-23T02:12:25.509345Z"
}
},
"id": "2a18ccb5d7dc469b"
@@ -470,8 +470,8 @@
"metadata": {
"collapsed": false,
"ExecuteTime": {
- "end_time": "2024-01-17T22:30:03.283868Z",
- "start_time": "2024-01-17T22:30:03.278695Z"
+ "end_time": "2024-03-23T02:12:25.816826Z",
+ "start_time": "2024-03-23T02:12:25.812549Z"
}
},
"id": "5e20e98e2b23751f"
@@ -523,13 +523,13 @@
}
],
"source": [
- "print(yaml_dumper.dumps(session.target_schema()))"
+ "print(yaml_dumper.dumps(session.target_schema))"
],
"metadata": {
"collapsed": false,
"ExecuteTime": {
- "end_time": "2024-01-17T22:30:03.290589Z",
- "start_time": "2024-01-17T22:30:03.286701Z"
+ "end_time": "2024-03-23T02:12:25.825306Z",
+ "start_time": "2024-03-23T02:12:25.820116Z"
}
},
"id": "7c1f7efef1836364"
@@ -608,8 +608,8 @@
"metadata": {
"collapsed": false,
"ExecuteTime": {
- "end_time": "2024-01-17T22:30:03.323328Z",
- "start_time": "2024-01-17T22:30:03.300567Z"
+ "end_time": "2024-03-23T02:12:25.850932Z",
+ "start_time": "2024-03-23T02:12:25.833403Z"
}
},
"id": "65a5ce5d97e27f76"
@@ -649,8 +649,8 @@
"metadata": {
"collapsed": false,
"ExecuteTime": {
- "end_time": "2024-01-17T22:30:03.365363Z",
- "start_time": "2024-01-17T22:30:03.321298Z"
+ "end_time": "2024-03-23T02:12:25.901551Z",
+ "start_time": "2024-03-23T02:12:25.853769Z"
}
},
"id": "bc99bad97970b1b7"
@@ -674,8 +674,8 @@
"metadata": {
"collapsed": false,
"ExecuteTime": {
- "end_time": "2024-01-17T22:30:03.622621Z",
- "start_time": "2024-01-17T22:30:03.370531Z"
+ "end_time": "2024-03-23T02:12:26.176193Z",
+ "start_time": "2024-03-23T02:12:25.901292Z"
}
},
"id": "831b444d9c47e0ea"
@@ -729,13 +729,13 @@
}
],
"source": [
- "print(yaml_dumper.dumps(session.target_schema()))\n"
+ "print(yaml_dumper.dumps(session.target_schema))\n"
],
"metadata": {
"collapsed": false,
"ExecuteTime": {
- "end_time": "2024-01-17T22:30:03.629604Z",
- "start_time": "2024-01-17T22:30:03.624546Z"
+ "end_time": "2024-03-23T02:12:26.176598Z",
+ "start_time": "2024-03-23T02:12:26.152743Z"
}
},
"id": "b589e0e95550962d"
@@ -760,8 +760,8 @@
"metadata": {
"collapsed": false,
"ExecuteTime": {
- "end_time": "2024-01-17T22:30:03.630816Z",
- "start_time": "2024-01-17T22:30:03.629262Z"
+ "end_time": "2024-03-23T02:12:26.176672Z",
+ "start_time": "2024-03-23T02:12:26.156764Z"
}
},
"id": "f492b27c0f0fbf88"
@@ -776,8 +776,8 @@
"metadata": {
"collapsed": false,
"ExecuteTime": {
- "end_time": "2024-01-17T22:30:03.661717Z",
- "start_time": "2024-01-17T22:30:03.635358Z"
+ "end_time": "2024-03-23T02:12:26.176741Z",
+ "start_time": "2024-03-23T02:12:26.159739Z"
}
},
"id": "3ac3f93ab8561300"
@@ -792,8 +792,8 @@
"metadata": {
"collapsed": false,
"ExecuteTime": {
- "end_time": "2024-01-17T22:30:03.662631Z",
- "start_time": "2024-01-17T22:30:03.646582Z"
+ "end_time": "2024-03-23T02:12:26.177256Z",
+ "start_time": "2024-03-23T02:12:26.168743Z"
}
},
"id": "84262d357323f76e"
@@ -825,8 +825,8 @@
"metadata": {
"collapsed": false,
"ExecuteTime": {
- "end_time": "2024-01-17T22:30:03.709283Z",
- "start_time": "2024-01-17T22:30:03.667849Z"
+ "end_time": "2024-03-23T02:12:26.249455Z",
+ "start_time": "2024-03-23T02:12:26.222590Z"
}
},
"id": "2f282430f48e13c0"
@@ -858,8 +858,8 @@
"metadata": {
"collapsed": false,
"ExecuteTime": {
- "end_time": "2024-01-17T22:30:03.739195Z",
- "start_time": "2024-01-17T22:30:03.711288Z"
+ "end_time": "2024-03-23T02:12:26.279106Z",
+ "start_time": "2024-03-23T02:12:26.242965Z"
}
},
"id": "fdd23ae82909770e"
@@ -909,8 +909,8 @@
"metadata": {
"collapsed": false,
"ExecuteTime": {
- "end_time": "2024-01-17T22:30:03.781498Z",
- "start_time": "2024-01-17T22:30:03.754420Z"
+ "end_time": "2024-03-23T02:12:26.339410Z",
+ "start_time": "2024-03-23T02:12:26.280636Z"
}
},
"id": "e8c1c3f98081d38"
@@ -923,8 +923,8 @@
"metadata": {
"collapsed": false,
"ExecuteTime": {
- "end_time": "2024-01-17T22:30:03.785065Z",
- "start_time": "2024-01-17T22:30:03.782845Z"
+ "end_time": "2024-03-23T02:12:26.339637Z",
+ "start_time": "2024-03-23T02:12:26.317148Z"
}
},
"id": "ee14ace4b1c7d256"
diff --git a/src/docs/faq.md b/src/docs/faq.md
new file mode 100644
index 0000000..cbccbe0
--- /dev/null
+++ b/src/docs/faq.md
@@ -0,0 +1,38 @@
+# FAQ
+
+## Why another framework?
+
+There are a number of excellent frameworks for performing mapping and data transformations.
+The LinkML Transformer framework was born out of a need for a framework that:
+
+- was not inherently tied to:
+ - a particular serialization format (e.g. RDF, JSON, ...)
+ - a particular programming language (e.g. Python, Java, ...)
+ - a particular database system or database language (e.g. PostgreSQL or SQL or SPARQL)
+ - not tied to a particular kind of transformation (e.g. ORM or Tables to RDF)
+- was a natural fit for the LinkML data modeling framework
+- was declarative and easy to perform machine reasoning over
+- is simple for simple use cases
+
+In its current state, this framework is less powerful and expressive than many other frameworks
+or methodologies for performing transformations. If you need to perform complex data transformations,
+you might be better off using an expressive query language like SPARQL or SQL, or even just coding
+transformations directly in a programming language or library like Python or Pandas (but note that
+even for the coding use case, the LinkML Transformer framework can be useful as a standard way
+of *documenting* transformations).
+
+Currently the main use case for this framework is *mostly isomorphic* transformations, with lightweight
+manipulations. These lend themselves well to a declarative framework. Uses cases that are a particularly good fit
+involve mapping between data-dictionary like standards, with large numbers of metadata elements, where these
+elements can often be mapped one-to-one, or with simple manipulations (e.g. unit conversions).
+
+The origins lie partly in the SSSOM standard, which is intended as an ultra-simple way of specifying
+precise mappings between *entities* (e.g. schema.org Person is the same as DBPedia person). We observed
+that many people wanted to extend the language to perform more complex mappings. To address this, we
+help a workshop at the Biocuration conference in Padua, Italy in 2022.
+
+- [Discussion](https://github.com/orgs/linkml/discussions/1829)
+- [SSSOM paper](https://academic.oup.com/database/article/doi/10.1093/database/baac035/6591806)
+- [SSSOM Update 2023](https://ceur-ws.org/Vol-3591/om2023_STpaper3.pdf)
+- [SSSOM Complex Mappings Workshop 2023](https://www.youtube.com/playlist?list=PLqu_J7ADQtKyX55F7RqZtaSS7TwGd3MoR)
+- [Mapping Data Structures: Challenges and Approaches](https://doi.org/10.5281/zenodo.10343505)
diff --git a/src/docs/index.md b/src/docs/index.md
new file mode 100644
index 0000000..a3064e1
--- /dev/null
+++ b/src/docs/index.md
@@ -0,0 +1,180 @@
+# LinkML-Transformer
+
+LinkML Transformer is a framework for specifying and executing mappings between data models.
+
+Features:
+
+- YAML-based lightweight syntax
+- Python library for executing mappings on data files
+- Ability to compile to other frameworks (SQL/DuckDB)
+- Derivation of target (implicit) schemas, allowing easy customization of data models (*profiling*)
+- Simple YAML dictionaries for simple mappings
+- Automatic unit conversion
+- Use of subset of Python to specify complex mappings
+- Visualizations of mappings
+- Mappings are reversible (provided all expressions used are reversible)
+- Compatibility with SSSOM
+
+This documentation are available at:
+
+- [linkml.io/linkml-transformer/](https://linkml.io/linkml-transformer/)
+
+Status:
+
+The transformation data model is not yet fully stable, and may be subject to change.
+Not all parts of the model are implemented in the reference Python framework.
+
+## Basic idea
+
+Given an object that conforms to a LinkML schema,e.g.:
+
+```yaml
+given_name: Jane
+family_name: Doe
+height_in_cm: 172.0
+age_in_years: 33
+aliases: [Janey, Janie]
+```
+
+Define a mapping in YAML:
+
+```yaml
+class_derivations:
+ Individual:
+ populated_from: Person
+ slot_derivations:
+ name:
+ expr: "{given_name} + ' ' + {family_name}"
+ description: Concatenating given and family names
+ note this is a bad assumption for names in general,
+ this is just for demonstration
+ height_in_meters:
+ populated_from: height_in_cm
+ unit_conversion:
+ target_unit: m
+ aliases:
+ populated_from: aliases
+ stringification:
+ delimiter: '|'
+```
+
+The schema mapping (aka [TransformationSpecification](TransformationSpecification.md)) specifies how to transform the data model.
+
+The schema mapping is a collection of one or more [ClassDerivation](ClassDerivation.md) objects,
+which themselves consist of one or more [SlotDerivation](SlotDerivation.md) objects.
+
+Transform the data:
+
+```bash
+linkml-tr map-data -T tr.yaml -s schema.yaml my-data.yaml
+```
+
+Giving:
+
+```yaml
+name: Jane Doe
+height_in_meters: 1.72
+aliases: Janey|Janie
+```
+
+## Installation and usage
+
+Installation and command line usage:
+
+```bash
+pip[x] install linkml-transformer
+cd tests/input/examples/personinfo_basic
+linkml-tr map-data \
+ -T transform/personinfo-to-agent.transform.yaml \
+ -s source/personinfo.yaml \
+ data/Container-001.yaml \
+ -o output/Translated-001.yaml
+```
+
+The command line has subcommands for:
+
+- `map-data` - map data from a source schema to a target schema
+- `derive-schema` - derive a target schema from a source schema and a mapping
+- `invert` - reverses a mapping
+- `compile` - compiles a mapping to another framework
+ - `markdown` - for generating static sites
+ - `graphviz` - for generating visualizations
+ - `python` - (partial)
+ - forthcoming: `r2rml`, ...
+
+## Details
+
+This repo contains both:
+
+- A [data model](datamodel) for a data model *transformation language*
+- A reference python implementation
+
+The transformation language is specified in terms of [LinkML](https://linkml.io) schemas.
+It is intended to be a *ployglot* transformation language, used for
+specifying how to map data models independent of underlying representation
+(TSVs, JSON/YAML, RDF, SQL Database, ...).
+
+Use cases include:
+
+- ETL and mapping from one data model to another
+- Database migrations (one version of a schema to another)
+- Creating "profiles"
+- Specifying mappings between different serializations of a model (e.g. OO to Relational)
+- Mapping between normalized/non-redundant forms and denormalized/query-optimized forms
+
+
+## Data Model
+
+The data model for transformations mirrors the data model for schemas:
+
+- A top level [TransformationSpecification](TransformationSpecification.md) class contains:
+ - Zero or more [ClassDerivation](ClassDerivation.md) objects, specifying how to map to a class, containing
+ - Zero or more [SlotDerivation](SlotDerivation.md) objects, specifying how to map to a slot
+ - Zero or more [EnumDerivation](EnumDerivation.md) objects, specifying how to map to an enum
+
+See the [generated docs](datamodel.md)
+
+## Conformance Suite
+
+The Transformers conformance suite contains a collection of tests for each feature of the language.
+
+See:
+
+* [Compliance Suite](specification/compliance.md)
+
+
+## Running the code
+
+```bash
+linkml-tr --help
+Usage: linkml-tr [OPTIONS] COMMAND [ARGS]...
+
+ CLI for linkml-transformer.
+
+Options:
+ -v, --verbose
+ -q, --quiet TEXT
+ --help Show this message and exit.
+
+Commands:
+ derive-schema Derive a schema from a source schema and a mapping.
+ map-data Map data in a source schema using a transformation.
+```
+
+### map-data
+
+Transforms (maps) data from a source schema to a target schema. This could range from a simple data dictionary mapping
+through to a complex mappings.
+
+```
+cd tests/input/examples/personinfo_basic
+linkml-tr map-data -T transform/personinfo-to-agent.transform.yaml -s source/personinfo.yaml data/Container-001.yaml
+```
+
+### derive-schema
+
+```
+cd tests/input/examples/personinfo_basic
+linkml-tr derive-schema -T transform/personinfo-to-agent.transform.yaml source/personinfo.yaml
+```
+
diff --git a/src/linkml_transformer/cli/cli.py b/src/linkml_transformer/cli/cli.py
index c61c888..394d2e0 100644
--- a/src/linkml_transformer/cli/cli.py
+++ b/src/linkml_transformer/cli/cli.py
@@ -1,4 +1,5 @@
"""Command line interface for linkml-transformer."""
+
import logging
import sys
@@ -93,7 +94,7 @@ def map_data(
with open(input) as file:
input_obj = yaml.safe_load(file)
tr.index(input_obj, source_type)
- tr_obj = tr.transform(input_obj, source_type)
+ tr_obj = tr.map_object(input_obj, source_type)
if output:
outfile = open(output, "w", encoding="utf-8")
else:
diff --git a/src/linkml_transformer/compiler/compiler.py b/src/linkml_transformer/compiler/compiler.py
index 52b533a..2a09c47 100644
--- a/src/linkml_transformer/compiler/compiler.py
+++ b/src/linkml_transformer/compiler/compiler.py
@@ -12,8 +12,9 @@
- LinkML-Transformer Specifications to Pandas
- LinkML-Transformer Specifications to Hamilton
"""
+
from abc import ABC
-from dataclasses import dataclass
+from dataclasses import dataclass, field
from types import ModuleType
from typing import Iterator, Optional
@@ -27,7 +28,7 @@
@dataclass
class CompiledSpecification:
- serialization: str
+ serialization: str = field(default="")
_module: Optional[ModuleType] = None
@@ -47,6 +48,9 @@ class Compiler(ABC):
an alternative representation.
An example compiler would be a R2RML compiler.
+
+ Note: Compilers and Importers will in general be implemented by providing
+ mapping specifications
"""
source_schemaview: SchemaView = None
diff --git a/src/linkml_transformer/compiler/sql_compiler.py b/src/linkml_transformer/compiler/sql_compiler.py
index 2fab732..80d44e5 100644
--- a/src/linkml_transformer/compiler/sql_compiler.py
+++ b/src/linkml_transformer/compiler/sql_compiler.py
@@ -1,12 +1,138 @@
+from linkml_runtime import SchemaView
+from linkml_runtime.linkml_model import SlotDefinition
+
from linkml_transformer.compiler.compiler import CompiledSpecification, Compiler
-from linkml_transformer.datamodel.transformer_model import TransformationSpecification
+from linkml_transformer.datamodel.transformer_model import (
+ ClassDerivation,
+ SerializationSyntaxType,
+ TransformationSpecification,
+)
+
+LINKML_TO_SQL_TYPE_MAP = {
+ "string": "TEXT",
+ "integer": "INTEGER",
+ "boolean": "BOOLEAN",
+ "float": "REAL",
+ "decimal": "REAL",
+ "datetime": "TIMESTAMP",
+ "date": "DATE",
+ "time": "TIME",
+ "uri": "TEXT",
+ "any": "TEXT",
+}
class SQLCompiler(Compiler):
"""
Compiles a Transformation Specification to SQL CREATE TABLE or VIEW statements.
+ Note: this is currently highly geared towards DuckDB.
"""
+ add_if_not_exists: bool = True
+ new_table_when_transforming: bool = False
+
def compile(self, specification: TransformationSpecification) -> CompiledSpecification:
- raise NotImplementedError
+ compiled = CompiledSpecification()
+ for cd in specification.class_derivations.values():
+ self.compile_class(compiled, cd, specification)
+ return compiled
+
+ def compile_class(
+ self,
+ compiled: CompiledSpecification,
+ cd: ClassDerivation,
+ specification: TransformationSpecification,
+ ) -> None:
+ """
+ Compile a class derivation to SQL.
+
+ :param compiled: (modified in place)
+ :param cd:
+ :param specification:
+ :return:
+ """
+ stmt = ""
+ if self.new_table_when_transforming:
+ stmt += "CREATE TABLE "
+ if self.add_if_not_exists:
+ stmt += "IF NOT EXISTS "
+ stmt += f"{cd.name} \n"
+ else:
+ stmt += f"INSERT INTO {cd.name} SELECT \n"
+ col_trs = []
+ for sd in cd.slot_derivations.values():
+ col_trs.append(self.compile_slot_derivation(sd))
+ if not col_trs:
+ return
+ stmt += ", \n".join(col_trs)
+ if self.new_table_when_transforming:
+ stmt += ");"
+ stmt += f" FROM {cd.name}"
+ compiled.serialization += f"{stmt};\n"
+
+ def compile_slot_derivation(self, sd) -> str:
+ expr = sd.populated_from
+ if expr is None:
+ expr = sd.name
+ if sd.stringification:
+ syntax = sd.stringification.syntax
+ delimiter = sd.stringification.delimiter
+ if sd.stringification.reversed:
+ pass
+ else:
+ # duckdb specific?
+ if syntax == SerializationSyntaxType.JSON:
+ expr = f"CAST({expr} AS TEXT)"
+ elif delimiter:
+ expr = f"STRING_AGG({expr}, '{delimiter}')"
+ return f" {sd.name} AS {expr}"
+
+ def create_ddl(self, schemaview: SchemaView) -> str:
+ """
+ Create DDL for the entire schema.
+
+ Note core LinkML has a SQL DDL generator, but this is primarily for pure relational models.
+
+ DuckDB allows complex datatypes.
+
+ TODO: move to LinkML core
+ :param schemaview:
+ :return:
+ """
+ ddl = []
+ for c in schemaview.all_classes().values():
+ if c.mixin or c.abstract:
+ continue
+ col_strs = []
+ for s in schemaview.class_induced_slots(c.name):
+ col_strs.append(f" {s.name} {self.sql_type(s, schemaview)}")
+ if not col_strs:
+ continue
+ ddl.append(f"CREATE TABLE IF NOT EXISTS {c.name} (")
+ ddl.append(",\n".join(col_strs))
+ ddl.append(");")
+ return "\n".join(ddl)
+
+ def sql_type(self, slot: SlotDefinition, schemaview: SchemaView) -> str:
+ """
+ Map LinkML types to DuckDB SQL types.
+
+ :param slot:
+ :param schemaview:
+ :return:
+ """
+ typ = "TEXT"
+ if slot.range:
+ if slot.range in LINKML_TO_SQL_TYPE_MAP:
+ typ = LINKML_TO_SQL_TYPE_MAP.get(slot.range, typ)
+ elif slot.range in schemaview.all_classes():
+ if slot.inlined:
+ typ = "TEXT"
+ else:
+ # TODO: consider structs
+ typ = "JSON"
+
+ if slot.multivalued:
+ typ = f"{typ}[]"
+ return typ
diff --git a/src/linkml_transformer/datamodel/specification_view.py b/src/linkml_transformer/datamodel/specification_view.py
deleted file mode 100644
index 8f701e5..0000000
--- a/src/linkml_transformer/datamodel/specification_view.py
+++ /dev/null
@@ -1,17 +0,0 @@
-from dataclasses import dataclass
-from typing import List
-
-from linkml_transformer.datamodel.transformer_model import (
- ElementDerivation,
- TransformationSpecification,
-)
-
-
-@dataclass
-class TransformerSpecificationView:
- specification: TransformationSpecification = None
-
- def derivations(self, derivation: ElementDerivation) -> List[ElementDerivation]:
- """Return all derivations of a given derivation"""
- closure = [derivation]
- return closure
diff --git a/src/linkml_transformer/datamodel/transformer_model.yaml b/src/linkml_transformer/datamodel/transformer_model.yaml
index e269e96..280a39a 100644
--- a/src/linkml_transformer/datamodel/transformer_model.yaml
+++ b/src/linkml_transformer/datamodel/transformer_model.yaml
@@ -312,6 +312,9 @@ classes:
- value: ';'
reversed:
range: boolean
+ over_slots:
+ range: string
+ multivalued: true
syntax:
range: SerializationSyntaxType
examples:
diff --git a/src/linkml_transformer/functions/unit_conversion.py b/src/linkml_transformer/functions/unit_conversion.py
index 49f771d..1f5d2a6 100644
--- a/src/linkml_transformer/functions/unit_conversion.py
+++ b/src/linkml_transformer/functions/unit_conversion.py
@@ -6,6 +6,7 @@
For UCUM, the ucumvert library is used to convert UCUM units to pint units,
see ``_.
"""
+
from enum import Enum
from functools import lru_cache
from typing import Any, Optional
diff --git a/src/linkml_transformer/inference/schema_mapper.py b/src/linkml_transformer/inference/schema_mapper.py
index 044c570..37713d7 100644
--- a/src/linkml_transformer/inference/schema_mapper.py
+++ b/src/linkml_transformer/inference/schema_mapper.py
@@ -3,6 +3,7 @@
AKA profiling
"""
+
import logging
from collections import defaultdict
from copy import copy
diff --git a/src/linkml_transformer/session.py b/src/linkml_transformer/session.py
index 1d6e3f4..f7aa8cf 100644
--- a/src/linkml_transformer/session.py
+++ b/src/linkml_transformer/session.py
@@ -1,17 +1,20 @@
import logging
from dataclasses import dataclass
from pathlib import Path
-from typing import Any, Optional, Union
+from typing import Any, Optional, Type, Union
import yaml
from linkml_runtime import SchemaView
from linkml_runtime.dumpers import yaml_dumper
from linkml_runtime.linkml_model import SchemaDefinition
+from linkml_runtime.processing.referencevalidator import ReferenceValidator
+from linkml_runtime.utils.introspection import package_schemaview
from linkml_transformer import ObjectTransformer
from linkml_transformer.datamodel.transformer_model import TransformationSpecification
from linkml_transformer.inference.inverter import TransformationSpecificationInverter
from linkml_transformer.inference.schema_mapper import SchemaMapper
+from linkml_transformer.transformer.transformer import Transformer
logger = logging.getLogger(__name__)
@@ -20,18 +23,45 @@
class Session:
"""
A wrapper object for a transformer session.
+
+ TODO:
+
+ - rename to Manager?
+ - consolidate configuration
+ - include source and target database
+
+ - current spec, src_sv, tgt_sv all live in both this class and transformer
"""
+ transformer_specification: Optional[TransformationSpecification] = None
source_schemaview: Optional[SchemaView] = None
+ transformer: Optional[Transformer] = None
object_transformer: Optional[ObjectTransformer] = None
schema_mapper: Optional[SchemaMapper] = None
_target_schema: Optional[SchemaDefinition] = None
+ _target_schemaview: Optional[SchemaView] = None
- @property
- def transformer_specification(self) -> TransformationSpecification:
- if self.object_transformer is None:
- raise ValueError("No transformer specified")
- return self.object_transformer.specification
+ def set_transformer_specification(
+ self, specification: Optional[Union[TransformationSpecification, dict, str, Path]] = None
+ ):
+ if isinstance(specification, Path):
+ specification = str(specification)
+ if isinstance(specification, TransformationSpecification):
+ self.transformer_specification = specification
+ elif isinstance(specification, dict):
+ # TODO: centralize this code
+ normalizer = ReferenceValidator(
+ package_schemaview("linkml_transformer.datamodel.transformer_model")
+ )
+ normalizer.expand_all = True
+ specification = normalizer.normalize(specification)
+ self.transformer_specification = TransformationSpecification(**specification)
+ elif isinstance(specification, str):
+ if "\n" in specification:
+ obj = yaml.safe_load(specification)
+ else:
+ obj = yaml.safe_load(open(specification))
+ self.set_transformer_specification(obj)
def set_source_schema(self, schema: Union[str, Path, dict, SchemaView, SchemaDefinition]):
"""
@@ -52,8 +82,21 @@ def set_source_schema(self, schema: Union[str, Path, dict, SchemaView, SchemaDef
self.source_schemaview = sv
self._target_schema = None
+ def set_transformer(
+ self,
+ transformer: Optional[Union[Transformer, Type[Transformer]]],
+ **kwargs,
+ ):
+ if isinstance(transformer, Type):
+ transformer = transformer()
+ transformer.specification = self.transformer_specification
+ self.transformer = transformer
+
def set_object_transformer(
- self, transformer: Optional[Union[ObjectTransformer, dict, str, Path]] = None
+ self,
+ transformer: Optional[
+ Union[ObjectTransformer, TransformationSpecification, dict, str, Path]
+ ] = None,
):
if transformer is None:
if self.object_transformer is not None:
@@ -62,38 +105,43 @@ def set_object_transformer(
else:
logger.warning("No transformer specified")
return
- if isinstance(transformer, ObjectTransformer):
- self.object_transformer = transformer
- elif isinstance(transformer, dict):
- self.object_transformer = ObjectTransformer()
- self.object_transformer.create_transformer_specification(transformer)
- elif isinstance(transformer, str):
- self.object_transformer = ObjectTransformer()
- self.object_transformer.create_transformer_specification(yaml.safe_load(transformer))
+ if transformer is not None:
+ if isinstance(transformer, ObjectTransformer):
+ self.object_transformer = transformer
+ else:
+ self.set_transformer_specification(transformer)
+ self.object_transformer = ObjectTransformer()
+ self.object_transformer.specification = self.transformer_specification
self._target_schema = None
+ @property
def target_schema(self) -> SchemaDefinition:
if self._target_schema is None:
if not self.schema_mapper:
self.schema_mapper = SchemaMapper(source_schemaview=self.source_schemaview)
- self._target_schema = self.schema_mapper.derive_schema(
- self.object_transformer.specification
- )
+ self._target_schema = self.schema_mapper.derive_schema(self.transformer_specification)
return self._target_schema
+ @property
+ def target_schemaview(self) -> SchemaView:
+ if self._target_schemaview is None:
+ # TODO: simplify
+ self._target_schemaview = SchemaView(yaml_dumper.dumps(self.target_schema))
+ return self._target_schemaview
+
def transform(self, obj: dict, **kwargs) -> dict:
if self.object_transformer is None:
raise ValueError("No transformer specified")
if not self.object_transformer.source_schemaview:
self.object_transformer.source_schemaview = self.source_schemaview
- return self.object_transformer.transform(obj, **kwargs)
+ return self.object_transformer.map_object(obj, **kwargs)
def reverse_transform(self, obj: dict, **kwargs) -> dict:
inv_spec = self.invert()
reverse_transformer = ObjectTransformer()
reverse_transformer.specification = inv_spec
- reverse_transformer.source_schemaview = SchemaView(yaml_dumper.dumps(self.target_schema()))
- return reverse_transformer.transform(obj, **kwargs)
+ reverse_transformer.source_schemaview = SchemaView(yaml_dumper.dumps(self.target_schema))
+ return reverse_transformer.map_object(obj, **kwargs)
def invert(self, in_place=False) -> TransformationSpecification:
"""
@@ -101,7 +149,7 @@ def invert(self, in_place=False) -> TransformationSpecification:
"""
inverter = TransformationSpecificationInverter(
source_schemaview=self.source_schemaview,
- target_schemaview=SchemaView(yaml_dumper.dumps(self.target_schema())),
+ target_schemaview=SchemaView(yaml_dumper.dumps(self.target_schema)),
)
inv_spec = inverter.invert(self.transformer_specification)
if in_place:
diff --git a/src/linkml_transformer/transformer/duckdb_transformer.py b/src/linkml_transformer/transformer/duckdb_transformer.py
new file mode 100644
index 0000000..f156e09
--- /dev/null
+++ b/src/linkml_transformer/transformer/duckdb_transformer.py
@@ -0,0 +1,70 @@
+import logging
+from dataclasses import dataclass
+from typing import Any, Dict, Optional, Union
+
+from duckdb import DuckDBPyConnection
+
+from linkml_transformer.compiler.sql_compiler import SQLCompiler
+from linkml_transformer.transformer.transformer import OBJECT_TYPE, Transformer
+
+DICT_OBJ = Dict[str, Any]
+DATABASE = Union[str, DuckDBPyConnection]
+
+
+logger = logging.getLogger(__name__)
+
+
+@dataclass
+class DuckDBTransformer(Transformer):
+ """
+ A Transformer that works on DuckDB data.
+ """
+
+ def map_object(
+ self,
+ source_obj: OBJECT_TYPE,
+ source_type: str = None,
+ target_type: str = None,
+ **kwargs,
+ ) -> OBJECT_TYPE:
+ """
+ Transform a source object into a target object.
+
+ :param source_obj: source data structure
+ :param source_type: source_obj instantiates this (may be class, type, or enum)
+ :param target_type: target_obj instantiates this (may be class, type, or enum)
+ :return: transformed data, either as type target_type or a dictionary
+ """
+ # sv = self.source_schemaview
+ raise NotImplementedError("DuckDBTransformer.transform")
+
+ def map_database(
+ self, source_database: DATABASE, target_database: Optional[DATABASE] = None, **kwargs
+ ) -> OBJECT_TYPE:
+ """
+ Transform source resource.
+
+ :param source_database:
+ :param target_database:
+ :param kwargs:
+ :return:
+ """
+ import duckdb
+
+ if target_database is None:
+ target_database = source_database
+
+ def _connect(db: DATABASE) -> DuckDBPyConnection:
+ if isinstance(db, str):
+ return duckdb.connect(db)
+ return db
+
+ source_connection = _connect(source_database)
+ target_connection = _connect(target_database)
+ sql_compiler = SQLCompiler()
+ source_connection.sql(sql_compiler.create_ddl(self.source_schemaview))
+ target_connection.sql(sql_compiler.create_ddl(self.target_schemaview))
+ if not self.specification:
+ raise ValueError("No specification provided.")
+ compiled = sql_compiler.compile(self.specification)
+ source_connection.execute(compiled.serialization)
diff --git a/src/linkml_transformer/transformer/object_transformer.py b/src/linkml_transformer/transformer/object_transformer.py
index 74ba290..63068be 100644
--- a/src/linkml_transformer/transformer/object_transformer.py
+++ b/src/linkml_transformer/transformer/object_transformer.py
@@ -55,7 +55,7 @@ def index(self, source_obj: Any, target: str = None):
else:
self.object_index = ObjectIndex(source_obj, schemaview=self.source_schemaview)
- def transform(
+ def map_object(
self,
source_obj: OBJECT_TYPE,
source_type: str = None,
@@ -174,16 +174,16 @@ def transform(
source_class_slot_range = source_class_slot.range
if source_class_slot.multivalued:
if isinstance(v, list):
- v = [self.transform(v1, source_class_slot_range, target_range) for v1 in v]
+ v = [self.map_object(v1, source_class_slot_range, target_range) for v1 in v]
elif isinstance(v, dict):
v = {
- k1: self.transform(v1, source_class_slot_range, target_range)
+ k1: self.map_object(v1, source_class_slot_range, target_range)
for k1, v1 in v.items()
}
else:
v = [v]
else:
- v = self.transform(v, source_class_slot_range, target_range)
+ v = self.map_object(v, source_class_slot_range, target_range)
if (
self._is_coerce_to_multivalued(slot_derivation, class_deriv)
and v is not None
@@ -342,7 +342,7 @@ def transform_object(
# source_obj_dict = source_obj.dict()
# else:
# raise ValueError(f"Do not know how to handle type: {typ}")
- tr_obj_dict = self.transform(source_obj, source_type_name)
+ tr_obj_dict = self.map_object(source_obj, source_type_name)
return target_class(**tr_obj_dict)
def transform_enum(self, source_value: str, enum_name: str, source_obj: Any) -> Optional[str]:
diff --git a/src/linkml_transformer/transformer/transformer.py b/src/linkml_transformer/transformer/transformer.py
index d1944d9..d2fb35e 100644
--- a/src/linkml_transformer/transformer/transformer.py
+++ b/src/linkml_transformer/transformer/transformer.py
@@ -2,12 +2,12 @@
Transformers (aka data mappers) are used to transform objects from one class to another
using a transformation specification.
"""
+
import logging
from abc import ABC
from copy import deepcopy
from dataclasses import dataclass, field
from pathlib import Path
-from types import ModuleType
from typing import Any, Dict, Optional, Union
import yaml
@@ -46,29 +46,24 @@ class Transformer(ABC):
subclass this
"""
- source_schemaview: SchemaView = None
- """A view over the schema describing the input/source object."""
-
specification: TransformationSpecification = None
"""A specification of how to generate target objects from source objects."""
+ source_schemaview: SchemaView = None
+ """A view over the schema describing the input/source object."""
+
_derived_specification: TransformationSpecification = None
"""A specification with inferred missing values."""
target_schemaview: Optional[SchemaView] = None
"""A view over the schema describing the output/target object."""
- target_module: Optional[ModuleType] = None
- """The python module which the target object should conform to."""
-
- prefix_map: Optional[Dict[str, str]] = None
- """Additional prefixes"""
-
unrestricted_eval: bool = field(default=False)
+ """Set to True to allow arbitrary evals as part of transformation."""
_curie_converter: Converter = None
- def transform(self, obj: OBJECT_TYPE, source_type: str = None) -> OBJECT_TYPE:
+ def map_object(self, obj: OBJECT_TYPE, source_type: str = None, **kwargs) -> OBJECT_TYPE:
"""
Transform source object into an instance of the target class.
@@ -78,6 +73,19 @@ def transform(self, obj: OBJECT_TYPE, source_type: str = None) -> OBJECT_TYPE:
"""
raise NotImplementedError
+ def map_database(
+ self, source_database: Any, target_database: Optional[Any] = None, **kwargs
+ ) -> OBJECT_TYPE:
+ """
+ Transform source resource.
+
+ :param source_database:
+ :param target_database:
+ :param kwargs:
+ :return:
+ """
+ raise NotImplementedError
+
def load_source_schema(self, path: Union[str, Path, dict]):
"""
Sets source_schemaview from a schema path.
diff --git a/src/linkml_transformer/utils/multi_file_transformer.py b/src/linkml_transformer/utils/multi_file_transformer.py
index 8752574..2c1dda6 100644
--- a/src/linkml_transformer/utils/multi_file_transformer.py
+++ b/src/linkml_transformer/utils/multi_file_transformer.py
@@ -1,6 +1,7 @@
"""Iterate through all examples in a folder testing them for validity.
"""
+
import glob
import logging
import os
@@ -190,7 +191,7 @@ def process_instructions(
for step in tr.steps:
input_obj = yaml.safe_load(open(str(root_directory / step.source_data)))
transformer.index(input_obj, step.source_class)
- target_obj = transformer.transform(input_obj, source_type=step.source_class)
+ target_obj = transformer.map_object(input_obj, source_type=step.source_class)
if step.target_data:
out_path = output_directory / step.target_data
out_path.parent.mkdir(parents=True, exist_ok=True)
diff --git a/tests/input/examples/biolink/source/biolink-model.yaml b/tests/input/examples/biolink/source/biolink-model.yaml
index 1819b89..0065382 100644
--- a/tests/input/examples/biolink/source/biolink-model.yaml
+++ b/tests/input/examples/biolink/source/biolink-model.yaml
@@ -5605,7 +5605,7 @@ classes:
chemical role:
is_a: attribute
description: >-
- A role played by the molecular entity or part thereof within a chemical context.
+ A role played by the molecular entity or part thereof within a chemical context.
id_prefixes:
- CHEBI
exact_mappings:
diff --git a/tests/test_compiler/test_duckdb_compiler.py b/tests/test_compiler/test_duckdb_compiler.py
new file mode 100644
index 0000000..09f4441
--- /dev/null
+++ b/tests/test_compiler/test_duckdb_compiler.py
@@ -0,0 +1,40 @@
+"""
+Tests compilation of a specification to python
+"""
+
+import pytest
+from linkml_runtime import SchemaView
+from linkml_runtime.dumpers import yaml_dumper
+
+from linkml_transformer.compiler.sql_compiler import SQLCompiler
+from linkml_transformer.session import Session
+from tests import SCHEMA1, SPECIFICATION
+
+
+@pytest.fixture
+def session():
+ session = Session()
+ session.set_source_schema(SCHEMA1)
+ session.set_transformer_specification(SPECIFICATION)
+ return session
+
+
+def test_compile(session):
+ compiler = SQLCompiler()
+ assert session.transformer_specification is not None
+ compiled = compiler.compile(session.transformer_specification)
+ # TODO: include imports so that code compiles
+ print(compiled.serialization)
+ source_sv = SchemaView(SCHEMA1)
+ source_ddl = compiler.create_ddl(source_sv)
+ print(source_ddl)
+ target_sv = session.target_schemaview
+ print(yaml_dumper.dumps(target_sv.schema))
+ target_ddl = compiler.create_ddl(target_sv)
+ print(target_ddl)
+
+ import duckdb
+
+ conn = duckdb.connect(":memory:")
+ conn.execute(target_ddl)
+ conn.execute(compiled.serialization)
diff --git a/tests/test_compiler/test_graphviz_compiler.py b/tests/test_compiler/test_graphviz_compiler.py
index 2858c1b..14ef715 100644
--- a/tests/test_compiler/test_graphviz_compiler.py
+++ b/tests/test_compiler/test_graphviz_compiler.py
@@ -1,6 +1,7 @@
"""
Tests compilation of a specification to graphviz
"""
+
import pytest
from linkml_runtime import SchemaView
diff --git a/tests/test_compiler/test_markdown_compiler.py b/tests/test_compiler/test_markdown_compiler.py
index bd2c507..7da9263 100644
--- a/tests/test_compiler/test_markdown_compiler.py
+++ b/tests/test_compiler/test_markdown_compiler.py
@@ -1,6 +1,7 @@
"""
Tests compilation of a specification to markdown
"""
+
import pytest
from linkml_runtime import SchemaView
diff --git a/tests/test_compiler/test_python_compiler.py b/tests/test_compiler/test_python_compiler.py
index 52e54b7..2767d45 100644
--- a/tests/test_compiler/test_python_compiler.py
+++ b/tests/test_compiler/test_python_compiler.py
@@ -1,6 +1,7 @@
"""
Tests compilation of a specification to python
"""
+
import pytest
from linkml_runtime import SchemaView
from linkml_runtime.utils.compile_python import compile_python
diff --git a/tests/test_compliance/test_compliance_suite.py b/tests/test_compliance/test_compliance_suite.py
index 3160d56..4a63c31 100644
--- a/tests/test_compliance/test_compliance_suite.py
+++ b/tests/test_compliance/test_compliance_suite.py
@@ -16,9 +16,11 @@
code can be abstract. You are encouraged to look at the markdown outputs
to see what is being generated for each test.
"""
+
import logging
import re
from dataclasses import dataclass
+from types import ModuleType
from typing import Any, Dict, Optional
import pytest
@@ -29,6 +31,7 @@
from linkml_runtime.linkml_model import Prefix, SchemaDefinition
from linkml_transformer.compiler.python_compiler import PythonCompiler
+from linkml_transformer.compiler.sql_compiler import SQLCompiler
from linkml_transformer.datamodel.transformer_model import (
CollectionType,
SerializationSyntaxType,
@@ -91,6 +94,25 @@ def build_transformer(**kwargs) -> TransformationSpecification:
return mapper.specification
+def create_compilers(spec: TransformationSpecification, expected_map: [Dict[ModuleType, str]]):
+ """
+ Test compilation of transformation specifications to other languages.
+
+ This test is a placeholder for future development, where the
+ transformation specification will be compiled to other languages
+ (e.g. SQL, R2RML, etc.)
+
+ :param spec: transformation specification
+ :return:
+ """
+ for compiler_type, expected in expected_map.items():
+ compiler = compiler_type()
+ compiled_spec = compiler.compile(spec)
+ print(f"**Compiled Specification ({compiler_type.__name__})**:\n\n")
+ print(compiled_spec.serialization)
+ assert expected in compiled_spec.serialization
+
+
@dataclass
class State:
schema_mapper: SchemaMapper = None
@@ -145,11 +167,11 @@ def map_object(
mapper.index(source_object, target=source_root)
if raises_error:
with pytest.raises(raises_error):
- target_object = mapper.transform(source_object)
+ target_object = mapper.map_object(source_object)
logger.debug(f"Unexpected Target Object: {target_object}")
target_object = None
else:
- target_object = mapper.transform(source_object)
+ target_object = mapper.map_object(source_object)
assert (
target_object == expected_target_object
), f"failed to map {source_object} to {expected_target_object}"
@@ -176,7 +198,7 @@ def map_object(
print("**Inverted Transformation Specification** (Derived):\n\n")
print_yaml(inv_spec)
inv_mapper = ObjectTransformer(source_schemaview=target_sv, specification=inv_spec)
- inv_target_object = inv_mapper.transform(target_object)
+ inv_target_object = inv_mapper.map_object(target_object)
if roundtrip_object is None:
roundtrip_object = source_object
assert (
@@ -697,18 +719,18 @@ def test_complex_unit_conversion(
@pytest.mark.parametrize(
- "delimiter,source_value,target_value",
+ "syntax,delimiter,source_value,target_value",
[
- (",", ["a", "b"], "a,b"),
- ("|", ["a", "b"], "a|b"),
- ("|", ["a"], "a"),
- ("|", [], ""),
- (SerializationSyntaxType.JSON, ["a", "b"], '["a", "b"]'),
- (SerializationSyntaxType.JSON, [], "[]"),
- (SerializationSyntaxType.YAML, ["a", "b"], "[a, b]"),
+ (None, ",", ["a", "b"], "a,b"),
+ (None, "|", ["a", "b"], "a|b"),
+ (None, "|", ["a"], "a"),
+ (None, "|", [], ""),
+ (SerializationSyntaxType.JSON, None, ["a", "b"], '["a", "b"]'),
+ (SerializationSyntaxType.JSON, None, [], "[]"),
+ (SerializationSyntaxType.YAML, None, ["a", "b"], "[a, b]"),
],
)
-def test_stringify(invocation_tracker, delimiter, source_value, target_value):
+def test_stringify(invocation_tracker, syntax, delimiter, source_value, target_value):
"""
Test compaction of multivalued slots into a string.
@@ -719,6 +741,7 @@ def test_stringify(invocation_tracker, delimiter, source_value, target_value):
- flattening lists or more complex objects using JSON or YAML
:param invocation_tracker: pytest fixture to emit metadata
+ :param syntax: SerializationSyntaxType
:param delimiter: delimiter to use in stringification
:param source_value: source value (a list)
:param target_value: expected value of slot in target object (a string)
@@ -733,18 +756,16 @@ def test_stringify(invocation_tracker, delimiter, source_value, target_value):
}
schema = build_schema("types", classes=classes)
source_sv = SchemaView(schema)
- stringification = {}
- if isinstance(delimiter, SerializationSyntaxType):
- stringification["syntax"] = delimiter.value
- else:
- stringification["delimiter"] = delimiter
cds = {
"D": {
"populated_from": "C",
"slot_derivations": {
"s1_verbatim": {
"populated_from": "s1",
- "stringification": stringification,
+ "stringification": {
+ "syntax": syntax,
+ "delimiter": delimiter,
+ },
}
},
}
@@ -758,6 +779,7 @@ def test_stringify(invocation_tracker, delimiter, source_value, target_value):
source_sv=source_sv,
invertible=True,
)
+ create_compilers(spec, {SQLCompiler: ""})
@pytest.mark.parametrize(
diff --git a/tests/test_transformer/test_duckdb_transformer.py b/tests/test_transformer/test_duckdb_transformer.py
new file mode 100644
index 0000000..b48b7c8
--- /dev/null
+++ b/tests/test_transformer/test_duckdb_transformer.py
@@ -0,0 +1,30 @@
+"""
+Tests compilation of a specification to python
+"""
+
+import pytest
+from linkml_runtime import SchemaView
+
+from linkml_transformer.session import Session
+from linkml_transformer.transformer.duckdb_transformer import DuckDBTransformer
+from tests import PERSONINFO_SRC_SCHEMA, PERSONINFO_TGT_SCHEMA, PERSONINFO_TR
+
+
+@pytest.fixture
+def session() -> Session:
+ session = Session()
+ session.set_source_schema(PERSONINFO_SRC_SCHEMA)
+ session.set_transformer_specification(PERSONINFO_TR)
+ if not session.transformer_specification:
+ raise ValueError("No specification provided.")
+ tr = DuckDBTransformer()
+ session.set_transformer(tr)
+ tr.specification = session.transformer_specification
+ tr.source_schemaview = SchemaView(str(PERSONINFO_SRC_SCHEMA))
+ tr.target_schemaview = SchemaView(str(PERSONINFO_TGT_SCHEMA))
+ return session
+
+
+def test_compile(session: Session):
+ pytest.skip("TODO")
+ session.transformer.map_database(":memory:")
diff --git a/tests/test_transformer/test_object_transformer.py b/tests/test_transformer/test_object_transformer.py
index 5630979..942932b 100644
--- a/tests/test_transformer/test_object_transformer.py
+++ b/tests/test_transformer/test_object_transformer.py
@@ -73,7 +73,7 @@ def test_transform_dict(self) -> None:
tr = self.tr
person_dict: dict[str, Any] = yaml.safe_load(open(str(PERSONINFO_DATA)))
assert person_dict["age_in_years"] == AGE_INT
- target_dict: dict[str, Any] = tr.transform(person_dict, source_type="Person")
+ target_dict: dict[str, Any] = tr.map_object(person_dict, source_type="Person")
assert isinstance(target_dict, type(TARGET_DATA))
assert target_dict["age"] == AGE_STRING
assert target_dict == TARGET_DATA
@@ -86,7 +86,7 @@ def test_transform_dict_in_container(self):
tr = self.tr
person_dict: dict[str, Any] = yaml.safe_load(open(str(PERSONINFO_DATA)))
container_dict = {"persons": [person_dict]}
- target_dict = tr.transform(container_dict, source_type="Container")
+ target_dict = tr.map_object(container_dict, source_type="Container")
assert target_dict == {"agents": [TARGET_DATA]}
def test_transform_multiple_dicts_in_container(self) -> None:
@@ -96,7 +96,7 @@ def test_transform_multiple_dicts_in_container(self) -> None:
"""
tr = self.tr
container_dict: dict[str, Any] = yaml.safe_load(open(str(PERSONINFO_CONTAINER_DATA)))
- target_dict: dict[str, Any] = tr.transform(container_dict, source_type="Container")
+ target_dict: dict[str, Any] = tr.map_object(container_dict, source_type="Container")
assert target_dict == CONTAINER_DATA
def check_familial_relationships(self, obj, data_model, expected):
@@ -294,7 +294,7 @@ def test_denormalized_transform_dict(self):
assert mset["mappings"] == [{"subject": "X:1", "object": "Y:1", "predicate": "P:1"}]
assert mset["entities"] == {"X:1": {"name": "x1"}, "Y:1": {"name": "y1"}}
tr.index(mset, "MappingSet")
- target_obj = tr.transform(mset, source_type="MappingSet")
+ target_obj = tr.map_object(mset, source_type="MappingSet")
assert isinstance(target_obj, dict)
assert target_obj["mappings"][0] == {
"subject_id": "X:1",
@@ -391,7 +391,7 @@ def mk(mv: bool, explicit: bool = False):
source_schemaview=SchemaView(source_schema),
target_schemaview=SchemaView(target_schema),
)
- target_instance = tr.transform(source_instance, class_name)
+ target_instance = tr.map_object(source_instance, class_name)
assert [val] if target_multivalued else val == target_instance[att_name]
def test_self_transform(self):
@@ -404,7 +404,7 @@ def test_self_transform(self):
)
normalizer.expand_all = True
source_object = normalizer.normalize(source_object)
- derived = tr.transform(source_object)
+ derived = tr.map_object(source_object)
print(derived)
print(yaml.dump(derived))