secoresearch/pylode Docker 镜像 - 轩辕镜像

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pyLODE

---

An OWL ontology documentation tool using Python and templating, based on LODE.

In addition to making human-readable forms of ontologies/taxonomies, pyLODE encourages ontology annotation best practice by only producing good results for well documented inputs! pyLODe defines what it ***s w'well documented' in sections below, such as Profiles_ & What pyLODE understands_.

Contents

1. Quick Intro_
2. Examples_
3. Installation_
4. Use_
5. What pyLODE understands_
6. Profiles_
7. Differences from LODE_
8. Releases_
9. License_
10. Citation_
11. Collaboration_
12. Contacts_

Quick Intro

The Live OWL Documentation Environment tool (LODE <[***]>) is a well-known (in Semantic Web circles) Java & XSLT-based tool used to generate human-readable HTML documents for OWL and RDF ontologies. That tool is now a bit dated (old-style HTML, use of older technologies like XSLT) and it's (online version <[***]>) is not always online.

This tool is a complete re-implementation of LODE's functionality using Python and Python's RDF manipulation module, rdflib <[***]>. An ontology to be documented is parsed and inspected using rdflib and HTML or Markdown is generated using basic Python scripting and Python's Jinja2 templating <[***]>.

The tool can be run as in these ways:

• Python command line
  • cli.py in the main folder
• BASH command line
  • bin/ directory, uses cli.py
• as-a-service locally
  • via the popular Falcon framework <[***]>__.
  • see server.py in the main folder
• as-a-service online
  • hosted at [***]

Examples

pyLODE has been tested with all of the 30+ ontologies in pylode/examples/ <pylode/examples/>_ and we are trying to ensure it captures all of their annotations. For each example, there is the original RDF file and the corresponding output, in HTML & Markdown. There are some examples of ADOC too.

For example, Epimorphic's <[***]>__'s Registry Ontology is:

• reg.ttl - source file
• reg.html - HTML output
  • this is a couple of releases ahead of the online version <[***]>_
• reg.md - Markdown output

Another, the Australian Government's Records Interoperability Framework (AGRIF) Ontology:

• agrif.ttl - source file
• agrif.html - HTML output
  • see this rendered online by GitHack <[***]>__
  • see the point-of-truth rendered online <[***]>__
• agrif.md - Markdown output
  • see this rendered online by GitHub <[***]>__
• agrif.md - ASCIIDOC output
  • resulting ADOC source <[***]>__
  • rendered in HTML <[***]>__
• agrif.skos.html - HTMl output, "vocpub" profile
  • see this rendered online by GitHack <[***]>__

You can build all of the example outputs locally by running pylode/examples/_make_examples.py <pylode/examples/_make_examples.py>_ which also serves as a good demonstration of calling pyLODE from a Python file.

Ontologies online using pyLODE:

• Australia's Department of Finance's <[***]>__'s AGRIF ontology - [***]
  • see the Markdown version <[***]>__
• National Archives of Australia <[***]>__'s Commonwealth Records Series ontology - [***]
  • see the Markdown version <[***]>__
• CSIRO's <[***]>__'s LocI ontology - [***]
• Geological Survey of Queensland <[***]>__'s Boreholes Profile - [***]
• Geoscience Australia <[***]>__'s Place Names Profile - [***]
• Epimorphic <[***]>__'s Registry Ontology
  • [***]
• Semantic Web for Earth and Environmental Terminology <[***]>__ (SWEET)
  • a series of ontologies that are live rendered into HTML via pyLODE being called by a Falcon server

See pairs of RDF & HTML files in the pylode/examples/ <pylode/examples/>__ directory for other, preprocessed examples.

Installation

This tool can be used either as a command line utility (Linux, Mac or Windows, see below) or as a Python module in other Python code. It can also be used via a hosted, online, service or even as a local web server that you can run. This repo contains executable files for Mac & Windows (soon Linux!) that you can use without any installation too.

The most important dependency to get correct when using this as a Python script of a command line program is the package rdflib which must be v5.0.0 or greater (see requirements.txt).

Python

Do this to use pyLODE as a Python command line program.

This tool is available on PyPI, the Python Package Index, at [***] and can be installed for use as a Python module via pip:

::

pip install pylode

To use pyLODE within Python, try something like this:

::

import pylode

html = pylode.MakeDocco(
    input_data_file=input_file_path,
    outputformat="html",
    profile="ontdoc"
).document()

You will now have the HTML content within the variable html.

For desktop command line use, just clone this repository and either use cli.py as per the command line instructions below or use makedocco.py as a Python script directly.

Use

pyLODE presents natively as a Python command-line utility, pylode/cli.py <pylode/cli.py>__ and there are also a BASH, Windows & Mac OS options available for command line use:

• pylode/bin/pylode.sh <pylode/bin/pylode.sh>__ - BASH script
• Linux executable coming soon!
• pylode/bin/pylode.app <pylode/bin/pylode.app>__ - MAC OS command line executable script
• pylode/bin/pylode.exe <pylode/bin/pylode.exe>__ - Windows command line executable

All use the same command line arguments.

Additionally, there is a Falcon framework <[***]>__ local HTTP server option.

Also, a web UI for pyLODE is available at <[***]>.

Command line arguments

These are the command line arguments to run pyLODE as a BASH or Python script on Linux, Mac etc. or via the Windows executable:

• -i or --inputfile, required if -u not used
  • The RDF ontology file you wish to generate HTML for Must be in either Turtle, RDF/XML, JSON-LD or N-Triples formats indicated by the file type extensions .rdf, .owl, .ttl, .n3, .nt, .json respectively
• -u or --url, required if -i not used
  • The RDF ontology you wish to generate HTML for, online. Must be an absolute URL that can be resolved to RDF, preferably via Content Negotiation.
• -c or --css, optional, default 'true'
  • Whether (true) or not (false) to include CSS in an HTML output.
• -o or --outputfile, optional
  • A name you wish to assign to the output file. Will be postfixed with .html, .md or .adoc. If not specified, the name of the input file or last segment of RDF URI will be used, + .html/.md/.adoc.
• -f or --outputformat, optional, default 'html'
  • The output format of the documentation. 'html', 'md' or 'adoc' accepted.
• -p or --profile, optional, default 'ontdoc'
  • The profile (specification) for ontology documentation used. "ontdoc" (for OWL Ontologies), "vocpub" (for Simple Knowledge Organization System (SKOS) <[***]>) vocabularies or SKOS versions of OWL ontologies, "prof" for Profiles Vocabularies <[***]> profiles. See -lp for all profiles supported.
• -lp or --listprofiles, optional, no arguments
  • Lists all the profiles (specifications) for ontology documentation supported by pyLODE

Example call

This basic call to the BASH script in pylode/bin/ <pylode/bin/>__ will print to standard out an HTML document for an ontology called placenames.html.

::

./pylode -i ../example/prof.ttl

An output file could be specified by using -o, rather than printing to standard out.

Online Service

An online version of pyLODE is now available at [***]

Docker

Install locally by first building the container

::

docker build -t pylode:latest --build-arg PYTHON_VERSION=3.8-slim .

Then run the container

::

docker run -it -d -p 8000:8000 -e GTAGID=${Google TagID} pylode

N.B. The Google TagID is NOT required unless Google Analytics is required. It looks as follows GTAGID=UA-***-1.

You can now access the service on localhost

::

curl localhost:8000/lode?url=[***]

Local server - Falcon

You can run pyLODE using your own, local, HTTP server like this:

::

gunicorn --chdir /path/to/pyLODE/pylode server:api

The server is then available at localhost:8000 and localhost:8000/pylode for the active endpoint. Note that the server must be fed a URL to an ontology to document supplied by a server capable of responding to Content Negotiation, i.e. it must supply RDF according to an HTTP Accept request for text/turtle, application/rdf+xml etc.

::

curl localhost:8000/pylode?url=[***]

Windows

In pylode/bin/, a Windows executable, pylode.exe is available for command line use.

Be sure to add pylode.exe to your Windows user's PATH variable so you can run pylode.exe from any folder. Just run the Registry Editor (search for "Regedit" in the Start menu) and then navicate to HKEY_CURRENT_USER > Environment > Path. Adding the full path of the folder pylode/bin/ to Path will ensure you can run pylode.exe within the Windows command prompt, regardless of what folder you are in.

You can rebuild the pylode.exe file from the source code, if you like. Use the Python program Pyinstaller <[***]>__ as per its instructions <[***]>__. The created pylode.exe will have the same characteristics as the Linux/Mac CLI program.

Pyinstaller uses a .spec file to make the binary and that is included in this repository: pylode-cli.spec.

See the PyInstaller installation guide <[***]>__ for info on how to install PyInstaller for Windows.

Once you have PyInstaller, use pyinstaller to generate the pyLODE.exe CLI file like so:

::

cd pylode
pyinstaller pylode-cli.spec

This will output pylode.exe in the dist directory in pylode. The .exe file in bin/ is just the latest copy of this.

You can now run the pyLODE Command Line utility via pylode.exe. See above for the pyLODE command line util usage instructions.

Mac OS

In pylode/bin/, there is a Mac executable, pylode.app.

As per instructions for PyInstaller use on Windows, you can rebuild the file pylode.app using pylode.spec, if you wish.

Linux

In pylode/bin/, there is a shell script pylode.sh. You can run this on the command line. It just pushes queries to the Python command line cli.py.

What pyLODE understands

pyLODE understands Ontologies, Taxonomies & Profiles and handles them based on the Ontology Document, Vocabulary Publication and PROF profiles that it contains. These three profiles share understanding of basic annotation properties.

Annotations

pyLODE understands the following ontology constructs:

• ontology/taxonomy/profile metadata
  • imports - owl:imports
  • title - rdfs:label, skos:prefLabel, dct:title or dc:title
  • description - rdfs:comment, skos:definition, dct:description or dc:description
    • inline HTML & Markdown are supported
  • historyNote - skos:historyNote
    • inline HTML & Markdown are supported
  • version URI - owl:versionIRI as a URI
  • version info - owl:versionInfo as a string
    • preferred namespace prefix - vann:preferredNamespacePrefix as a token
    • preferred namespace URI - vann:preferredNamespaceUri as a URI
  • agents: publishers, creators, contributors
    • see Agent Formatting below for details
    • see the pylode/examples/ <pylode/examples/>__ directory for examples!
  • dates: created, modified, issued - dct:created etc., all as xsd:date or xsd:dateTime datatype properties
  • rights: license - dct:license as a URI & rights - dct:rights as a string
  • code respository - schema:codeRepository as a literal of type xsd:anyURI
  • source - dcterms:source as a literal of type xsd:anyURI or text
• ontology classes
  • per rdfs:Class or owl:Class
  • title - rdfs:label or skos:prefLabel or dct:title
  • description - rdf:comment, skos:definition, dct:description as a string or using inline HTML or Markdown <[***]>__
  • scope note - a skos:scopeNote as a literal
    • inline HTML & Markdown are supported
  • example - a skos:example
    • see Example Handling below
  • super classes - by declaring a class to be owl:subClassOf something
  • sub classes - pyLODE will work these out itself
  • restrictions - by declaring a class to be owl:subClassOf of an owl:Restriction with any of the normal cardinality or property existence etc. restrictions
  • in domain/range of - pyLODE will auto-calculate these
• ontology properties
  • per owl:ObjectProperty, owl:DatatypeProperty or owl:AnnotationProperty
  • title - rdfs:label or skos:prefLabel or dct:title string literal
  • description - rdf:comment, skos:definition, dct:description string literal
    • inline HTML & Markdown are supported
  • scope note - a skos:scopeNote string literal
    • inline HTML & Markdown are supported
  • example - a skos:example
    • see Example Handling below
  • super properties - by declaring a class to be owl:subPropertyOf something
  • sub properties - pyLODE will work these out itself
  • equivalent properties - by declaring a class to be owl:equivalentProperty something
  • inverse of - by declaring a class to be owl:inverseOf something
  • domains - rdfs:domain or schema:domainIncludes
  • ranges - rdfs:range or schema:rangeIncludes
• namespaces
  • pyLODE will honour any namespace prefixes you set and look up others in [***] <[***]>__
  • it will either read your ontology's default/base URI in annotations or guess it using a number of methods
• named individuals
  • as per class but also owl:sameAs

Example Handling

pyLODE can handle many forms of examples for Classes & Properties and can handle multiple examples per class/property. In all cases, the example value is indicated with a ``skos:example`` property like this:

::

    <x>
        a owl:Class ;
        skos:example {Literal, Blank Node or URI}
    .

**Simple Literals**

The most basic form is an example that is a literal with no format type indicated. This will be printed out in monospaced text, e.g. the Class ``Fish`` in the `Examples Ontology <[***]>`_ has a plain Turtle example like this:

::

    <x> a eggs:Fish ;
        skos:prefLabel "Fish X"@en ;
        eggs:livesInFreshWater true ;
        ...
    .

If you indicate one of the RDF built-in formats (``rdf:HTML``, ``rdf:XMLLiteral`` or ``rdf:JSON``), it will be interpreted in the markup form specified, which means, in practice, that HTML will be rendered where as XML or JSON will be monospaced. The Examples Ontology has this HTML example for the property ``has scale colour``:

----

**scale colour:**

* blue
* orange
* white

----

You can use Markdown in example literals too, but to do so, you must set the format to ``text/markdown`` so see the *Resource Descriptor* method below.


**URIs**

If you put a URI in the example field like this: ``<x> skos:example <...> ;`` or like this ``<x> skos:example "..."^^xsd:anyURI ;`` then pyLODE will render it as a clickable hyperlink in HTML, Markdown or ASCIIDOC, as per your chose output format.

**Images**

You can use images in the example field. To do so, either use a URI to an image on the web or a relative URI to a local image file. pyLODE will render either form as an inline image. See the `Fish Food class example  <[***]>`_ that looks like this:

.. image:: examples/examples-ont/fish-food.png

**"Resource Descriptor" Examples**

To do more you can use a `Profiles Vocabulary (PROF) <[***]>`__ ``ResourceDescriptor`` to define multiple properties for an example resource. This involves defining a ``ResourceDescriptor`` either as a Blank Node or a URI node like this, the `Examples Ont 'eats' property <[***]>`_:

::

    :eats skos:example :eats-example .

    :eats-example
        a prof:ResourceDescriptor ;
        dcterms:format "text/turtle" ;
        dcterms:conformsTo <[***]> ;
        prof:hasArtifact """<x> a :Creature ;
        :eats <y> ;
    .
    <y> a :Food .""" ;
    .

Here the ``ResourceDescriptor`` says that this example is in the ``text/turtle`` format, has an inline artifact (the actual example text) and conforms to something, in this case the profile defined by ``<[***]>``.

You can use this ``ResourceDescriptor`` method to create multiple examples for a class or property that conform to different things (perhaps profiles of your ontology).

Agents
------
Agents, individual persons or organisations, should be associated with ontologies/taxonomies/profiles to indicate *authors*, *creators*, *publishers* etc. There are 2 ways to do this that pyLODE understands: datatype & object type.

Datatype - not preferred

A simple literal value for an agent that a human can read but not a machine can't understand:

• <ONTOLOGY_URI> dc:creator "AGENT NAME" .
  • the range value is a string literal, either string typed (^^xsd:string) or language typed (@en or @de)
  • the following Dublin Core Elements 1.1 <[***]>__ properties may be used:
    • dc:contributor
    • dc:creator
    • dc:publisher
  • the following schema.org <[***]>__ properties may be used:
    • schema:author
    • schema:contributor
    • schema:creator
    • schema:editor
    • schema:funder
    • schema:publisher
    • schema:translator

::

<ontology_x>
    dc:creator "Nicholas J. Car" ;

Object type - preferred

An RDF object is used for the agent and can contain multiple details. A Blank Node or a URI can be used. Best case, a persistent agent URI!

.. figure:: img/contributor-object.png
    :align: center
    :figclass: figure-eg

.....

* ``<ONTOLOGY_URI> dct:creator [...] .``

or

* ``<ONTOLOGY_URI> dct:creator <SOME_URI> .``
   * the range value is a Blank Node or a URI of type:
      * ``schema:Person``
      * ``schema:Organization``
      * ``foaf:Person``
      * ``foaf:Organization``
   * the properties of the Blank Node or the URI are as below
   * the following `Dublin Core Terms <[***]>`__ properties may be used:
      * ``dct:contributor``
      * ``dct:creator``
      * ``dct:publisher``
      * ``dct:rightsHolder``
   * the following `schema.org <[***]>`__ properties may be used:
      * ``schema:author``
      * ``schema:contributor``
      * ``schema:creator``
      * ``schema:editor``
      * ``schema:funder``
      * ``schema:publisher``
      * ``schema:translator``
   * the following `FOAF <[***]>`__ properties may be used:
      * ``foaf:maker``

e.g. (Blank Node):

::

    <ontology_x>
        schema:editor [
            a schema:Organization ;
            ...
        ] ;

or (URI):

::

    <ontology_x>
        schema:editor <[***]> ;
        ...

    <[***]>
        a foaf:Person ;
        ...


Agent datatype properties
^^^^^^^^^^^^^^^^^^^^^^^^^

* ``foaf:name`` / ``schema:name``
* ``foaf:mbox`` / ``schema:email``
* ``foaf:homepage`` / ``schema:url``
* ``schema:identifier``


e.g.:

::

    <ontology_x>
        dct:creator [
            schema:name "Nicholas J. Car" ;
            schema:identifier <[***]> ;
            schema:email <mailto:***> ;
        ] ;


Linking a Person to an Organization
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Use ``schema:member``, ``schema:affiliation`` (there is no FOAF Person -> Group/Org property):

e.g.:

::

    <ontology_x>
        dct:creator [
            schema:name "Nicholas J. Car" ;
            schema:identifier <[***]> ;
            schema:email <mailto:***> ;
            schema:affiliation [
                schema:name "SURROUND Australia Pty Ltd" ;
                schema:url <[***]> ;
            ] ;
        ] ;


Provenance
----------

Ontology/Taxonomy Source

The ontology's HTML representation linking back to the RDF: generated automatically

.. figure:: img/source.png :align: center :figclass: figure-eg

.....

Code Repositories

Indicating to readers where the 'live' version of the ontology/taxonomy is managed:

.. figure:: img/code-repository.png
    :align: center
    :figclass: figure-eg

.....

This should not be done for profiles, instread, create a ``prof:ResourceDescriptor`` instance with ``role:repository`` to indicate a profile's repository.

Code repositories that house an ontology can be indicated either using `schema.org's codeRepository property <[***]>`__ or a combination of the `Description of a Project <[***]>`__ and PROV:

::

    @prefix schema: <[***]> .

    <ONTOLOGY_URI>
        schema:codeRepository <REPO_URI> ;
        ...

or

::

    @prefix doap: <[***]> .
    @prefix prov: <[***]> .

    <ONTOLOGY_URI>
        prov:wasGeneratedBy [
            a doap:Project , prov:Activity ;
            doap:repository <REPO_URI>
        ]
        ...

e.g., for the `ontology version on ISO ***-1 <[***]>`__:

::

    <[***]>
        prov:wasGeneratedBy [
            a doap:Project , prov:Activity ;
            doap:repository <[***]>
        ] ;
        ...

Styling
-------
This tool generates HTML that is shamelessly similar to LODE's styling.
That's because we want things to look familiar and LODE's outputs look
great. The Markdown's pretty vanilla.

Also, pyLODE generates and uses only static HTML + CSS, no JavaScript,
live loading Google Fonts etc. This is to ensure that all you need for
nice display is within a couple of static, easy to use and maintain,
files. Prevents documentation breaking over time.

Feel free to extend your styli