pylode 2.8.3__tar.gz → 2.8.5__tar.gz

{pyLODE-2.8.3 → pyLODE-2.8.5}/PKG-INFO

@@ -1,12 +1,12 @@
 Metadata-Version: 2.1
 Name: pyLODE
-Version: 2.8.3
+Version: 2.8.5
 Summary: An OWL ontology documentation tool using Python and templating, based on LODE.
 Home-page: https://github.com/rdflib/pyLODE
 Author: Nicholas J. Car
 Author-email: nicholas.car@surroundaustralia.com
 License: LICENSE
-Download-URL: https://github.com/rdflib/pyLODE/archive/v2.8.3.tar.gz
+Download-URL: https://github.com/rdflib/pyLODE/archive/v2.8.5.tar.gz
 Project-URL: Bug Reports, https://github.com/rdflib/pyLODE/issues
 Project-URL: Source, https://github.com/rdflib/pyLODE/
 Description: .. image:: img/pyLODE-250.png
@@ -66,7 +66,7 @@ Description: .. image:: img/pyLODE-250.png
             - via the popular `Falcon framework <https://falconframework.org/>`__.
             - see server.py in the main folder
         - as-a-service online
-            - hosted at https://kurrawong.net/pylode-online
+            - hosted at https://pylode.surroundaustralia.com
         
         
         Examples
@@ -164,9 +164,11 @@ Description: .. image:: img/pyLODE-250.png
         * `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 <https://falconframework.org/>`__ local HTTP server option.
         
-        All use the same command line arguments.
+        Also, a web UI for pyLODE is available at `<https://pylode.surroundaustralia.com>`.
         
         Command line arguments
         ----------------------
@@ -176,8 +178,8 @@ Description: .. image:: img/pyLODE-250.png
             -  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 'false'*
-            -  Whether (true) or not (false) to copy the default CSS file to the output directory.
+        -  ``-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 or .md. If not specified, the name of the input file or last segment of RDF URI will be used, + .html/.md.
         -  ``-f`` or ``--outputformat``, *optional, default 'html'*
@@ -189,18 +191,41 @@ Description: .. image:: img/pyLODE-250.png
         
         Example call
         ------------
-        This call to the BASH script in `pylode/bin/ <pylode/bin/>`__ will
-        create an HTML document for an ontology called ``placenames.html`` and
-        save it with a basic CSS file into
-        `pylode/output\_files/ <pylode/output_files/>`__:
+        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 --css true
+            ./pylode -i ../example/prof.ttl
+        
+        An output file could be specified by using `-o`, rather than printing to standard out.
         
         Online Service
         --------------
-        An online API to access pyLODE is now available in test mode at https://kurrawong.net/pylode-online.
+        An online version of pyLODE is now available at https://pylode.surroundaustralia.com/.
+        
+        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-168806395-1`.
+        
+        You can now access the service on localhost
+        
+        ::
+        
+            curl localhost:8000/lode?url=http://sweetontology.net/sweetAll.ttl
         
         Local server - Falcon
         ---------------------
@@ -208,13 +233,14 @@ Description: .. image:: img/pyLODE-250.png
         
         ::
         
-            cd pylode && gunicorn --chdir /path/to/pyLODE/pylode server:api
+            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.
         
-        Then, in another terminal:
         
         ::
         
-            curl localhost:8000/lode?url=http://sweetontology.net/sweetAll.ttl
+            curl localhost:8000/pylode?url=http://sweetontology.net/sweetAll.ttl
         
         Windows
         -------
@@ -253,6 +279,7 @@ Description: .. image:: img/pyLODE-250.png
         -----
         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.
@@ -534,7 +561,7 @@ Description: .. image:: img/pyLODE-250.png
         **Token** **URI**
         ========= ==========================================
         prof        `<https://www.w3.org/TR/dx-prof/>`_
-        ontdoc      `<https://w3id.org/profile/ontdocp>`_
+        ontdoc      `<https://w3id.org/profile/ontdoc>`_
         vocpub      `<https://w3id.org/profile/vocpub>`_
         ========= ==========================================
         
@@ -670,7 +697,7 @@ Description: .. image:: img/pyLODE-250.png
         Current Release
         ---------------
         
-        The current release, as of July 2020, is **2.8.3**.
+        The current release, as of January, 2021, is **2.8.5**.
         
         Release Schedule
         ----------------
@@ -679,8 +706,9 @@ Description: .. image:: img/pyLODE-250.png
            :header: "Version", "Date", "Description"
            :widths: 15, 10, 30
         
-           3.0, *June 2020*, "Will include pre-testing inputs with SHACL"
-           **2.8.3**, **3 July 2020**, "Packaging bugfixes only"
+           3.0, *?*, "Will include pre-testing inputs with SHACL"
+           **2.8.5**, **5 Jan 20201**, "Small enhancements to the Falcon server deployment option"
+           2.8.3, 3 July 2020, "Packaging bugfixes only"
            2.7, 1 July 2020, "Much refactoring for new profile creation ease"
            2.6, June 2020, "Supports PROF profiles as well as taxonomies & ontologies"
            2.4, 27 May 2020, "Small improvements over 2.0"

{pyLODE-2.8.3 → pyLODE-2.8.5}/README.rst

@@ -55,7 +55,7 @@ The tool can be run as in these ways:
     - via the popular `Falcon framework <https://falconframework.org/>`__.
     - see server.py in the main folder
 - as-a-service online
-    - hosted at https://kurrawong.net/pylode-online
+    - hosted at https://pylode.surroundaustralia.com
 
 
 Examples
@@ -153,9 +153,11 @@ pyLODE presents natively as a Python command-line utility,
 * `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 <https://falconframework.org/>`__ local HTTP server option.
 
-All use the same command line arguments.
+Also, a web UI for pyLODE is available at `<https://pylode.surroundaustralia.com>`.
 
 Command line arguments
 ----------------------
@@ -165,8 +167,8 @@ These are the command line arguments to run pyLODE as a BASH or Python script on
     -  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 'false'*
-    -  Whether (true) or not (false) to copy the default CSS file to the output directory.
+-  ``-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 or .md. If not specified, the name of the input file or last segment of RDF URI will be used, + .html/.md.
 -  ``-f`` or ``--outputformat``, *optional, default 'html'*
@@ -178,18 +180,41 @@ These are the command line arguments to run pyLODE as a BASH or Python script on
 
 Example call
 ------------
-This call to the BASH script in `pylode/bin/ <pylode/bin/>`__ will
-create an HTML document for an ontology called ``placenames.html`` and
-save it with a basic CSS file into
-`pylode/output\_files/ <pylode/output_files/>`__:
+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 --css true
+    ./pylode -i ../example/prof.ttl
+
+An output file could be specified by using `-o`, rather than printing to standard out.
 
 Online Service
 --------------
-An online API to access pyLODE is now available in test mode at https://kurrawong.net/pylode-online.
+An online version of pyLODE is now available at https://pylode.surroundaustralia.com/.
+
+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-168806395-1`.
+
+You can now access the service on localhost
+
+::
+
+    curl localhost:8000/lode?url=http://sweetontology.net/sweetAll.ttl
 
 Local server - Falcon
 ---------------------
@@ -197,13 +222,14 @@ You can run pyLODE using your own, local, HTTP server like this:
 
 ::
 
-    cd pylode && gunicorn --chdir /path/to/pyLODE/pylode server:api
+    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.
 
-Then, in another terminal:
 
 ::
 
-    curl localhost:8000/lode?url=http://sweetontology.net/sweetAll.ttl
+    curl localhost:8000/pylode?url=http://sweetontology.net/sweetAll.ttl
 
 Windows
 -------
@@ -242,6 +268,7 @@ 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.
@@ -523,7 +550,7 @@ profiles include, see the profiles' definitions at:
 **Token** **URI**
 ========= ==========================================
 prof        `<https://www.w3.org/TR/dx-prof/>`_
-ontdoc      `<https://w3id.org/profile/ontdocp>`_
+ontdoc      `<https://w3id.org/profile/ontdoc>`_
 vocpub      `<https://w3id.org/profile/vocpub>`_
 ========= ==========================================
 
@@ -659,7 +686,7 @@ and change/add development priorities.
 Current Release
 ---------------
 
-The current release, as of July 2020, is **2.8.3**.
+The current release, as of January, 2021, is **2.8.5**.
 
 Release Schedule
 ----------------
@@ -668,8 +695,9 @@ Release Schedule
    :header: "Version", "Date", "Description"
    :widths: 15, 10, 30
 
-   3.0, *June 2020*, "Will include pre-testing inputs with SHACL"
-   **2.8.3**, **3 July 2020**, "Packaging bugfixes only"
+   3.0, *?*, "Will include pre-testing inputs with SHACL"
+   **2.8.5**, **5 Jan 20201**, "Small enhancements to the Falcon server deployment option"
+   2.8.3, 3 July 2020, "Packaging bugfixes only"
    2.7, 1 July 2020, "Much refactoring for new profile creation ease"
    2.6, June 2020, "Supports PROF profiles as well as taxonomies & ontologies"
    2.4, 27 May 2020, "Small improvements over 2.0"

{pyLODE-2.8.3 → pyLODE-2.8.5}/pyLODE.egg-info/PKG-INFO

@@ -1,12 +1,12 @@
 Metadata-Version: 2.1
 Name: pyLODE
-Version: 2.8.3
+Version: 2.8.5
 Summary: An OWL ontology documentation tool using Python and templating, based on LODE.
 Home-page: https://github.com/rdflib/pyLODE
 Author: Nicholas J. Car
 Author-email: nicholas.car@surroundaustralia.com
 License: LICENSE
-Download-URL: https://github.com/rdflib/pyLODE/archive/v2.8.3.tar.gz
+Download-URL: https://github.com/rdflib/pyLODE/archive/v2.8.5.tar.gz
 Project-URL: Bug Reports, https://github.com/rdflib/pyLODE/issues
 Project-URL: Source, https://github.com/rdflib/pyLODE/
 Description: .. image:: img/pyLODE-250.png
@@ -66,7 +66,7 @@ Description: .. image:: img/pyLODE-250.png
             - via the popular `Falcon framework <https://falconframework.org/>`__.
             - see server.py in the main folder
         - as-a-service online
-            - hosted at https://kurrawong.net/pylode-online
+            - hosted at https://pylode.surroundaustralia.com
         
         
         Examples
@@ -164,9 +164,11 @@ Description: .. image:: img/pyLODE-250.png
         * `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 <https://falconframework.org/>`__ local HTTP server option.
         
-        All use the same command line arguments.
+        Also, a web UI for pyLODE is available at `<https://pylode.surroundaustralia.com>`.
         
         Command line arguments
         ----------------------
@@ -176,8 +178,8 @@ Description: .. image:: img/pyLODE-250.png
             -  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 'false'*
-            -  Whether (true) or not (false) to copy the default CSS file to the output directory.
+        -  ``-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 or .md. If not specified, the name of the input file or last segment of RDF URI will be used, + .html/.md.
         -  ``-f`` or ``--outputformat``, *optional, default 'html'*
@@ -189,18 +191,41 @@ Description: .. image:: img/pyLODE-250.png
         
         Example call
         ------------
-        This call to the BASH script in `pylode/bin/ <pylode/bin/>`__ will
-        create an HTML document for an ontology called ``placenames.html`` and
-        save it with a basic CSS file into
-        `pylode/output\_files/ <pylode/output_files/>`__:
+        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 --css true
+            ./pylode -i ../example/prof.ttl
+        
+        An output file could be specified by using `-o`, rather than printing to standard out.
         
         Online Service
         --------------
-        An online API to access pyLODE is now available in test mode at https://kurrawong.net/pylode-online.
+        An online version of pyLODE is now available at https://pylode.surroundaustralia.com/.
+        
+        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-168806395-1`.
+        
+        You can now access the service on localhost
+        
+        ::
+        
+            curl localhost:8000/lode?url=http://sweetontology.net/sweetAll.ttl
         
         Local server - Falcon
         ---------------------
@@ -208,13 +233,14 @@ Description: .. image:: img/pyLODE-250.png
         
         ::
         
-            cd pylode && gunicorn --chdir /path/to/pyLODE/pylode server:api
+            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.
         
-        Then, in another terminal:
         
         ::
         
-            curl localhost:8000/lode?url=http://sweetontology.net/sweetAll.ttl
+            curl localhost:8000/pylode?url=http://sweetontology.net/sweetAll.ttl
         
         Windows
         -------
@@ -253,6 +279,7 @@ Description: .. image:: img/pyLODE-250.png
         -----
         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.
@@ -534,7 +561,7 @@ Description: .. image:: img/pyLODE-250.png
         **Token** **URI**
         ========= ==========================================
         prof        `<https://www.w3.org/TR/dx-prof/>`_
-        ontdoc      `<https://w3id.org/profile/ontdocp>`_
+        ontdoc      `<https://w3id.org/profile/ontdoc>`_
         vocpub      `<https://w3id.org/profile/vocpub>`_
         ========= ==========================================
         
@@ -670,7 +697,7 @@ Description: .. image:: img/pyLODE-250.png
         Current Release
         ---------------
         
-        The current release, as of July 2020, is **2.8.3**.
+        The current release, as of January, 2021, is **2.8.5**.
         
         Release Schedule
         ----------------
@@ -679,8 +706,9 @@ Description: .. image:: img/pyLODE-250.png
            :header: "Version", "Date", "Description"
            :widths: 15, 10, 30
         
-           3.0, *June 2020*, "Will include pre-testing inputs with SHACL"
-           **2.8.3**, **3 July 2020**, "Packaging bugfixes only"
+           3.0, *?*, "Will include pre-testing inputs with SHACL"
+           **2.8.5**, **5 Jan 20201**, "Small enhancements to the Falcon server deployment option"
+           2.8.3, 3 July 2020, "Packaging bugfixes only"
            2.7, 1 July 2020, "Much refactoring for new profile creation ease"
            2.6, June 2020, "Supports PROF profiles as well as taxonomies & ontologies"
            2.4, 27 May 2020, "Small improvements over 2.0"

{pyLODE-2.8.3 → pyLODE-2.8.5}/pyLODE.egg-info/requires.txt

@@ -1,10 +1,5 @@
-argparse
-falcon
-gunicorn
 jinja2
 markdown
-pytest
-python-dateutil
 rdflib>=5.0.0
 rdflib-jsonld>=0.5.0
 requests

{pyLODE-2.8.3 → pyLODE-2.8.5}/pylode/cli.py

@@ -63,17 +63,9 @@ def main(args=None):
     parser.add_argument(
         "-c",
         "--css",
-        help="Whether (true) or not (false) to copy the default CSS file to the output directory.",
+        help="Whether (true) or not (false) to include CSS within an output HTML file.",
         choices=["true", "false"],
-        default="false",
-    )
-
-    parser.add_argument(
-        "-xc",
-        "--excludecss",
-        help="Whether (true) or not (false) to exclude the standard pyLODE CSS content from an HTML file output.",
-        choices=["true", "false"],
-        default="false",
+        default="true",
     )
 
     parser.add_argument(
@@ -117,10 +109,10 @@ def main(args=None):
         print(__version__)
         exit()
     elif args.inputfile or args.url:
-        if args.excludecss == "true":
-            exclude_css = True
+        if args.css == "true":
+            include_css = True
         else:
-            exclude_css = False
+            include_css = False
 
         # args are present so getting RDF from input file or uri into an rdflib Graph
         if args.inputfile:
@@ -128,14 +120,14 @@ def main(args=None):
                 input_data_file=args.inputfile,
                 outputformat=args.outputformat,
                 profile=args.profile,
-                exclude_css=exclude_css
+                include_css=include_css
             )
         elif args.url:
             h = MakeDocco(
                 input_uri=args.url,
                 outputformat=args.outputformat,
                 profile=args.profile,
-                exclude_css=exclude_css
+                include_css=include_css
             )
         else:
             # we have neither an input file or a URI supplied
@@ -152,23 +144,9 @@ def main(args=None):
 
     # here we have a parsed graph from either a local file or a URI
 
-    # set up output directories and resources
-    main_dir = path.dirname(path.realpath(__file__))
-    style_dir = path.join(main_dir, "style")
-    if h.publication_dir == "":
-        h.publication_dir = "."
-    os.makedirs(h.publication_dir, exist_ok=True)
-
-    # include CSS
-    if args.css == "true":
-        shutil.copyfile(
-            path.join(style_dir, "pylode.css"), path.join(h.publication_dir, "style.css")
-        )
-
+    # name the output file
     if args.outputfile is not None:
-        output_file_name = (
-            args.outputfile if args.outputfile else "doc.html"
-        )
+        output_file_name = args.outputfile
 
         if args.outputformat == "html":
             if not output_file_name.endswith(".html"):

{pyLODE-2.8.3 → pyLODE-2.8.5}/pylode/common.py

@@ -1,8 +1,8 @@
 from os import path
-import requests
+from urllib import request
 from rdflib import util, Graph
 
-VERSION = "2.8.3"
+VERSION = "2.8.5"
 APP_DIR = path.dirname(path.realpath(__file__))
 TEMPLATES_DIR = path.join(path.dirname(path.realpath(__file__)), "templates")
 STYLE_DIR = path.join(path.dirname(path.realpath(__file__)), "style")
@@ -30,7 +30,7 @@ from .profiles import OntDoc, Prof, VocPub, PROFILES
 
 
 class MakeDocco:
-    def __init__(self, input_data_file=None, input_uri=None, data=None, outputformat="html", exclude_css=False, get_curies_online=False, profile="ontdoc"):
+    def __init__(self, input_data_file=None, input_uri=None, data=None, outputformat="html", include_css=True, get_curies_online=False, profile="ontdoc"):
         """This class receives all of the variables needed to specify how to make documentation from an input RDF source
 
         :param input_data_file: An RDF file
@@ -41,8 +41,8 @@ class MakeDocco:
         :type data: Python varaible (string)
         :param outputformat: The desired output format form the list of supported formats (currently either "html" (default) or "md" for Markdown
         :type outputformat: string (one of "html" or "md")
-        :param exclude_css: Whether (True, default) or not (False) to include styling CSS within HTML outputs (as oposed to producing a separate style.css file)
-        :type exclude_css: boolean
+        :param include_css: Whether (True, default) or not (False) to include styling CSS within HTML outputs
+        :type include_css: boolean
         :param get_curies_online: Whether (True) or not (False, default) to search prefix.cc online for additional URI prefixes
         :type get_curies_online: boolean
         :param profile: When document profile, from a supported set, to use. Currently supported is "ontdoc" (profile of OWL) or "skosp" (profile of SKOS). See `list_profiles()` for full list of profiles.
@@ -55,7 +55,7 @@ class MakeDocco:
         else:
             self.outputformat = outputformat
 
-        self.exclude_css = exclude_css
+        self.include_css = include_css
         self.get_curies_online = get_curies_online
 
         if profile not in PROFILES.keys():
@@ -97,14 +97,12 @@ class MakeDocco:
 
             self.G = Graph().parse(file_name, format=fmt)
             self.source_info = (file_name, fmt)
-            self.publication_dir = path.dirname(file_name)
 
     def _parse_input_uri(self, uri):
-        r = requests.get(
-            uri, headers={"Accept": ", ".join(RDF_SERIALIZER_MAP.keys())}
-        )
+        headers = {"Accept": ", ".join(RDF_SERIALIZER_MAP.keys())}
+        resp = request.urlopen(request.Request(uri, None, headers))
         # get RDF format from Media Type
-        media_type = r.headers.get("Content-Type").split(";")[0]  # splitting off any ;charset=...
+        media_type = resp.headers["Content-Type"].split(";")[0]  # splitting off any ;charset=...
         if RDF_SERIALIZER_MAP.get(media_type):
             fmt = RDF_SERIALIZER_MAP.get(media_type)
         else:
@@ -121,16 +119,12 @@ class MakeDocco:
                 "({} was given) or from a file extension".format(media_type)
             )
 
-        self.G = Graph().parse(data=r.text, format=fmt)
+        self.G = Graph().parse(data=resp.read().decode(), format=fmt)
         self.source_info = (uri, fmt)
-        self.publication_dir = path.join(
-            path.dirname(path.realpath(__file__)), "output_files"
-        )
 
     def _parse_data(self, data):
         self.G = Graph().parse(data=data, format="turtle")
         self.source_info = ("input.ttl", "turtle")
-        self.publication_dir = path.dirname(path.realpath(__file__))
 
     @classmethod
     def list_profiles(cls):
@@ -155,7 +149,7 @@ class MakeDocco:
                 self.G,
                 self.source_info,
                 outputformat=self.outputformat,
-                exclude_css=self.exclude_css,
+                include_css=self.include_css,
                 default_language="en",
                 get_curies_online=self.get_curies_online
             )
@@ -164,7 +158,7 @@ class MakeDocco:
                 self.G,
                 self.source_info,
                 outputformat=self.outputformat,
-                exclude_css=self.exclude_css,
+                include_css=self.include_css,
                 default_language="en",
                 get_curies_online=self.get_curies_online
             )
@@ -173,7 +167,7 @@ class MakeDocco:
                 self.G,
                 self.source_info,
                 outputformat=self.outputformat,
-                exclude_css=self.exclude_css,
+                include_css=self.include_css,
                 default_language="en",
                 get_curies_online=self.get_curies_online
             )
@@ -185,7 +179,9 @@ class MakeDocco:
                     f.write(doc)
             except Exception as e:
                 print(e)
-                raise Exception("The file you specified as 'destination' could not be written to. You specified {}.".format(destination))
+                raise Exception(
+                    "The file you specified as 'destination' could not be written to. You specified {}."
+                                .format(destination))
 
         else:
             return p.generate_document()

{pyLODE-2.8.3 → pyLODE-2.8.5}/pylode/profiles/base.py

@@ -8,9 +8,9 @@ from pylode.common import TEMPLATES_DIR
 
 
 class BaseProfile:
-    def __init__(self, g, source_info, outputformat="html", exclude_css=False, default_language="en", get_curies_online=False):
+    def __init__(self, g, source_info, outputformat="html", include_css=False, default_language="en", get_curies_online=False):
         self.outputformat = outputformat
-        self.exclude_css = exclude_css
+        self.include_css = include_css
         self.default_language = default_language
         self.get_curies_online = get_curies_online
         self.default_namespace = None

{pyLODE-2.8.3 → pyLODE-2.8.5}/pylode/profiles/ontdoc.py

@@ -2,7 +2,6 @@ from os import path
 from pylode.common import VERSION, TEMPLATES_DIR, STYLE_DIR
 import collections
 from os import path
-import dateutil.parser
 from itertools import chain
 import markdown
 from jinja2 import Environment, FileSystemLoader
@@ -13,8 +12,8 @@ from pylode.profiles.base import BaseProfile
 
 
 class OntDoc(BaseProfile):
-    def __init__(self, g, source_info, outputformat="html", exclude_css=False, default_language="en", get_curies_online=False):
-        super().__init__(g, source_info, outputformat=outputformat, exclude_css=exclude_css, get_curies_online=False, default_language=default_language)
+    def __init__(self, g, source_info, outputformat="html", include_css=False, default_language="en", get_curies_online=False):
+        super().__init__(g, source_info, outputformat=outputformat, include_css=include_css, get_curies_online=False, default_language=default_language)
         self.G.bind("prov", PROV)
         self.CLASSES = collections.OrderedDict()
         self.PROPERTIES = collections.OrderedDict()
@@ -363,9 +362,7 @@ class OntDoc(BaseProfile):
                 # dates
                 if p in [DCTERMS.created, DCTERMS.modified, DCTERMS.issued]:
                     date_type = p.split("/")[-1]
-                    self.METADATA[date_type] = dateutil.parser.parse(str(o)).strftime(
-                        "%Y-%m-%d"
-                    )
+                    self.METADATA[date_type] = str(o)
 
                 if p == DCTERMS.source:
                     if str(o).startswith('http'):
@@ -464,7 +461,7 @@ class OntDoc(BaseProfile):
                     self.CLASSES[cls]["description"] = markdown.markdown(str(o))
 
                 if p == SKOS.scopeNote:
-                    self.CLASSES[cls]["scopeNote"] = str(o)
+                    self.CLASSES[cls]["scopeNote"] = markdown.markdown(str(o))
 
                 if p == SKOS.example:
                     self.CLASSES[cls]["example"] = str(o)
@@ -652,7 +649,7 @@ class OntDoc(BaseProfile):
                 if p == RDFS.label:
                     self.PROPERTIES[prop]["title"] = str(o)
 
-                if p == RDFS.comment:
+                if p == DCTERMS.description:
                     self.PROPERTIES[prop]["description"] = str(o)
 
                 if p == SKOS.scopeNote:
@@ -1090,7 +1087,7 @@ class OntDoc(BaseProfile):
     def _make_document(self):
         css = None
         if self.outputformat == "html":
-            if not self.exclude_css:
+            if self.include_css:
                 css = open(path.join(STYLE_DIR, "pylode.css")).read()
 
         return self._load_template("document." + self.outputformat).render(

{pyLODE-2.8.3 → pyLODE-2.8.5}/pylode/profiles/prof.py

@@ -3,7 +3,6 @@ import collections
 from os import path
 from rdflib import URIRef, BNode, Literal
 from rdflib.namespace import DC, DCTERMS, OWL, PROF, RDF, RDFS, SDO, SKOS
-import dateutil.parser
 from itertools import chain
 import markdown
 from jinja2 import Environment, FileSystemLoader
@@ -12,8 +11,8 @@ from pylode.profiles.base import BaseProfile
 
 
 class Prof(BaseProfile):
-    def __init__(self, g, source_info, outputformat="html", exclude_css=False, default_language="en", get_curies_online=False):
-        super().__init__(g, source_info, outputformat=outputformat, exclude_css=exclude_css, get_curies_online=False, default_language=default_language)
+    def __init__(self, g, source_info, outputformat="html", include_css=False, default_language="en", get_curies_online=False):
+        super().__init__(g, source_info, outputformat=outputformat, include_css=include_css, get_curies_online=False, default_language=default_language)
         self.RESOURCE_DESCRIPTORS = collections.OrderedDict()
 
     def _load_template(self, template_file):
@@ -164,7 +163,7 @@ class Prof(BaseProfile):
                 # dates
                 if p in [DCTERMS.created, DCTERMS.modified, DCTERMS.issued]:
                     date_type = p.split("/")[-1]
-                    self.METADATA[date_type] = dateutil.parser.parse(str(o)).strftime("%Y-%m-%d")
+                    self.METADATA[date_type] = str(o)
 
                 if p == OWL.versionIRI:
                     self.METADATA["versionIRI"] = self._make_formatted_uri(o)
@@ -252,7 +251,7 @@ class Prof(BaseProfile):
     def _make_document(self):
         css = None
         if self.outputformat == "html":
-            if not self.exclude_css:
+            if self.include_css:
                 css = open(path.join(STYLE_DIR, "pylode.css")).read()
 
         return self._load_template("prof." + self.outputformat).render(

{pyLODE-2.8.3 → pyLODE-2.8.5}/pylode/profiles/profile.py

@@ -71,6 +71,17 @@ PROF_PROFILE = Profile(
     languages=["en"],
     default_language="en"
 )
+PROF_FLAT_PROFILE = Profile(
+    "https://w3id.org/profile/prof-flat",
+    "Flattened PROF Hierarchy",
+    "A profile of the Profiles Vocabulary for documentation purposes that requires all details of profiles within a "
+    "profile hierarchy to be documented be present within a single graph (or file)."
+    "through profile hierarchy.",
+    [HTML_MEDIA_TYPE, "text/markdown"],
+    HTML_MEDIA_TYPE,
+    languages=["en"],
+    default_language="en"
+)
 OWL_PROFILE = Profile(
     "https://www.w3.org/TR/owl2-rdf-based-semantics/",
     "Web Ontology Language (OWL)",
@@ -83,7 +94,7 @@ OWL_PROFILE = Profile(
     default_language="en"
 )
 ONT_DOC_PROFILE = Profile(
-    "https://w3id.org/profile/ontdocp",
+    "https://w3id.org/profile/ontdoc",
     "Ontology Documentation Profile",
     "OWL Classes and Properties as well as additional SKOS, Dublin Core Terms and schema.org annotation "
     "properties to be used to document ontologies.",

{pyLODE-2.8.3 → pyLODE-2.8.5}/pylode/profiles/vocpub.py

@@ -3,7 +3,6 @@ import collections
 from os import path
 from rdflib import URIRef, BNode, Literal
 from rdflib.namespace import DC, DCTERMS, DOAP, OWL, PROV, RDF, RDFS, SDO, SKOS
-import dateutil.parser
 from itertools import chain
 import markdown
 from jinja2 import Environment, FileSystemLoader
@@ -12,8 +11,8 @@ from pylode.profiles.base import BaseProfile
 
 
 class VocPub(BaseProfile):
-    def __init__(self, g, source_info, outputformat="html", exclude_css=False, default_language="en", get_curies_online=False):
-        super().__init__(g, source_info, outputformat=outputformat, exclude_css=exclude_css, get_curies_online=False, default_language=default_language)
+    def __init__(self, g, source_info, outputformat="html", include_css=False, default_language="en", get_curies_online=False):
+        super().__init__(g, source_info, outputformat=outputformat, include_css=include_css, get_curies_online=False, default_language=default_language)
         self.CONCEPTS = collections.OrderedDict()
         self.COLLECTIONS = collections.OrderedDict()
 
@@ -359,9 +358,7 @@ class VocPub(BaseProfile):
                 # dates
                 if p in [DCTERMS.created, DCTERMS.modified, DCTERMS.issued]:
                     date_type = p.split("/")[-1]
-                    self.METADATA[date_type] = dateutil.parser.parse(str(o)).strftime(
-                        "%Y-%m-%d"
-                    )
+                    self.METADATA[date_type] = str(o)
 
                 if p == DCTERMS.source:
                     if str(o).startswith('http'):
@@ -573,7 +570,7 @@ class VocPub(BaseProfile):
     def _make_document(self):
         css = None
         if self.outputformat == "html":
-            if not self.exclude_css:
+            if self.include_css:
                 css = open(path.join(STYLE_DIR, "pylode.css")).read()
 
         return self._load_template("taxonomy." + self.outputformat).render(

pyLODE-2.8.5/pylode/server.py

@@ -0,0 +1,60 @@
+from bs4 import BeautifulSoup as Soup
+import falcon
+import os
+import subprocess
+
+
+class InfoResource:
+    def on_get(self, req, resp):
+        resp.body = """<h3>pyLODE Server</h3>
+                        <p>This is <a href=\"https://github.com/rdflib/pyLODE/\">pyLODE</a> online via Falcon.</p>
+                        <p>To use this server to document ontologies, supply an ontology RDF file to it via the See <a href=\"/pylode\">/pylode</a> endpoint.</p>
+                        <p>For example, to document the PHS ontology, do this:</p>
+                        <ul>
+                            <li><code>http://localhost:8000/pylode?url=https://linked.data.gov.au/def/phs</code></li>
+                        </ul>
+                        <p>Note that this server will use <a href="https://developer.mozilla.org/en-US/docs/Web/HTTP/Content_negotiation">Content Negotiation</a> to try and get an RDF response from the URI supplied so the ontology must be served with the apprpriate Media Type.</p> 
+                    """
+        resp.set_header("Powered-By", "Falcon")
+        resp.set_header("content-type", "text/html")
+        resp.status = falcon.HTTP_200
+
+
+class DocResource:
+    def on_get(self, req, resp):
+        """Handles GET requests"""
+        url = req.get_param("url")
+        if url is not None:
+            cmd = "cd ./bin && ./pylode.sh -u {url} -c true".format(url=url)
+
+            # remove Overview image placeholder, if present
+            raw_html = subprocess.check_output(cmd, shell=True)
+            processed_html = raw_html.decode().replace(
+                '<section id="overview">', '<section id="overview" style="display:none;">')
+            soup = Soup(processed_html, features="html.parser")
+            if os.getenv('GTAGID') is not None:
+                tag = os.getenv('GTAGID')
+                title = soup.find('title')
+                async_tag = soup.new_tag("script")
+                async_tag['async src'] = "https://www.googletagmanager.com/gtag/js?id=%s" % tag
+                title.insert_after(async_tag)
+                gtag = soup.new_tag('script')
+                gtag.string = """window.dataLayer = window.dataLayer || [];\n
+                      function gtag(){dataLayer.push(arguments);}\n
+                      gtag('js', new Date());\n
+                      gtag('config', '%s');\n""" % tag
+                async_tag.insert_after(gtag)
+            resp.body = soup
+
+            resp.set_header("Powered-By", "Falcon")
+            resp.set_header("content-type", "text/html")
+            resp.status = falcon.HTTP_200
+        else:
+            resp.body = "<h3>USER ERROR</h3><p>For this endpoint, you must supply a Query String Argument of <code>url</code>, e.g. <code>/pylode?url={URL_OF_AN_RDF_FILE}</code>.</p>"
+            resp.set_header("content-type", "text/html")
+            resp.status = falcon.HTTP_400
+
+
+api = falcon.API()
+api.add_route("/", InfoResource())
+api.add_route("/pylode", DocResource())

{pyLODE-2.8.3 → pyLODE-2.8.5}/pylode/templates/ontdoc/class.html

@@ -42,7 +42,7 @@
                 <th>Example</th>
                 <td>
                     <pre>
-                      {{ example }}
+{{ example }}
                     </pre>
                 </td>
             </tr>

{pyLODE-2.8.3 → pyLODE-2.8.5}/pylode/templates/ontdoc/property.html

@@ -54,7 +54,7 @@
                 <th>Example</th>
                 <td>
                     <pre>
-                      {{ example }}
+{{ example }}
                     </pre>
                 </td>
             </tr>
@@ -126,4 +126,4 @@
             </tr>
             {%- endif %}
         </table>
-    </div>
+    </div>

{pyLODE-2.8.3 → pyLODE-2.8.5}/pylode/templates/vocpub/collection.html

@@ -1,5 +1,5 @@
 <div class="entity collection" id="{{ fid }}">
-        <h3>{{ prefLabels[0][0] }}<sup title="Collection" class="sup-cp">cp</sup></h3>
+        <h3>{{ prefLabels[0][0] }}<sup title="Collection" class="sup-cl">cl</sup></h3>
             {%- if prefLabels|length > 1 %}
             <h4>
               {%- for prefLabel in prefLabels %}
@@ -48,4 +48,4 @@
             </tr>
             {% endif %}
         </table>
-    </div>
+    </div>

{pyLODE-2.8.3 → pyLODE-2.8.5}/pylode/templates/vocpub/concept.md

@@ -8,8 +8,8 @@ Preferred Labels | {%- for prefLabel in prefLabels %}{{ prefLabel[0] }} ({{ pref
 {%- if altLabels|length > 0 %}
 Alternate Labels | {%- for altLabel in altLabels %}{{ altLabel }}<br />{%- endfor %}
 {%- endif %}
-{%- if descriptions|length > 0 %}
-Description | {%- for description in descriptions %}{{ descriptions }}<br />{%- endfor %}
+{%- if definitions|length > 0 %}
+Definitions | {%- for definition in definitions %}{{ definitions }}<br />{%- endfor %}
 {%- endif %}
 {%- if scopeNotes|length > 0 %}
 Scope Notes | {%- for scopeNote in scopeNotes %}{{ scopeNote }}<br />{%- endfor %}

{pyLODE-2.8.3 → pyLODE-2.8.5}/pylode/templates/vocpub/concepts.md

@@ -1,4 +1,4 @@
-## Classes
+## Concepts
 {%- if concept_hierarchy is not none %}
 {{ concept_hierarchy|safe }}
 {%- endif %}

pyLODE-2.8.5/pylode/tests/test_ont_html_description.py

@@ -0,0 +1,9 @@
+from pylode import MakeDocco
+from os.path import join, dirname, abspath
+TESTS_DIR = dirname(abspath(__file__))
+
+
+h = MakeDocco(input_data_file=join(TESTS_DIR, "test_ont_html_description.ttl"))
+# generate the HTML doc
+h.document(destination="test_ont_html_description.html")
+

pyLODE-2.8.5/pylode/tests/test_skos.py

@@ -0,0 +1,7 @@
+from pylode import MakeDocco
+from os.path import join, dirname, abspath
+TESTS_DIR = dirname(abspath(__file__))
+
+h = MakeDocco(input_data_file=join(TESTS_DIR, "test_skos_cif.ttl"), profile='skos')
+# generate the HTML doc
+h.document(destination=join(TESTS_DIR, "test_skos_cif.html"))

pyLODE-2.8.3/pylode/server.py

@@ -1,24 +0,0 @@
-import falcon
-import subprocess
-
-
-class DocResource:
-    def on_get(self, req, resp):
-        """Handles GET requests"""
-        url = req.get_param("url")
-        if url is not None:
-            cmd = "cd ./bin && ./pylode.sh -u {url} -c true".format(url=url)
-
-            # remove Overview image placeholder, if present
-            raw_html = subprocess.check_output(cmd, shell=True)
-            processed_html = raw_html.decode().replace(
-                '<section id="overview">', '<section id="overview" style="display:none;">').encode()
-            resp.body = processed_html
-
-            resp.set_header("Powered-By", "Falcon")
-            resp.set_header("content-type", "text/html")
-            resp.status = falcon.HTTP_200
-
-
-api = falcon.API()
-api.add_route("/lode", DocResource())

pyLODE-2.8.3/pylode/tests/test_ont_html_description.py

@@ -1,7 +0,0 @@
-from makedocco import MakeDocco
-
-
-h = MakeDocco(input_data_file="test_ont_html_description.ttl")
-# generate the HTML doc
-h.document(destination="test_ont_html_description.html")
-

pyLODE-2.8.3/pylode/tests/test_skos.py

@@ -1,8 +0,0 @@
-from makedocco import MakeDocco
-
-
-h = MakeDocco(profile='skos')
-source_info = ("test_skos_cif.ttl", "turtle")
-# generate the HTML doc
-with open("test_skos_cif.html", "w") as f:
-    f.write(h.document(source_info))