fixes latest pysubyt uage

vliz-be-opsci · Aug 28, 2024 · 7c614f4 · 7c614f4
1 parent 6995503
commit 7c614f4
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Showing 4 changed files with 7 additions and 99 deletions.
diff --git a/Makefile b/Makefile
@@ -1,5 +1,5 @@
 SHELL := /bin/bash
-PYTHON = python3
+PYTHON = python
 TEST_PATH = ./tests/
 FLAKE8_EXCLUDE = venv,.venv,.eggs,.tox,.git,__pycache__,*.pyc
 

diff --git a/entrypoint.py b/entrypoint.py
@@ -14,8 +14,8 @@
 from dotenv import load_dotenv
 from pathlib import Path
 from jinja2 import Environment, FileSystemLoader, BaseLoader
-from pysubyt import JinjaBasedGenerator, SourceFactory, SinkFactory, Settings
-from pylode import OntDoc, PylodeError, __version__ as plv
+from pysubyt import JinjaBasedGenerator, SourceFactory, SinkFactory, GeneratorSettings
+from pylode import OntPub, PylodeError, __version__ as plv
 from pylode import (
     DCTERMS,
     OWL,
@@ -55,7 +55,7 @@ def enable_logging(logconf):
         logging.config.dictConfig(yaml.load(EMBEDDED_YAML_LOGCONF, Loader=yaml.SafeLoader))
         log.warning(f"logconf file '{logconf}' does not exist. Embedded logging config applied as fallback.")
 
-def extract_pub_dict(od: OntDoc):
+def extract_pub_dict(od: OntPub):
     def ont_prop(ont, predicate):
         value = None
         for s in chain(
@@ -121,7 +121,7 @@ def ontopub(baseuri, nsfolder, nssub, nsname, outfolder):
     nspub = dict(error=True) # this assumes things will go bad :)
     #check if _draft is in the name
     try:                      # apply pylode
-        od = OntDoc(outpath)
+        od = OntPub(outpath)
         log.debug(f"> {name} --> ontology loaded to pylode from '{outpath}'")
         # ask pylode to make the html
         od.make_html(destination=outhtmlpath, include_css=False)
@@ -301,7 +301,7 @@ def vocabpub(baseuri, nsfolder, nssub, nsname, outfolder,template_path):
         service = JinjaBasedGenerator(args["template_path"])
         source = {"_": SourceFactory.make_source(args["input"])}
         sink = SinkFactory.make_sink(args["output"], force_output=True)
-        settings = Settings()
+        settings = GeneratorSettings()
         service.process(
             args["template_name"],
             source,

diff --git a/requirements.txt b/requirements.txt
@@ -4,4 +4,4 @@ jinja2
 python-dotenv
 flake8
 pytest
-git+https://github.com/vliz-be-opsci/pysubyt.git@4518e4f#egg=pysubyt
+pysubyt
diff --git a/tests/new_out/onto-one.ttl b/tests/new_out/onto-one.ttl
@@ -42,98 +42,6 @@ tst1:CClass1
   rdfs:comment      "Concept Class Test for onto-one."@en ;
   rdfs:label        "ConceptClass#1"@en ;
   rdfs:subClassOf   dc:Location, skos:Concept .
-<https://example.org/pylode2pages-test/onto-one#1>
-        rdf:type               skos:Concept ;
-        dc:date                "2016-01-01" ;
-        dc:identifier          "1" ;
-        skos:prefLabel         "Abdominal pain"@en ;
-        skos:broader            <https://example.org/pylode2pages-test/onto-one#4> ,;
-        skos:narrower           <https://example.org/pylode2pages-test/onto-one#2> ,;
-        skos:definition        "Pain in the region of the abdomen. It is a common complaint and has many causes."@en ;
-
-        .
-
-<https://example.org/pylode2pages-test/onto-one#2>
-        rdf:type               skos:Concept ;
-        dc:date                "2017-01-01" ;
-        dc:identifier          "2" ;
-        skos:prefLabel         "Rectum"@en ;
-        skos:broader            <https://example.org/pylode2pages-test/onto-one#4> ,;
-        skos:definition        "bodypart that is responsible for excretion of feces"@en ;
-
-        .
-
-<https://example.org/pylode2pages-test/onto-one#3>
-        rdf:type               skos:Concept ;
-        dc:date                "2018-01-02" ;
-        dc:identifier          "3" ;
-        skos:prefLabel         "Spine"@en ;
-        skos:broader            <https://example.org/pylode2pages-test/onto-one#4> ,;
-        skos:narrower           <https://example.org/pylode2pages-test/onto-one#2> ,;
-        skos:definition        "bodypart most people don't have "@en ;
-        skos:altLabel          "Back"
-        .
-
-<https://example.org/pylode2pages-test/onto-one#4>
-        rdf:type               skos:Concept ;
-        dc:date                "2017-02-28" ;
-        dc:identifier          "4" ;
-        skos:prefLabel         "Body"@en ;
-        skos:narrower           <https://example.org/pylode2pages-test/onto-one#3> , <https://example.org/pylode2pages-test/onto-one#2> , <https://example.org/pylode2pages-test/onto-one#1> ,;
-        skos:definition        " the physical structure of a person or an animal."@en ;
-
-        .
-
-<https://example.org/pylode2pages-test/onto-one#5>
-        rdf:type               skos:Concept ;
-        dc:date                "2019-01-31" ;
-        dc:identifier          "5" ;
-        skos:prefLabel         "No Def"@en ;
-        skos:broader            <https://example.org/pylode2pages-test/onto-one#4> ,;
-        skos:narrower           <https://example.org/pylode2pages-test/onto-one#2> , <https://example.org/pylode2pages-test/onto-one#1> ,;
-
-        skos:altLabel          "no definition"
-        .
-
-<https://example.org/pylode2pages-test/onto-one#6>
-        rdf:type               skos:Concept ;
-        dc:date                "2017-12-12" ;
-        dc:identifier          "6" ;
-        skos:prefLabel         "example one"@en ;
-        skos:definition        " just an example"@en ;
-        skos:altLabel          " ex1"
-        .
-
-<https://example.org/pylode2pages-test/onto-one#7>
-        rdf:type               skos:Concept ;
-        dc:date                "2017-12-23" ;
-        dc:identifier          "7" ;
-        skos:prefLabel         "example two"@en ;
-        skos:narrower           <https://example.org/pylode2pages-test/onto-one#6> ,;
-        skos:definition        " just example 2"@en ;
-
-        .
-
-<https://example.org/pylode2pages-test/onto-one#8>
-        rdf:type               skos:Concept ;
-        dc:date                "2015-12-14" ;
-        dc:identifier          "8" ;
-        skos:prefLabel         "example three"@en ;
-        skos:broader            <https://example.org/pylode2pages-test/onto-one#5> ,;
-        skos:narrower           <https://example.org/pylode2pages-test/onto-one#6> , <https://example.org/pylode2pages-test/onto-one#7> ,;
-
-
-        .
-
-<https://example.org/pylode2pages-test/onto-one#9>
-        rdf:type               skos:Concept ;
-        dc:date                "1996-01-03" ;
-        dc:identifier          "9" ;
-        skos:prefLabel         "test"@en ;
-
-
-        .
-
 <https://example.org/pylode2pages-test/onto-one#10>
         rdf:type               skos:Concept ;
         dc:date                "2000-01-01" ;