Contribution of current work on application_ontologies/tensile_test_ontologies

.github/workflow_resources/oops_report.py

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+"""
+Tool for checking a provided ontology for OOPS pitfalls.
+
+Author: Matthias Jung
+Date: 2023-12-07
+
+usage: oops_report.py [-h] [-u ONTOLOGY_URL] [-f ONTOLOGY_FILE] 
+                      [-t ONTOLOGY_FILE_TYPE] [-r RESTRICTION] 
+                      [--timeout TIMEOUT] [-v]
+
+Generates a report using the OOPS API based on the provided ontology 
+URL or ontology file. The output is stored in oops_report.json. The 
+maximum level of the report is stored in oops_badge.svg. The badge       
+command is stored in _oops_badge_command.sh. Use either ontology_file 
+or ontology_url, if both are provided only ontology_file is used.
+
+options:
+  -h, --help            show this help message and exit
+  -u ONTOLOGY_URL, --ontology-url ONTOLOGY_URL
+                        The URL of the ontology to be used for generating the report.
+  -f ONTOLOGY_FILE, --ontology-file ONTOLOGY_FILE
+                        The path to the ontology file to be used for generating the report.
+  -t ONTOLOGY_FILE_TYPE, --ontology-file-type ONTOLOGY_FILE_TYPE
+                        The format of the input ontology file (default: xml).
+  -r RESTRICTION, --restriction RESTRICTION
+                        A restriction to be applied during report generation.
+  --timeout TIMEOUT     The number of seconds to wait for a response from 
+                        the OOPS API (default: 120).
+  -v, --verbose         Whether to print verbose output.
+"""
+import argparse
+import json
+import xml.etree.ElementTree as ET
+import requests
+import rdflib
+
+REQ_TIMEOUT = 120
+LEVELS = {'Critical': 3, 'Important': 2, 'Minor': 1, 'Pass': 0}
+LEVELS_INV = {v: k for k, v in LEVELS.items()}
+LEVEL_COLOR = {
+    'Critical': 'red',
+    'Important': 'orange',
+    'Minor': 'yellow',
+    'Pass': 'brightgreen'
+}
+
+def pitfall_repr(pitfall, namespace, restriction=''):
+    """
+    Generate a dictionary representing a pitfall's information.
+
+    :param pitfall: The pitfall element to extract information from.
+    :type pitfall: Element
+
+    :param namespace: The namespace to use for XML element searching.
+    :type namespace: dict
+
+    :param restriction: A restriction to filter affected elements by (optional).
+    :type restriction: str
+
+    :return: A dictionary containing the pitfall's name, 
+             description, code, importance, and affected elements.
+    :rtype: dict
+    """
+    d = pitfall.find('.//oops:Description', namespace).text
+    n = pitfall.find('.//oops:Name', namespace).text
+    c = pitfall.find('.//oops:Code', namespace).text
+    i = pitfall.find('.//oops:Importance', namespace).text
+    affelem_filtered = [
+        affelem.text for affelem in pitfall.findall('.//oops:AffectedElement', namespace)
+        if affelem.text.startswith(restriction)
+    ]
+    return {
+        'name': n,
+        'description': d,
+        'code': c,
+        'importance': i,
+        'affected_elements': affelem_filtered
+    }
+
+def suggestion_repr(suggestion, namespace, restriction=''):
+    """
+    Returns a dictionary representation of a suggestion with the given namespace and restriction.
+
+    Parameters:
+        suggestion (Element): The suggestion element.
+        namespace (dict): The namespace dictionary.
+        restriction (str): The restriction to filter affected elements (default '').
+
+    Returns:
+        dict: A dictionary containing the name, description, 
+              and affected elements of the suggestion.
+    """
+    d = suggestion.find('.//oops:Description', namespace).text
+    n = suggestion.find('.//oops:Name', namespace).text
+    affelem_filtered = [
+        affelem.text for affelem in suggestion.findall('.//oops:AffectedElement', namespace)
+        if affelem.text.startswith(restriction)]
+    return {
+        'name': n,
+        'description': d,
+        'affected_elements': affelem_filtered
+    }
+
+def make_report(strdata, restriction=''):
+    """
+    Generate a report based on the given XML data.
+
+    Parameters:
+        strdata (str): The XML data as a string.
+        restriction (str, optional): A restriction on the affected elements. Defaults to ''.
+
+    Returns:
+        tuple: A tuple containing the report, the maximum level of 
+               importance, and the corresponding level name.
+    """
+    root = ET.fromstring(strdata)
+    namespace = {'oops': 'http://www.oeg-upm.net/oops'}
+
+    pitfalls = [
+        pitfall for pitfall in root.findall('.//oops:Pitfall', namespace)
+        for affelem in pitfall.findall('.//oops:AffectedElement', namespace)
+        if affelem.text.startswith(restriction)
+    ]
+    suggestions = [
+        suggestion for suggestion in root.findall('.//oops:Suggestion', namespace)
+        for affelem in suggestion.findall('.//oops:AffectedElement', namespace)
+        if affelem.text.startswith(restriction)
+    ]
+
+    report = {
+        'pitfalls': [
+            pitfall_repr(pitfall, namespace, restriction) for pitfall in pitfalls
+        ],
+        'suggestions': [ 
+            suggestion_repr(suggestion, namespace, restriction) for suggestion in suggestions
+        ]
+    }
+
+    maxlevel = 0
+    for pf in report['pitfalls']:
+        maxlevel = max(maxlevel, LEVELS[pf['importance']])
+
+    return report, maxlevel, LEVELS_INV[maxlevel]
+
+def oops_report(ontology_url=None, ontology_file=None,
+                ontology_file_type='xml', restriction='', verbose=False, timeout=REQ_TIMEOUT):
+    """
+    Generates a report using the OOPS API based on the provided ontology URL or ontology file.
+
+    Args:
+        ontology_url (str): The URL of the ontology to be used for generating the report.
+        ontology_file (str): The path to the ontology file to be used for generating the report.
+        restriction (str): A restriction to be applied during report generation.
+        verbose (bool): Whether to print verbose output.
+
+    Returns:
+        int: The maximum level of the report.
+
+    Raises:
+        ValueError: If neither ontology_file nor ontology_url is specified.
+        RuntimeError: If an invalid response is received from the OOPS API.
+    """
+    if ontology_file is not None:
+        ontology = convert_file(ontology_file, ontology_file_type)
+        xml_body = '''
+        <?xml version="1.0" encoding="UTF-8"?>
+        <OOPSRequest>
+        <OntologyURI></OntologyURI>
+        <OntologyContent>'''+ontology+'''</OntologyContent>
+        <Pitfalls></Pitfalls>
+        <OutputFormat>XML</OutputFormat>
+        </OOPSRequest>
+        '''
+    elif ontology_url is not None:
+        xml_body = '''
+        <?xml version="1.0" encoding="UTF-8"?>
+        <OOPSRequest>
+        <OntologyURI>'''+ontology_url+'''</OntologyURI>
+        <OntologyContent></OntologyContent>
+        <Pitfalls></Pitfalls>
+        <OutputFormat>XML</OutputFormat>
+        </OOPSRequest>
+        '''
+    else:
+        raise ValueError('Either ontology_file or ontology_url must be specified')
+
+    url = 'https://oops.linkeddata.es/rest'
+    headers = {
+        'Content-Type': 'application/xml'
+    }
+    with open('_oops_badge_command.sh', 'w', encoding='utf8') as f:
+        f.write('badge OOPS! Error :blue > oops_badge.svg')
+
+    response = requests.post(url, data=xml_body.encode('utf-8'), headers=headers, timeout=timeout)
+    with open('oops_request_raw.txt', 'wb') as f:
+        f.write(response.content)
+
+    if verbose:
+        print(f'OOPS API answered with status code {response.status_code}')
+    if response.status_code == 200:
+        report, maxlevel, maxlevel_text = make_report(response.content, restriction)
+        with open('_oops_badge_command.sh', 'w', encoding='utf8') as f:
+            f.write(f'badge OOPS! {maxlevel_text} :{LEVEL_COLOR[maxlevel_text]} > oops_badge.svg')
+    else:
+        with open('_oops_badge_command.sh', 'w', encoding='utf8') as f:
+            f.write('badge OOPS! Error :blue > oops_badge.svg')
+        raise RuntimeError('Invalid response from OOPS API')
+
+    if verbose:
+        print(f"Report shows {len(report['pitfalls'])} pitfalls and {len(report['suggestions'])}",
+              f"suggestions. Max level is {maxlevel}:{maxlevel_text}")
+
+    with open('oops_report.json', 'w', encoding='utf8') as f:
+        json.dump(report, f, indent=4)
+
+def convert_file(file_path, input_type):
+    """
+    Converts a file to a specified input type.
+
+    Args:
+        file_path (str): The path to the file to be converted.
+        input_type (str): The format of the input file.
+
+    Returns:
+        str: The serialized XML representation of the converted file.
+    """
+    graph = rdflib.Graph()
+    graph.parse(file_path, format=input_type)
+    return graph.serialize(format='xml')
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(description=
+        'Generates a report using the OOPS API based on the provided ontology \
+         URL or ontology file. The output is stored in oops_report.json. \
+         The maximum level of the report is stored in oops_badge.svg. \
+         The badge command is stored in _oops_badge_command.sh. \
+         Use either ontology_file or ontology_url, if both are provided \
+         only ontology_file is used.')
+    parser.add_argument('-u', '--ontology-url', type=str, default=None,
+                        help='The URL of the ontology to be used for generating the report.')
+    parser.add_argument('-f', '--ontology-file', type=str, default=None,
+                        help='The path to the ontology file to be used for generating the report.')
+    parser.add_argument('-t', '--ontology-file-type', type=str, default='xml',
+                        help='The format of the input ontology file (default: xml).')
+    parser.add_argument('-r', '--restriction', type=str, default='',
+                        help='A restriction to be applied during report generation.')
+    parser.add_argument('--timeout', type=int, default=REQ_TIMEOUT,
+                        help=f'The number of seconds to wait for a \
+                               response from the OOPS API (default: {REQ_TIMEOUT}).')
+    parser.add_argument('-v', '--verbose', action='store_true',
+                        help='Whether to print verbose output.')
+    args = parser.parse_args()
+
+    oops_report(ontology_url=args.ontology_url,
+                ontology_file=args.ontology_file,
+                ontology_file_type=args.ontology_file_type,
+                restriction=args.restriction,
+                verbose=args.verbose,
+                timeout=args.timeout)

.github/workflow_resources/query_version.sparql

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+SELECT ?v WHERE {
+    <https://w3id.org/pmd/tto> <http://www.w3.org/2002/07/owl#versionInfo> ?v
+}