Update requirements

README.md

@@ -137,7 +137,6 @@ Install with
 See [docs/docker-instructions.md](#docs/docker-instructions.md)
 for how to build a docker image.
 
-
 Known issues
 ------------
 
@@ -150,13 +149,13 @@ Known issues
   master](https://github.com/RDFLib/rdflib) if you need to serialise
   to turtle.
 
-
 Attributions and credits
 ------------------------
 EMMOntoPy is maintained by [EMMC-ASBL](https://emmc.eu/).  So far it has mainly been developed by
 [SINTEF](https://www.sintef.no/).
 
 ### Contributing projects
+
 - [EMMC-CSA](https://emmc.info/about-emmc-csa/);
   Grant Agreement No: 723867
   <img src="https://i2.wp.com/emmc.info/wp-content/uploads/2018/10/emmc_logo-low.jpg?fit=1701%2C1701&ssl=1" height="50">

ontopy/utils.py

@@ -6,6 +6,7 @@
 import datetime
 import tempfile
 import types
+from typing import TYPE_CHECKING
 import urllib.request
 import xml.etree.ElementTree as ET
 
@@ -15,6 +16,11 @@
 import owlready2
 
 
+if TYPE_CHECKING:
+    from packaging.version import Version, LegacyVersion
+    from typing import Union
+
+
 # Format mappings: file extension -> rdflib format name
 FMAP = {
     'n3': 'ntriples',
@@ -28,6 +34,15 @@
 OWLREADY2_FORMATS = 'rdfxml', 'owl', 'xml', 'ntriples'
 
 
+class IncompatibleVersion(Exception):
+    """An installed dependency version is incompatible with a functionality of
+    this package."""
+
+
+class UnknownVersion(Exception):
+    """Cannot retrieve version from a package."""
+
+
 def isinteractive():
     """Returns true if we are running from an interactive interpreater,
     false otherwise."""
@@ -324,13 +339,71 @@ def write_catalog(mappings, output='catalog-v001.xml'):
         f.write('\n'.join(s) + '\n')
 
 
+def _validate_installed_version(
+    package: str, min_version: "Union[str, Version, LegacyVersion]"
+) -> bool:
+    """Validate an installed package.
+
+    Examine whether a minimum version is installed in the used Python
+    interpreter for a specific package.
+
+    Parameters:
+        package: The package to be investigated as a string, e.g., `"rdflib"`.
+        min_version: The minimum version expected to be installed.
+
+    Raises:
+        UnknownVersion: If the supplied package does not have a `__version__`
+            attribute.
+
+    Returns:
+        Whether or not the installed version is equal to or greater than the
+        `min_version`.
+
+    """
+    import importlib
+    from packaging.version import (
+        parse as parse_version, LegacyVersion, Version
+    )
+
+    if isinstance(min_version, str):
+        min_version = parse_version(min_version)
+    elif isinstance(min_version, (LegacyVersion, Version)):
+        # We have the format we want
+        pass
+    else:
+        raise TypeError(
+            "min_version should be either a str, LegacyVersion or Version. "
+            "The latter classes being from the packaging.version module."
+        )
+
+    installed_package = importlib.import_module(
+        name=".", package=package
+    )
+    installed_package_version = getattr(installed_package, "__version__", None)
+    if not installed_package_version:
+        raise UnknownVersion(
+            f"Cannot retrieve version information from package {package!r}."
+        )
+
+    return parse_version(installed_package_version) >= min_version
+
+
 def convert_imported(input, output, input_format=None, output_format='xml',
                      url_from_catalog=None, catalog_file='catalog-v001.xml'):
     """Convert imported ontologies.
 
     Store the output in a directory structure matching the source
     files.  This require catalog file(s) to be present.
 
+    Warning:
+        To convert to Turtle (`.ttl`) format, you must have installed
+        `rdflib>=6.0.0`. See [Known issues](../README.md#Known-issues) in the
+        README for more information.
+
+    Raises:
+        IncompatibleVersion: If `rdflib<6.0.0` and the desired output format is
+            Turtle.
+
     Args:
         input: input ontology file name
         output: output ontology file path.  The directory part of `output`
@@ -395,6 +468,20 @@ def recur(graph, outext):
 
     # Write output files
     fmt = input_format if input_format else guess_format(input, fmap=FMAP)
+
+    if (
+        not _validate_installed_version(package="rdflib", min_version="6.0.0")
+        and (output_format == FMAP.get("ttl", "") or outext == "ttl")
+    ):
+        from rdflib import __version__ as __rdflib_version__
+
+        raise IncompatibleVersion(
+            "To correctly convert to Turtle format, rdflib must be version "
+            "6.0.0 or greater, however, the detected rdflib version used "
+            f"by your Python interpreter is {__rdflib_version__!r}. For "
+            "more information see the 'Known issues' section of the README."
+        )
+
     g = Graph()
     g.parse(input, format=fmt)
     g.serialize(destination=output, format=output_format)
@@ -410,6 +497,16 @@ def squash_imported(input, output, input_format=None, output_format='xml',
     only be used if it exists in the same directory as the input file.
 
     The the squash rdflib graph is returned.
+
+    Warning:
+        To convert to Turtle (`.ttl`) format, you must have installed
+        `rdflib>=6.0.0`. See [Known issues](../README.md#Known-issues) in the
+        README for more information.
+
+    Raises:
+        IncompatibleVersion: If `rdflib<6.0.0` and the desired output format is
+            Turtle.
+
     """
     inroot = os.path.dirname(os.path.abspath(input))
 
@@ -440,6 +537,25 @@ def recur(g):
     graph.parse(input, format=input_format)
     recur(graph)
     if output:
+        if (
+            not _validate_installed_version(
+                package="rdflib", min_version="6.0.0"
+            )
+            and (
+                output_format == FMAP.get("ttl", "")
+                or os.path.splitext(output)[1] == "ttl"
+            )
+        ):
+            from rdflib import __version__ as __rdflib_version__
+
+            raise IncompatibleVersion(
+                "To correctly convert to Turtle format, rdflib must be version"
+                " 6.0.0 or greater, however, the detected rdflib version used "
+                f"by your Python interpreter is {__rdflib_version__!r}. For "
+                "more information see the 'Known issues' section of the "
+                "README."
+            )
+
         graph.serialize(destination=output, format=output_format)
     return graph
 

requirements.txt

@@ -1,9 +1,9 @@
-Cython>=0.29.21
-Owlready2>=0.28,!=0.32,!=0.34
-graphviz>=0.16
-PyYAML>=5.4.1
-blessings>=1.7
-Pygments>=2.7.4
-rdflib~=4.2.1
-semver>=2.8.1
-pydot>=1.4.1
+Cython>=0.29.21,<0.30
+Owlready2>=0.28,<0.35,!=0.32,!=0.34
+graphviz>=0.16,<0.17
+PyYAML>=5.4.1,<6
+blessings>=1.7,<2
+Pygments>=2.7.4,<3
+rdflib>=4.2.1,<7
+semver>=2.8.1,<3
+pydot>=1.4.1,<2

tools/ontoconvert

@@ -2,10 +2,18 @@
 """Converts file format of input ontology and write it to output file(s).
 """
 import argparse
+import os
+import sys
 
 from rdflib.util import Graph, guess_format
 
-from ontopy.utils import convert_imported, squash_imported
+from ontopy.utils import (
+    convert_imported,
+    FMAP,
+    IncompatibleVersion,
+    squash_imported,
+    _validate_installed_version,
+)
 from ontopy.factpluspluswrapper.factppgraph import FaCTPPGraph
 
 
@@ -64,28 +72,49 @@ def main():
         output_format = 'xml'
 
     # Perform conversion
-    if args.recursive:
-        convert_imported(args.input, args.output,
-                         input_format=input_format,
-                         output_format=output_format,
-                         url_from_catalog=args.url_from_catalog)
-    elif args.inferred:
-        g = squash_imported(args.input, None,
-                            input_format=input_format)
-        fg = FaCTPPGraph(g)
-        if args.base_iri:
-            fg.base_iri = args.base_iri
-        g2 = fg.inferred_graph()
-        g2.serialize(destination=args.output, format=output_format)
-    elif args.squash:
-        squash_imported(args.input, args.output,
-                        input_format=input_format,
-                        output_format=output_format,
-                        url_from_catalog=args.url_from_catalog)
-    else:
-        g = Graph()
-        g.parse(args.input, format=input_format)
-        g.serialize(destination=args.output, format=output_format)
+    try:
+        if args.recursive:
+            convert_imported(args.input, args.output,
+                            input_format=input_format,
+                            output_format=output_format,
+                            url_from_catalog=args.url_from_catalog)
+        elif args.inferred:
+            g = squash_imported(args.input, None,
+                                input_format=input_format)
+            fg = FaCTPPGraph(g)
+            if args.base_iri:
+                fg.base_iri = args.base_iri
+            g2 = fg.inferred_graph()
+            g2.serialize(destination=args.output, format=output_format)
+        elif args.squash:
+            squash_imported(args.input, args.output,
+                            input_format=input_format,
+                            output_format=output_format,
+                            url_from_catalog=args.url_from_catalog)
+        else:
+            if (
+                not _validate_installed_version(
+                    package="rdflib", min_version="6.0.0"
+                )
+                and (
+                    output_format == FMAP.get("ttl", "")
+                    or os.path.splitext(args.output)[1] == "ttl"
+                )
+            ):
+                from rdflib import __version__ as __rdflib_version__
+
+                raise IncompatibleVersion(
+                    "To correctly convert to Turtle format, rdflib must be version"
+                    " 6.0.0 or greater, however, the detected rdflib version used "
+                    f"by your Python interpreter is {__rdflib_version__!r}. For "
+                    "more information see the 'Known issues' section of the README."
+                )
+
+            g = Graph()
+            g.parse(args.input, format=input_format)
+            g.serialize(destination=args.output, format=output_format)
+    except IncompatibleVersion as exc:
+        sys.exit(f"\033[91mERROR\033[0m: {exc}")
 
 
 if __name__ == '__main__':