valid URI generation for saving file working

docs/_sources/autoapi/json2graph/decode/index.rst.txt

@@ -79,7 +79,7 @@ Attributes
 
 .. py:function:: decode_all_ontouml_json2graph()
 
-   Decode multiple OntoUML JSON files.
+   Decode multiple OntoUML JSON files in batch mode.
 
    This function processes a directory of OntoUML JSON files and converts each file into a corresponding
    knowledge graph using the specified options.

docs/_sources/autoapi/json2graph/modules/messages/index.rst.txt

@@ -5,7 +5,7 @@
 
 .. autoapi-nested-parse::
 
-   Decoding messages to be displayed to users must be concentrated in this module whenever possible.
+   Warning messages generated during the decoding process to be displayed to users must be concentrated in this module whenever possible.
 
 
 

docs/_sources/autoapi/json2graph/modules/utils_graph/index.rst.txt

@@ -21,6 +21,8 @@ Functions
    json2graph.modules.utils_graph.ontouml_ref
    json2graph.modules.utils_graph.load_ontouml_vocabulary
    json2graph.modules.utils_graph.load_graph_safely
+   json2graph.modules.utils_graph.fix_uri
+   json2graph.modules.utils_graph.rename_uriref_resource
 
 
 
@@ -65,15 +67,40 @@ Attributes
    :rtype: Graph
 
 
-.. py:function:: load_graph_safely(ontology_file, format = 'not_provided')
+.. py:function:: load_graph_safely(ontology_file, out_format = 'not_provided')
 
    Safely load graph from file to working memory using arguments provided by the user, which are the file path     and (optionally) the file type.
 
    :param ontology_file: Path to the ontology file to be loaded into the working memory.
    :type ontology_file: str
-   :param format: Optional argument. Format of the file to be loaded.
-   :type format: str
+   :param out_format: Optional argument. Format of the file to be loaded.
+   :type out_format: str
    :return: RDFLib graph loaded as object.
    :rtype: Graph
 
 
+.. py:function:: fix_uri(url_string)
+
+   Received a valid URL, but invalid URI string and converts to a valid URL and valid URI string.
+
+   This function takes a URL string, parses it, encodes non-URI characters, and reconstructs a valid URI.
+
+   :param url_string: The URL string to be fixed.
+   :type url_string: str
+   :return: The resulting valid URI string.
+   :rtype: str
+
+
+.. py:function:: rename_uriref_resource(graph, old_resource, new_resource)
+
+   Rename a URIRef resource of an RDF graph by replacing it to a new one with a different name.
+
+   :param graph: The RDF graph that contains the resource to be renamed.
+   :type graph: Graph
+   :param old_resource: The old resource to be replaced.
+   :type old_resource: URIRef
+   :param new_resource: The new resource to replace the old one.
+   :type new_resource: URIRef
+   :return: None
+
+

docs/autoapi/json2graph/decode/index.html

@@ -104,7 +104,7 @@ <h3>Functions<a class="headerlink" href="#functions" title="Link to this heading
 <td><p>Save the ontology graph received as argument into a file using the syntax defined by the user.</p></td>
 </tr>
 <tr class="row-odd"><td><p><a class="reference internal" href="#json2graph.decode.decode_all_ontouml_json2graph" title="json2graph.decode.decode_all_ontouml_json2graph"><code class="xref py py-obj docutils literal notranslate"><span class="pre">decode_all_ontouml_json2graph</span></code></a>()</p></td>
-<td><p>Decode multiple OntoUML JSON files.</p></td>
+<td><p>Decode multiple OntoUML JSON files in batch mode.</p></td>
 </tr>
 </tbody>
 </table>
@@ -173,7 +173,7 @@ <h3>Attributes<a class="headerlink" href="#attributes" title="Link to this headi
 <dl class="py function">
 <dt class="sig sig-object py" id="json2graph.decode.decode_all_ontouml_json2graph">
 <span class="sig-prename descclassname"><span class="pre">json2graph.decode.</span></span><span class="sig-name descname"><span class="pre">decode_all_ontouml_json2graph</span></span><span class="sig-paren">(</span><span class="sig-paren">)</span><a class="headerlink" href="#json2graph.decode.decode_all_ontouml_json2graph" title="Link to this definition"></a></dt>
-<dd><p>Decode multiple OntoUML JSON files.</p>
+<dd><p>Decode multiple OntoUML JSON files in batch mode.</p>
 <p>This function processes a directory of OntoUML JSON files and converts each file into a corresponding
 knowledge graph using the specified options.
 The output graphs are saved in the output directory chosen by the user as argument.</p>

docs/autoapi/json2graph/modules/messages/index.html

@@ -92,7 +92,7 @@
 
   <section id="module-json2graph.modules.messages">
 <span id="json2graph-modules-messages"></span><h1><a class="reference internal" href="#module-json2graph.modules.messages" title="json2graph.modules.messages"><code class="xref py py-mod docutils literal notranslate"><span class="pre">json2graph.modules.messages</span></code></a><a class="headerlink" href="#module-json2graph.modules.messages" title="Link to this heading"></a></h1>
-<p>Decoding messages to be displayed to users must be concentrated in this module whenever possible.</p>
+<p>Warning messages generated during the decoding process to be displayed to users must be concentrated in this module whenever possible.</p>
 <section id="module-contents">
 <h2>Module Contents<a class="headerlink" href="#module-contents" title="Link to this heading"></a></h2>
 <section id="functions">

docs/autoapi/json2graph/modules/utils_graph/index.html

@@ -105,9 +105,15 @@ <h3>Functions<a class="headerlink" href="#functions" title="Link to this heading
 <tr class="row-even"><td><p><a class="reference internal" href="#json2graph.modules.utils_graph.load_ontouml_vocabulary" title="json2graph.modules.utils_graph.load_ontouml_vocabulary"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_ontouml_vocabulary</span></code></a>([enable_remote])</p></td>
 <td><p>Load the OntoUML Vocabulary to the working memory.</p></td>
 </tr>
-<tr class="row-odd"><td><p><a class="reference internal" href="#json2graph.modules.utils_graph.load_graph_safely" title="json2graph.modules.utils_graph.load_graph_safely"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_graph_safely</span></code></a>(ontology_file[, format])</p></td>
+<tr class="row-odd"><td><p><a class="reference internal" href="#json2graph.modules.utils_graph.load_graph_safely" title="json2graph.modules.utils_graph.load_graph_safely"><code class="xref py py-obj docutils literal notranslate"><span class="pre">load_graph_safely</span></code></a>(ontology_file[, out_format])</p></td>
 <td><p>Safely load graph from file to working memory using arguments provided by the user, which are the file path     and (optionally) the file type.</p></td>
 </tr>
+<tr class="row-even"><td><p><a class="reference internal" href="#json2graph.modules.utils_graph.fix_uri" title="json2graph.modules.utils_graph.fix_uri"><code class="xref py py-obj docutils literal notranslate"><span class="pre">fix_uri</span></code></a>(url_string)</p></td>
+<td><p>Received a valid URL, but invalid URI string and converts to a valid URL and valid URI string.</p></td>
+</tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="#json2graph.modules.utils_graph.rename_uriref_resource" title="json2graph.modules.utils_graph.rename_uriref_resource"><code class="xref py py-obj docutils literal notranslate"><span class="pre">rename_uriref_resource</span></code></a>(graph, old_resource, new_resource)</p></td>
+<td><p>Rename a URIRef resource of an RDF graph by replacing it to a new one with a different name.</p></td>
+</tr>
 </tbody>
 </table>
 </section>
@@ -167,13 +173,13 @@ <h3>Attributes<a class="headerlink" href="#attributes" title="Link to this headi
 
 <dl class="py function">
 <dt class="sig sig-object py" id="json2graph.modules.utils_graph.load_graph_safely">
-<span class="sig-prename descclassname"><span class="pre">json2graph.modules.utils_graph.</span></span><span class="sig-name descname"><span class="pre">load_graph_safely</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ontology_file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">format</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'not_provided'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#json2graph.modules.utils_graph.load_graph_safely" title="Link to this definition"></a></dt>
+<span class="sig-prename descclassname"><span class="pre">json2graph.modules.utils_graph.</span></span><span class="sig-name descname"><span class="pre">load_graph_safely</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">ontology_file</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">out_format</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">'not_provided'</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#json2graph.modules.utils_graph.load_graph_safely" title="Link to this definition"></a></dt>
 <dd><p>Safely load graph from file to working memory using arguments provided by the user, which are the file path     and (optionally) the file type.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Parameters<span class="colon">:</span></dt>
 <dd class="field-odd"><ul class="simple">
 <li><p><strong>ontology_file</strong> (<em>str</em>) – Path to the ontology file to be loaded into the working memory.</p></li>
-<li><p><strong>format</strong> (<em>str</em>) – Optional argument. Format of the file to be loaded.</p></li>
+<li><p><strong>out_format</strong> (<em>str</em>) – Optional argument. Format of the file to be loaded.</p></li>
 </ul>
 </dd>
 <dt class="field-even">Returns<span class="colon">:</span></dt>
@@ -185,6 +191,45 @@ <h3>Attributes<a class="headerlink" href="#attributes" title="Link to this headi
 </dl>
 </dd></dl>
 
+<dl class="py function">
+<dt class="sig sig-object py" id="json2graph.modules.utils_graph.fix_uri">
+<span class="sig-prename descclassname"><span class="pre">json2graph.modules.utils_graph.</span></span><span class="sig-name descname"><span class="pre">fix_uri</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">url_string</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#json2graph.modules.utils_graph.fix_uri" title="Link to this definition"></a></dt>
+<dd><p>Received a valid URL, but invalid URI string and converts to a valid URL and valid URI string.</p>
+<p>This function takes a URL string, parses it, encodes non-URI characters, and reconstructs a valid URI.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><p><strong>url_string</strong> (<em>str</em>) – The URL string to be fixed.</p>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>The resulting valid URI string.</p>
+</dd>
+<dt class="field-odd">Return type<span class="colon">:</span></dt>
+<dd class="field-odd"><p>str</p>
+</dd>
+</dl>
+</dd></dl>
+
+<dl class="py function">
+<dt class="sig sig-object py" id="json2graph.modules.utils_graph.rename_uriref_resource">
+<span class="sig-prename descclassname"><span class="pre">json2graph.modules.utils_graph.</span></span><span class="sig-name descname"><span class="pre">rename_uriref_resource</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">graph</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">old_resource</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">new_resource</span></span></em><span class="sig-paren">)</span><a class="headerlink" href="#json2graph.modules.utils_graph.rename_uriref_resource" title="Link to this definition"></a></dt>
+<dd><p>Rename a URIRef resource of an RDF graph by replacing it to a new one with a different name.</p>
+<dl class="field-list simple">
+<dt class="field-odd">Parameters<span class="colon">:</span></dt>
+<dd class="field-odd"><ul class="simple">
+<li><p><strong>graph</strong> (<em>Graph</em>) – The RDF graph that contains the resource to be renamed.</p></li>
+<li><p><strong>old_resource</strong> (<em>URIRef</em>) – The old resource to be replaced.</p></li>
+<li><p><strong>new_resource</strong> (<em>URIRef</em>) – The new resource to replace the old one.</p></li>
+</ul>
+</dd>
+<dt class="field-even">Returns<span class="colon">:</span></dt>
+<dd class="field-even"><p>None</p>
+</dd>
+<dt class="field-odd">Return type<span class="colon">:</span></dt>
+<dd class="field-odd"><p>None</p>
+</dd>
+</dl>
+</dd></dl>
+
 </section>
 </section>
 </section>

docs/genindex.html

@@ -79,6 +79,7 @@ <h1 id="index">Index</h1>
  | <a href="#C"><strong>C</strong></a>
  | <a href="#D"><strong>D</strong></a>
  | <a href="#E"><strong>E</strong></a>
+ | <a href="#F"><strong>F</strong></a>
  | <a href="#G"><strong>G</strong></a>
  | <a href="#I"><strong>I</strong></a>
  | <a href="#J"><strong>J</strong></a>
@@ -177,6 +178,14 @@ <h2 id="E">E</h2>
   </ul></td>
 </tr></table>
 
+<h2 id="F">F</h2>
+<table style="width: 100%" class="indextable genindextable"><tr>
+  <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autoapi/json2graph/modules/utils_graph/index.html#json2graph.modules.utils_graph.fix_uri">fix_uri() (in module json2graph.modules.utils_graph)</a>
+</li>
+  </ul></td>
+</tr></table>
+
 <h2 id="G">G</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
@@ -576,6 +585,8 @@ <h2 id="P">P</h2>
 <h2 id="R">R</h2>
 <table style="width: 100%" class="indextable genindextable"><tr>
   <td style="width: 33%; vertical-align: top;"><ul>
+      <li><a href="autoapi/json2graph/modules/utils_graph/index.html#json2graph.modules.utils_graph.rename_uriref_resource">rename_uriref_resource() (in module json2graph.modules.utils_graph)</a>
+</li>
       <li><a href="autoapi/json2graph/modules/errors/index.html#json2graph.modules.errors.report_error_end_of_switch">report_error_end_of_switch() (in module json2graph.modules.errors)</a>
 </li>
       <li><a href="autoapi/json2graph/modules/errors/index.html#json2graph.modules.errors.report_error_invalid_parameter">report_error_invalid_parameter() (in module json2graph.modules.errors)</a>

json2graph/modules/input_output.py

@@ -1,13 +1,12 @@
 """IO functions used in diverse occasions."""
 import json
 import os
-import urllib
 
-from icecream import ic
-from rdflib import Graph
+from rdflib import Graph, URIRef
 
 from .errors import report_error_io_read, report_error_io_write
 from .logger import initialize_logger
+from .utils_graph import rename_uriref_resource, fix_uri
 
 LOGGER = initialize_logger()
 
@@ -48,34 +47,6 @@ def safe_load_json_file(json_path: str) -> dict:
     return json_data
 
 
-def fix_uri(url_string) -> str:
-    """To do."""
-    # Step 1: Parse the URL
-    parsed_url = urllib.parse.urlparse(url_string)
-
-    # Step 2: URL Encode Non-URI Characters
-    # Encode non-ASCII characters and spaces in the path and query components
-    encoded_path = urllib.parse.quote(parsed_url.path)
-    encoded_query = urllib.parse.quote(parsed_url.query)
-    encoded_scheme = urllib.parse.quote(parsed_url.scheme)
-    encoded_netloc = urllib.parse.quote(parsed_url.netloc)
-    encoded_fragment = urllib.parse.quote(parsed_url.fragment)
-
-    # Step 3: Reconstruct the URI
-    valid_uri = urllib.parse.urlunparse(
-        (
-            encoded_scheme,
-            encoded_netloc,
-            encoded_path,
-            "",  # Empty string for params
-            encoded_query,
-            encoded_fragment,
-        )
-    )
-
-    return valid_uri
-
-
 def safe_write_graph_file(ontouml_graph: Graph, output_file_path: str, syntax: str) -> None:
     """Safely saves the graph into a file in the informed destination with the desired syntax.
 
@@ -86,26 +57,32 @@ def safe_write_graph_file(ontouml_graph: Graph, output_file_path: str, syntax: s
     :param syntax: Syntax to be used for saving the ontology file.
     :type syntax: str
     """
+    # Regular case (all URIRef resources have valid URIs)
     try:
         ontouml_graph.serialize(destination=output_file_path, encoding="utf-8", format=syntax)
     except Exception:
-        for s, p, o in ontouml_graph:
-            if "URIRef" in str(type(s)):
-                old_s = s.toPython()
-                new_s = fix_uri(old_s)
-                if old_s != new_s:
-                    ic(old_s, new_s)
-            if "URIRef" in str(type(p)):
-                old_p = p.toPython()
-                new_p = fix_uri(old_p)
-                if old_p != new_p:
-                    ic(old_p, new_p)
-            if "URIRef" in str(type(o)):
-                old_o = o.toPython()
-                new_o = fix_uri(old_o)
-                if old_o != new_o:
-                    ic(old_o, new_o)
-        # ontouml_graph.serialize(destination=output_file_path, encoding="utf-8", format=syntax)
-    except OSError as errorOS:
-        file_description = "output graph file - OSError"
-        report_error_io_write(output_file_path, file_description, errorOS)
+        # Special treatment for the cases where the graph has URIRef resources that are not valid URIs
+        try:
+            for old_s, old_p, old_o in ontouml_graph:
+                if "URIRef" in str(type(old_s)):
+                    old_s_name = old_s.toPython()
+                    new_s = URIRef(fix_uri(old_s_name))
+                    new_s_name = new_s.toPython()
+                    if old_s_name != new_s_name:
+                        rename_uriref_resource(ontouml_graph, old_s, new_s)
+                if "URIRef" in str(type(old_p)):
+                    old_p_name = old_p.toPython()
+                    new_p = URIRef(fix_uri(old_p_name))
+                    new_p_name = new_p.toPython()
+                    if old_p_name != new_p_name:
+                        rename_uriref_resource(ontouml_graph, old_p, new_p)
+                if "URIRef" in str(type(old_o)):
+                    old_o_name = old_o.toPython()
+                    new_o = URIRef(fix_uri(old_o_name))
+                    new_o_name = new_o.toPython()
+                    if old_o_name != new_o_name:
+                        rename_uriref_resource(ontouml_graph, old_o, new_o)
+            ontouml_graph.serialize(destination=output_file_path, encoding="utf-8", format=syntax)
+        except OSError as errorOS:
+            file_description = "output graph file"
+            report_error_io_write(output_file_path, file_description, errorOS)