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mapping-commons · Nov 14, 2023 · c79bce0 · c79bce0
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diff --git a/_modules/sssom/util.html b/_modules/sssom/util.html
@@ -370,13 +370,7 @@ <h1>Source code for sssom.util</h1><div class="highlight"><pre>
 <span class="sd">        - If the string represents a CURIE, tries to standardize it. If not possible, returns the original value</span>
 <span class="sd">        - Otherwise, return the original value</span>
 <span class="sd">    &quot;&quot;&quot;</span>
-    <span class="k">if</span> <span class="n">converter</span><span class="o">.</span><span class="n">is_uri</span><span class="p">(</span><span class="n">curie_or_iri</span><span class="p">):</span>
-        <span class="c1"># TODO switch to compress, or fully replace _standardize_curie_or_iri with</span>
-        <span class="c1">#  https://curies.readthedocs.io/en/latest/tutorial.html#extended-expansion-and-compression</span>
-        <span class="k">return</span> <span class="n">converter</span><span class="o">.</span><span class="n">standardize_uri</span><span class="p">(</span><span class="n">curie_or_iri</span><span class="p">,</span> <span class="n">strict</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
-    <span class="k">if</span> <span class="n">converter</span><span class="o">.</span><span class="n">is_curie</span><span class="p">(</span><span class="n">curie_or_iri</span><span class="p">):</span>
-        <span class="k">return</span> <span class="n">converter</span><span class="o">.</span><span class="n">standardize_curie</span><span class="p">(</span><span class="n">curie_or_iri</span><span class="p">,</span> <span class="n">strict</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
-    <span class="k">return</span> <span class="n">curie_or_iri</span>
+    <span class="k">return</span> <span class="n">converter</span><span class="o">.</span><span class="n">compress_or_standardize</span><span class="p">(</span><span class="n">curie_or_iri</span><span class="p">,</span> <span class="n">passthrough</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
 
 
 <span class="k">def</span> <span class="nf">_standardize_metadata</span><span class="p">(</span>
@@ -1567,16 +1561,7 @@ <h1>Source code for sssom.util</h1><div class="highlight"><pre>
 <span class="sd">    :param converter: Converter used for compression</span>
 <span class="sd">    :return: A CURIE</span>
 <span class="sd">    &quot;&quot;&quot;</span>
-    <span class="c1"># TODO replace with https://curies.readthedocs.io/en/latest/tutorial.html#extended-expansion-and-compression</span>
-    <span class="c1">#  when it&#39;s available</span>
-    <span class="k">if</span> <span class="ow">not</span> <span class="n">converter</span><span class="o">.</span><span class="n">is_curie</span><span class="p">(</span><span class="n">uri</span><span class="p">):</span>
-        <span class="k">return</span> <span class="n">converter</span><span class="o">.</span><span class="n">compress_strict</span><span class="p">(</span><span class="n">uri</span><span class="p">)</span>
-    <span class="n">rv</span> <span class="o">=</span> <span class="n">converter</span><span class="o">.</span><span class="n">standardize_curie</span><span class="p">(</span><span class="n">uri</span><span class="p">)</span>
-    <span class="k">if</span> <span class="n">rv</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
-        <span class="k">raise</span> <span class="ne">ValueError</span><span class="p">(</span>
-            <span class="sa">f</span><span class="s2">&quot;CURIE appeared where there should be a URI, and could not be standardized: </span><span class="si">{</span><span class="n">uri</span><span class="si">}</span><span class="s2">&quot;</span>
-        <span class="p">)</span>
-    <span class="k">return</span> <span class="n">rv</span></div>
+    <span class="k">return</span> <span class="n">converter</span><span class="o">.</span><span class="n">compress_or_standardize</span><span class="p">(</span><span class="n">uri</span><span class="p">,</span> <span class="n">strict</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span></div>
 </pre></div>
 
            </div>

diff --git a/cli_usage.html b/cli_usage.html
@@ -370,7 +370,7 @@ <h3>convert<a class="headerlink" href="#sssom-convert" title="Permalink to this
 <dd><p>Desired output format.</p>
 <dl class="field-list simple">
 <dt class="field-odd">Options<span class="colon">:</span></dt>
-<dd class="field-odd"><p>tsv | owl | ontoportal_json | fhir_json | json | rdf | nt | turtle | xml | ttl</p>
+<dd class="field-odd"><p>tsv | owl | ontoportal_json | fhir_json | json | rdf | xml | nt | turtle | ttl</p>
 </dd>
 </dl>
 </dd></dl>