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@hrshdhgd
hrshdhgd committed Mar 14, 2024
1 parent 95942ac commit ea1482a
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19 changes: 11 additions & 8 deletions _modules/oaklib/implementations/simpleobo/simple_obo_implementation.html
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Original file line number Diff line number Diff line change
Expand Up @@ -582,13 +582,14 @@ <h1>Source code for oaklib.implementations.simpleobo.simple_obo_implementation</
<span class="sd"> :param rel_type:</span>
<span class="sd"> :return:</span>
<span class="sd"> &quot;&quot;&quot;</span>
<span class="n">is_core</span> <span class="o">=</span> <span class="n">rel_type</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">&quot;BFO:&quot;</span><span class="p">)</span> <span class="ow">or</span> <span class="n">rel_type</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">&quot;RO:&quot;</span><span class="p">)</span>
<span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">obo_document</span><span class="o">.</span><span class="n">stanzas</span><span class="o">.</span><span class="n">values</span><span class="p">():</span>
<span class="k">if</span> <span class="n">s</span><span class="o">.</span><span class="n">type</span> <span class="o">==</span> <span class="s2">&quot;Typedef&quot;</span><span class="p">:</span>
<span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">s</span><span class="o">.</span><span class="n">simple_values</span><span class="p">(</span><span class="n">TAG_XREF</span><span class="p">):</span>
<span class="k">if</span> <span class="n">x</span> <span class="o">==</span> <span class="n">rel_type</span><span class="p">:</span>
<span class="k">if</span> <span class="n">is_core</span> <span class="ow">or</span> <span class="s2">&quot;:&quot;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">s</span><span class="o">.</span><span class="n">id</span><span class="p">:</span>
<span class="k">return</span> <span class="n">s</span><span class="o">.</span><span class="n">id</span>
<span class="k">if</span> <span class="n">rel_type</span><span class="p">:</span>
<span class="n">is_core</span> <span class="o">=</span> <span class="n">rel_type</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">&quot;BFO:&quot;</span><span class="p">)</span> <span class="ow">or</span> <span class="n">rel_type</span><span class="o">.</span><span class="n">startswith</span><span class="p">(</span><span class="s2">&quot;RO:&quot;</span><span class="p">)</span>
<span class="k">for</span> <span class="n">s</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">obo_document</span><span class="o">.</span><span class="n">stanzas</span><span class="o">.</span><span class="n">values</span><span class="p">():</span>
<span class="k">if</span> <span class="n">s</span><span class="o">.</span><span class="n">type</span> <span class="o">==</span> <span class="s2">&quot;Typedef&quot;</span><span class="p">:</span>
<span class="k">for</span> <span class="n">x</span> <span class="ow">in</span> <span class="n">s</span><span class="o">.</span><span class="n">simple_values</span><span class="p">(</span><span class="n">TAG_XREF</span><span class="p">):</span>
<span class="k">if</span> <span class="n">x</span> <span class="o">==</span> <span class="n">rel_type</span><span class="p">:</span>
<span class="k">if</span> <span class="n">is_core</span> <span class="ow">or</span> <span class="s2">&quot;:&quot;</span> <span class="ow">not</span> <span class="ow">in</span> <span class="n">s</span><span class="o">.</span><span class="n">id</span><span class="p">:</span>
<span class="k">return</span> <span class="n">s</span><span class="o">.</span><span class="n">id</span>
<span class="k">return</span> <span class="n">rel_type</span>

<span class="k">def</span> <span class="nf">relationships</span><span class="p">(</span>
Expand Down Expand Up @@ -730,7 +731,7 @@ <h1>Source code for oaklib.implementations.simpleobo.simple_obo_implementation</
<span class="k">else</span><span class="p">:</span>
<span class="bp">self</span><span class="o">.</span><span class="n">obo_document</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="n">path</span><span class="p">)</span>
<span class="k">else</span><span class="p">:</span>
<span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">syntax</span><span class="p">)</span>
<span class="nb">super</span><span class="p">()</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="n">syntax</span><span class="o">=</span><span class="n">syntax</span><span class="p">)</span>

<span class="k">def</span> <span class="nf">save</span><span class="p">(</span>
<span class="bp">self</span><span class="p">,</span>
Expand Down Expand Up @@ -793,6 +794,8 @@ <h1>Source code for oaklib.implementations.simpleobo.simple_obo_implementation</
<span class="n">meta</span><span class="o">.</span><span class="n">definition</span> <span class="o">=</span> <span class="n">obograph</span><span class="o">.</span><span class="n">DefinitionPropertyValue</span><span class="p">(</span><span class="n">val</span><span class="o">=</span><span class="n">defn</span><span class="p">)</span>
<span class="k">for</span> <span class="n">_</span><span class="p">,</span> <span class="n">syn</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">synonym_property_values</span><span class="p">([</span><span class="n">curie</span><span class="p">]):</span>
<span class="n">meta</span><span class="o">.</span><span class="n">synonyms</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">syn</span><span class="p">)</span>
<span class="k">for</span> <span class="n">_</span><span class="p">,</span> <span class="n">subset</span> <span class="ow">in</span> <span class="bp">self</span><span class="o">.</span><span class="n">terms_subsets</span><span class="p">([</span><span class="n">curie</span><span class="p">]):</span>
<span class="n">meta</span><span class="o">.</span><span class="n">subsets</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">subset</span><span class="p">)</span>
<span class="k">return</span> <span class="n">obograph</span><span class="o">.</span><span class="n">Node</span><span class="p">(</span><span class="nb">id</span><span class="o">=</span><span class="n">curie</span><span class="p">,</span> <span class="n">lbl</span><span class="o">=</span><span class="bp">self</span><span class="o">.</span><span class="n">label</span><span class="p">(</span><span class="n">curie</span><span class="p">),</span> <span class="nb">type</span><span class="o">=</span><span class="n">typ</span><span class="p">,</span> <span class="n">meta</span><span class="o">=</span><span class="n">meta</span><span class="p">)</span>

<span class="k">def</span> <span class="nf">as_obograph</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">expand_curies</span><span class="o">=</span><span class="kc">False</span><span class="p">)</span> <span class="o">-&gt;</span> <span class="n">Graph</span><span class="p">:</span>
Expand Down
15 changes: 12 additions & 3 deletions _modules/oaklib/implementations/sqldb/sql_implementation.html
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Original file line number Diff line number Diff line change
Expand Up @@ -239,6 +239,10 @@ <h1>Source code for oaklib.implementations.sqldb.sql_implementation</h1><div cla
<span class="kn">from</span> <span class="nn">oaklib.utilities.axioms.logical_definition_utilities</span> <span class="kn">import</span> <span class="p">(</span>
<span class="n">logical_definition_matches</span><span class="p">,</span>
<span class="p">)</span>
<span class="kn">from</span> <span class="nn">oaklib.utilities.format_utilities</span> <span class="kn">import</span> <span class="p">(</span>
<span class="n">OBOGRAPHS_SYNTAX_ALIAS_MAP</span><span class="p">,</span>
<span class="n">RDFLIB_SYNTAX_ALIAS_MAP</span><span class="p">,</span>
<span class="p">)</span>
<span class="kn">from</span> <span class="nn">oaklib.utilities.graph.relationship_walker</span> <span class="kn">import</span> <span class="n">walk_down</span><span class="p">,</span> <span class="n">walk_up</span>
<span class="kn">from</span> <span class="nn">oaklib.utilities.identifier_utils</span> <span class="kn">import</span> <span class="p">(</span>
<span class="n">string_as_base64_curie</span><span class="p">,</span>
Expand Down Expand Up @@ -1267,11 +1271,14 @@ <h1>Source code for oaklib.implementations.sqldb.sql_implementation</h1><div cla
<span class="sd"> &quot;&quot;&quot;</span>
<span class="k">if</span> <span class="n">syntax</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
<span class="n">syntax</span> <span class="o">=</span> <span class="s2">&quot;ttl&quot;</span>
<span class="k">if</span> <span class="n">syntax</span> <span class="o">==</span> <span class="s2">&quot;ttl&quot;</span><span class="p">:</span>
<span class="k">if</span> <span class="n">syntax</span> <span class="ow">in</span> <span class="p">[</span><span class="s2">&quot;ttl&quot;</span><span class="p">,</span> <span class="s2">&quot;rdfxml&quot;</span><span class="p">,</span> <span class="s2">&quot;owl&quot;</span><span class="p">]:</span>
<span class="k">if</span> <span class="n">syntax</span> <span class="ow">in</span> <span class="n">RDFLIB_SYNTAX_ALIAS_MAP</span><span class="p">:</span>
<span class="n">syntax</span> <span class="o">=</span> <span class="n">RDFLIB_SYNTAX_ALIAS_MAP</span><span class="p">[</span><span class="n">syntax</span><span class="p">]</span>
<span class="n">g</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">as_rdflib_graph</span><span class="p">()</span>
<span class="n">logging</span><span class="o">.</span><span class="n">info</span><span class="p">(</span><span class="sa">f</span><span class="s2">&quot;Dumping to </span><span class="si">{</span><span class="n">path</span><span class="si">}</span><span class="s2">&quot;</span><span class="p">)</span>
<span class="n">g</span><span class="o">.</span><span class="n">serialize</span><span class="p">(</span><span class="n">path</span><span class="p">,</span> <span class="nb">format</span><span class="o">=</span><span class="n">syntax</span><span class="p">)</span>
<span class="k">elif</span> <span class="n">syntax</span> <span class="o">==</span> <span class="s2">&quot;json&quot;</span><span class="p">:</span>
<span class="k">elif</span> <span class="n">syntax</span> <span class="ow">in</span> <span class="n">OBOGRAPHS_SYNTAX_ALIAS_MAP</span><span class="o">.</span><span class="n">keys</span><span class="p">():</span>
<span class="n">syntax</span> <span class="o">=</span> <span class="n">OBOGRAPHS_SYNTAX_ALIAS_MAP</span><span class="p">[</span><span class="n">syntax</span><span class="p">]</span>
<span class="n">g</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">as_obograph</span><span class="p">(</span><span class="n">expand_curies</span><span class="o">=</span><span class="kc">True</span><span class="p">)</span>
<span class="n">gd</span> <span class="o">=</span> <span class="n">obograph</span><span class="o">.</span><span class="n">GraphDocument</span><span class="p">(</span><span class="n">graphs</span><span class="o">=</span><span class="p">[</span><span class="n">g</span><span class="p">])</span>
<span class="n">json_dumper</span><span class="o">.</span><span class="n">dump</span><span class="p">(</span><span class="n">gd</span><span class="p">,</span> <span class="n">path</span><span class="p">)</span>
Expand Down Expand Up @@ -2348,9 +2355,11 @@ <h1>Source code for oaklib.implementations.sqldb.sql_implementation</h1><div cla
<span class="bp">self</span><span class="o">.</span><span class="n">set_label</span><span class="p">(</span><span class="n">patch</span><span class="o">.</span><span class="n">about_node</span><span class="p">,</span> <span class="n">patch</span><span class="o">.</span><span class="n">new_value</span><span class="p">)</span>
<span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">patch</span><span class="p">,</span> <span class="n">kgcl</span><span class="o">.</span><span class="n">NewSynonym</span><span class="p">):</span>
<span class="c1"># TODO: synonym type</span>
<span class="k">if</span> <span class="ow">not</span> <span class="n">patch</span><span class="o">.</span><span class="n">predicate</span><span class="p">:</span>
<span class="n">patch</span><span class="o">.</span><span class="n">predicate</span> <span class="o">=</span> <span class="n">HAS_EXACT_SYNONYM</span>
<span class="bp">self</span><span class="o">.</span><span class="n">_execute</span><span class="p">(</span>
<span class="n">insert</span><span class="p">(</span><span class="n">Statements</span><span class="p">)</span><span class="o">.</span><span class="n">values</span><span class="p">(</span>
<span class="n">subject</span><span class="o">=</span><span class="n">about</span><span class="p">,</span> <span class="n">predicate</span><span class="o">=</span><span class="n">HAS_EXACT_SYNONYM</span><span class="p">,</span> <span class="n">value</span><span class="o">=</span><span class="n">patch</span><span class="o">.</span><span class="n">new_value</span>
<span class="n">subject</span><span class="o">=</span><span class="n">about</span><span class="p">,</span> <span class="n">predicate</span><span class="o">=</span><span class="n">patch</span><span class="o">.</span><span class="n">predicate</span><span class="p">,</span> <span class="n">value</span><span class="o">=</span><span class="n">patch</span><span class="o">.</span><span class="n">new_value</span>
<span class="p">)</span>
<span class="p">)</span>
<span class="k">elif</span> <span class="nb">isinstance</span><span class="p">(</span><span class="n">patch</span><span class="p">,</span> <span class="n">kgcl</span><span class="o">.</span><span class="n">RemoveSynonym</span><span class="p">):</span>
Expand Down
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