add compound links in model, fix compound bioschemas

and reuse that in the links template
bioschemas for compound fixed for links and more
WIP on #245

ippisite/ippidb/models.py

@@ -1082,6 +1082,41 @@ class Compound(AutoFillableModel):
         """
         return reverse("compound_card", kwargs={"pk": self.pk})
 
+    @property
+    def pubchem_url(self):
+        """
+        Get absolute URL to the corresponding PubChem entry
+        """
+        return f"https://pubchem.ncbi.nlm.nih.gov/compound/{ self.pubchem_id }" if self.pubchem_id else None
+
+    @property
+    def chembl_url(self):
+        """
+        Get absolute URL to the corresponding Chembl entry
+        """
+        return f"https://www.ebi.ac.uk/chembldb/compound/inspect/{ self.chembl_id }" if self.chembl_id else None
+
+    @property
+    def chemspider_url(self):
+        """
+        Get absolute URL to the corresponding ChemSpider entry
+        """
+        return f"http://www.chemspider.com/Chemical-Structure.{ self.chemspider_id}.html" if self.chemspider_id else None
+
+    @property
+    def pdbligand_url(self):
+        """
+        Get absolute URL to the corresponding PDB ligand entry
+        """
+        return f"https://www.rcsb.org/ligand/{ self.ligand_id}" if self.ligand_id else None
+
+    @property
+    def drugbank_url(self):
+        """
+        Get absolute URL to the corresponding Drugbank entry
+        """
+        return f"https://www.drugbank.ca/drugs/{ self.drugbank_id}" if self.drugbank_id else None
+
     def clean(self):
         """
         Perform additional checks:

ippisite/ippidb/templates/compound_card.html

@@ -573,8 +573,9 @@
 <script id='JSON_LD' type="application/ld+json">
 
   {
-"url": "{{ compound.get_absolute_url }}",
+"url": "{{ request.build_absolute_uri }}",
 "inChI": "{{ compound.inchi }}",
+"name": "{{ compound.iupac_name }}",
 "iupacName": "{{ compound.iupac_name }}",
 "molecularWeight": {{ compound.molecular_weight }},
 "identifier": "{{ compound.id }}",
@@ -584,6 +585,21 @@
 "smiles": [
   "{{ compound.canonical_smile }}"
 ],
+{% if compound.pubchem_id %}
+"sameAs": "{{ compound.pubchem_url }}",
+{% endif %}
+{% if compound.chembl_id %}
+"sameAs": "{{ compound.chembl_url }}",
+{% endif %}
+{% if compound.chemspider_id %}
+"sameAs": "{{ compound.chemspider_url }}",
+{% endif %}
+{% if compound.ligand_id %}
+"sameAs": "{{ compound.pdbligand_url }}",
+{% endif %}
+{% if compound.drugbank_id %}
+"sameAs": "{{ compound.drugbank_url }}",
+{% endif %}
 "@context": "http://schema.org"
 }
 

ippisite/ippidb/templates/compound_db_links.html

@@ -4,35 +4,35 @@
     <tr class="row">
       <td scope="col" class="col-2 text-center">
         {% if compound.pubchem_id %}
-        <a href="https://pubchem.ncbi.nlm.nih.gov/compound/{{ compound.pubchem_id }}" target="_blank"><img
+        <a href="{{ compound.pubchem_url }}" target="_blank"><img
             src="/static/images/Other/Pubchemlogo.png" style="height: 1.5em;"
             title="PubChem ID: {{ compound.pubchem_id }}" /><br />{{ compound.pubchem_id }}</a>
         {% endif %}
       </td>
       <td scope="col" class="col-2 text-center">
         {% if compound.chembl_id %}
-        <a href="https://www.ebi.ac.uk/chembldb/compound/inspect/{{ compound.chembl_id }}" target="_blank"><img
+        <a href="{{ compound.chembl_url }}" target="_blank"><img
             src="/static/images/Other/Chembl_logo.png" style="height: 1.5em;"
             title="ChEMBL ID: {{ compound.chembl_id }}" /><br />{{ compound.chembl_id }}</a>
         {% endif %}
       </td>
       <td scope="col" class="col-2 text-center">
         {% if compound.chemspider_id %}
-        <a href="http://www.chemspider.com/Chemical-Structure.{{ compound.chemspider_id}}.html" target="_blank"><img
+        <a href="{{ compound.chemspider_url }}.html" target="_blank"><img
             src="/static/images/Other/ChemSpider_Logo.png" style="height: 1.5em;"
             title="ChemSpider ID: {{ compound.chemspider_id }}" /><br />{{ compound.chemspider_id }}</a>
         {% endif %}
       </td>
       <td scope="col" class="col-2 text-center">
         {% if compound.ligand_id %}
-        <a href="https://www.rcsb.org/ligand/{{ compound.ligand_id}}" target="_blank"><img
+        <a href="{{ compound.pdbligand_url }}" target="_blank"><img
             src="/static/images/Other/PDBLogo.ico" style="height: 1.5em;"
             title="PDB Ligand ID: {{ compound.ligand_id }}" /><br />{{ compound.ligand_id }}</a>
         {% endif %}
       </td>
       <td scope="col" class="col-2 text-center">
         {% if compound.drugbank_id %}
-        <a href="https://www.drugbank.ca/drugs/{{ compound.drugbank_id}}" target="_blank"><img
+        <a href="{{ compound.drugbank_url }}" target="_blank"><img
             src="/static/images/Other/DrugBankLogo.ico" style="height: 1.5em;"
             title="DrugBank ID: {{ compound.drugbank_id }}" /><br />{{ compound.drugbank_id }}</a>
         {% endif %}