From 5b1c7218fe63a5eee5d561ecaa20a17d94d91835 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Herv=C3=A9=20M=C3=A9nager?= <herve.menager@pasteur.fr>
Date: Fri, 2 Oct 2020 15:41:47 +0200
Subject: [PATCH] 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 | 35 +++++++++++++++++++
ippisite/ippidb/templates/compound_card.html | 18 +++++++++-
.../ippidb/templates/compound_db_links.html | 10 +++---
3 files changed, 57 insertions(+), 6 deletions(-)
diff --git a/ippisite/ippidb/models.py b/ippisite/ippidb/models.py
index 3bb8468c..6e7b2877 100644
--- a/ippisite/ippidb/models.py
+++ b/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:
diff --git a/ippisite/ippidb/templates/compound_card.html b/ippisite/ippidb/templates/compound_card.html
index 680c2290..c8a3924b 100644
--- a/ippisite/ippidb/templates/compound_card.html
+++ b/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"
}
diff --git a/ippisite/ippidb/templates/compound_db_links.html b/ippisite/ippidb/templates/compound_db_links.html
index 5a0235a9..b823487e 100644
--- a/ippisite/ippidb/templates/compound_db_links.html
+++ b/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 %}
--
GitLab