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authorAlexander_Kabui2024-01-08 11:22:48 +0300
committerAlexander_Kabui2024-01-08 11:22:48 +0300
commit461d573d52c1c789304ea7b2e4e2d40885bdf72d (patch)
tree6e9952a3c7e4e7a1e3d97af15513fee198553808 /gn2
parent3e8831c0e47975b618a2fb1476e9c4179187474e (diff)
parent2855a7ae9c01a7203d411e6cd96f61677f3c6bc3 (diff)
downloadgenenetwork2-461d573d52c1c789304ea7b2e4e2d40885bdf72d.tar.gz
merge testing
Diffstat (limited to 'gn2')
-rw-r--r--gn2/wqflask/templates/probeset.html114
-rw-r--r--gn2/wqflask/views.py14
2 files changed, 128 insertions, 0 deletions
diff --git a/gn2/wqflask/templates/probeset.html b/gn2/wqflask/templates/probeset.html
new file mode 100644
index 00000000..53d7136e
--- /dev/null
+++ b/gn2/wqflask/templates/probeset.html
@@ -0,0 +1,114 @@
+{% extends "base.html" %}
+
+{% block css %}
+<style type="text/css">
+ .page-header {
+ text-underline-offset: 0.5rem;
+ padding: 1em;
+ }
+</style>
+{% endblock %}
+
+{% block title %}
+mRNA Expression:
+{{ metadata.name or name }}
+{% endblock %}
+
+{% block content %}
+
+
+<div class="container">
+ <h2>
+ mRNA Expression:
+ {{ metadata.name or name }}
+ </h2>
+ {% if metadata.description %}
+ <h3>{{ metadata.description }}</h3>
+ {% endif %}
+ <table class="table">
+ {% if metadata.dataset %}
+ <tr>
+ <td><b>Group </b></td>
+ <td>
+ <a href="{{ metadata.group }}" target="_blank">{{ metadata.dataset }}</a>
+ </td>
+ </tr>
+ <tr>
+ <td><b>Dataset </b></td>
+ <td>
+ <a href="{{ metadata.group }}" target="_blank">{{ metadata.datasetName }}</a>
+ </td>
+ </tr>
+ <tr>
+ <td><b>Tissue</b></td>
+ <td>{{ metadata.tissue}}</td>
+ </tr>
+ {% endif %}
+
+ {% if metadata.symbol %}
+ <tr>
+ <td><b>Gene Symbol</b></td>
+ <td>
+ {% if metadata.symbol.__class__.__name__ == 'list' %}
+ {% for symbol in metadata.symbol %}
+ {{ symbol.symbol }};
+ {% endfor %}
+ {% else %}
+ {{ metadata.symbol }}
+ {% endif %}
+ </td>
+ </tr>
+ {% endif %}
+
+ {% if metadata.alias %}
+ <td><b>Aliases</b></td>
+ <!-- XXX TODO: How do you fetch the Wikidata Alias for a given genesymbol? -->
+ <td>GeneneNetwork: {{ metadata.alias }}</td>
+ {% endif %}
+
+ {% if metadata.location %}
+ <tr>
+ <td><b>Location</b></td>
+ <td> {{ metadata.location }}</td>
+ </tr>
+ {% endif %}
+
+ {% if metadata.blatSeq %}
+ <tr>
+ <td><b>BLAT Sequence</b></td>
+ <td style="inline-size: fit-content; writing-mode: horizontal-tb; overflow-wrap: break-word; max-width: 70vw;">
+ {{ metadata.blatSeq }}
+ </td>
+ </tr>
+ {% endif %}
+
+ {% if metadata.specificity or metadata.blatScore %}
+ <tr>
+ <td><b>Target Score</b></td>
+ <td>
+ {% if metadata.specificity %}
+ <a href="http://gn1.genenetwork.org/blatInfo.html" target="_blank">BLAT Specificity</a>: {{ metadata.specificity }}
+ {% endif %}
+
+ {% if metadata.blatScore %}
+ &emsp;Score: {{ metadata.blatScore }}
+ {% endif %}
+ </td>
+ </tr>
+ {% endif %}
+
+ {% if metadata.references %}
+ <tr>
+ <td><b>Resource Links</b></td>
+ <td>
+ {% for reference in metadata.references %}
+ <a href="{{ reference.id }}" target="_blank" title="{{ reference.comments }}">{{ reference.name }}</a>&emsp;
+ {% endfor %}
+ </td>
+
+ </tr>
+ {% endif %}
+ </table>
+</div>
+
+{% endblock %}
diff --git a/gn2/wqflask/views.py b/gn2/wqflask/views.py
index d73438c2..3b324719 100644
--- a/gn2/wqflask/views.py
+++ b/gn2/wqflask/views.py
@@ -1181,6 +1181,20 @@ def get_phenotype(name, group=None):
)
+@app.route("/probesets/<name>", methods=('GET',))
+def get_probeset(name):
+ metadata = requests.get(
+ urljoin(
+ GN3_LOCAL_URL,
+ f"/api/metadata/probesets/{name}")
+ ).json()
+ return render_template(
+ "probeset.html",
+ name=name,
+ metadata=metadata,
+ )
+
+
@app.route("/genotypes/<name>", methods=('GET',))
def get_genotype(name):
metadata = requests.get(