Added aliases in a few places, though they generate a few to many que…

…ries for my liking due to the lazy=dynamic relation between sequences and xrefs
proost · Dec 23, 2015 · e872b90 · e872b90
1 parent 0085000
commit e872b90
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Showing 3 changed files with 6 additions and 3 deletions.
diff --git a/planet/controllers/expression_cluster.py b/planet/controllers/expression_cluster.py
@@ -1,7 +1,7 @@
 from flask import Blueprint, url_for, render_template, flash, redirect, g, Response
 
 from planet.models.coexpression_clusters import CoexpressionCluster, CoexpressionClusteringMethod
-from planet.models.relationships import CoexpressionClusterSimilarity
+from planet.models.relationships import CoexpressionClusterSimilarity, SequenceCoexpressionClusterAssociation
 from planet.helpers.cytoscape import CytoscapeHelper
 
 from planet.models.sequences import Sequence
@@ -56,7 +56,7 @@ def expression_cluster_sequences(cluster_id, page=1):
     :param page: page number
     """
     cluster = CoexpressionCluster.query.get_or_404(cluster_id)
-    sequence_associations = cluster.sequence_associations.order_by('probe').paginate(page, g.page_items, False).items
+    sequence_associations = cluster.sequence_associations.order_by(SequenceCoexpressionClusterAssociation.probe).paginate(page, g.page_items, False).items
 
     return render_template('pagination/cluster_probes.html', sequence_associations=sequence_associations,
                            species_id=cluster.method.network_method.species.id)
@@ -71,7 +71,7 @@ def expression_cluster_download(cluster_id):
     :param page: page number
     """
     cluster = CoexpressionCluster.query.get_or_404(cluster_id)
-    sequence_associations = cluster.sequence_associations.order_by('probe')
+    sequence_associations = cluster.sequence_associations.order_by(SequenceCoexpressionClusterAssociation.probe)
 
     output = ["probe\tsequence\tdescription"]
 

diff --git a/planet/templates/pagination/cluster_probes.html b/planet/templates/pagination/cluster_probes.html
@@ -6,8 +6,10 @@
                     <td><a href="{{ url_for('expression_profile.expression_profile_find', probe=sequence_association.probe, species_id=species_id) }}">{{ sequence_association.probe }}</a></td>
                     {% if sequence_association.sequence %}
                     <td><a href="{{ url_for('sequence.sequence_view', sequence_id=sequence_association.sequence.id) }}">{{ sequence_association.sequence.name }}</a></td>
+                    <td>{% if sequence_association.sequence.aliases %}{{ sequence_association.sequence.aliases }}{% else %}<span class="text-muted">No alias</span>{% endif %}</td>
                     {% else %}
                     <td><em class="text-muted">No sequence associated with this probe</em></td>
+                    <td><span class="text-muted">No alias</span></td>
                     {% endif %}
                     <td>{% if sequence_association.sequence.description %}{{ sequence_association.sequence.description|truncate(60) }}{% else %}<em class="text-muted">No description available</em>{% endif %}</td>
                 </tr>

diff --git a/planet/templates/pagination/sequences.html b/planet/templates/pagination/sequences.html
@@ -4,6 +4,7 @@
             {% for sequence in sequences %}
                 <tr>
                     <td><a href="{{ url_for('sequence.sequence_view', sequence_id=sequence.id) }}">{{ sequence.name }}</a></td>
+                    <td>{% if sequence.aliases %}{{ sequence.aliases }}{% else %}<span class="text-muted">No alias</span>{% endif %}</td>
                     <td><a href="{{ url_for('species.species_view', species_id=sequence.species_id) }}"><em>{{ sequence.species.name }}</em></a></td>
                     <td>{% if sequence.description %}{{ sequence.description|truncate(60) }}{% else %}<span class="text-muted">No description available</span>{% endif %}</td>
                     <td>{{ sequence.type }}</td>