From bd7bdf71037aa006c365ed804f578a6ed9a872ba Mon Sep 17 00:00:00 2001
From: sepro <sebastian.proost@gmail.com>
Date: Thu, 26 Oct 2017 17:09:07 +0200
Subject: [PATCH] added count for enriched clusters alternative to precog as
 this query was too slow.

---
 planet/controllers/search.py                 | 37 ++++++++++++
 planet/models/search.py                      | 29 ++++++++++
 planet/templates/find_enriched_clusters.html | 60 +++++++++++++++++---
 3 files changed, 117 insertions(+), 9 deletions(-)

diff --git a/planet/controllers/search.py b/planet/controllers/search.py
index d4e73f3..5756c27 100644
--- a/planet/controllers/search.py
+++ b/planet/controllers/search.py
@@ -167,6 +167,43 @@ def search_json_genes(label=''):
     return Response(json.dumps(list(set(output))), mimetype='application/json')
 
 
+@search.route('/enriched/count', methods=['POST'])
+def count_enriched_clusters():
+    """
+    Counts the number of clusters enriched for a set of criteria
+
+    :return: json response with the count
+    """
+
+    content = request.get_json(silent=True)
+
+    try:
+        term = content["go_term"]
+        method = int(content["method"])
+
+        check_enrichment = bool(content["check_enrichment"])
+        check_p = bool(content["check_p"])
+        check_corrected_p = bool(content["check_corrected_p"])
+
+        min_enrichment = float(content["min_enrichment"]) if check_enrichment else None
+        max_p = float(content["max_p"]) if check_p else None
+        max_corrected_p = float(content["max_corrected_p"]) if check_corrected_p else None
+
+        go = GO.query.filter(or_(GO.name == term,
+                                 GO.label == term)).first()
+
+        cluster_count = Search.count_enriched_clusters(go.id,
+                                                       method=method,
+                                                       min_enrichment=min_enrichment,
+                                                       max_p=max_p,
+                                                       max_corrected_p=max_corrected_p)
+
+        return Response(json.dumps({'count': cluster_count, 'error': 0}), mimetype='application/json')
+    except Exception as e:
+        # Bad data return zero
+        return Response(json.dumps({'count': 0, 'error': 1}), mimetype='application/json')
+
+
 @search.route('/enriched/clusters', methods=['GET', 'POST'])
 def search_enriched_clusters():
     """
diff --git a/planet/models/search.py b/planet/models/search.py
index 020c66d..8efa8e5 100644
--- a/planet/models/search.py
+++ b/planet/models/search.py
@@ -191,6 +191,35 @@ def advanced_sequence_search(species_id, gene_list, terms, term_rules, gene_fami
 
         return sequences
 
+    @staticmethod
+    def count_enriched_clusters(go_id, method=-1, min_enrichment=None, max_p=None, max_corrected_p=None):
+        """
+        Function to get enriched clusters for a specific GO term
+
+
+        :param go_id: Internal GO id
+        :param method: Internal ID of the clustering method (ignored if -1)
+        :param min_enrichment: minimal (log2) enrichment score (ignored if None)
+        :param max_p: maximum (uncorrected) p-value (ignored if None)
+        :param max_corrected_p: maximum corrected p-value (ignored if None)
+        :return: all clusters with the desired properties (ignored if None)
+        """
+        clusters = ClusterGOEnrichment.query.filter(ClusterGOEnrichment.go_id == go_id)\
+
+        if method != -1:
+            clusters = clusters.filter(ClusterGOEnrichment.cluster.has(method_id=method))
+
+        if min_enrichment is not None:
+            clusters = clusters.filter(ClusterGOEnrichment.enrichment >= min_enrichment)
+
+        if max_p is not None:
+            clusters = clusters.filter(ClusterGOEnrichment.p_value <= max_p)
+
+        if max_corrected_p is not None:
+            clusters = clusters.filter(ClusterGOEnrichment.corrected_p_value <= max_corrected_p)
+
+        return clusters.count()
+
     @staticmethod
     def enriched_clusters(go_id, method=-1, min_enrichment=None, max_p=None, max_corrected_p=None):
         """
diff --git a/planet/templates/find_enriched_clusters.html b/planet/templates/find_enriched_clusters.html
index f4b6162..f63dd24 100644
--- a/planet/templates/find_enriched_clusters.html
+++ b/planet/templates/find_enriched_clusters.html
@@ -77,26 +77,27 @@ <h1>Enriched Clusters</h1>
                         <form method="POST"  action="{{ url_for('search.search_enriched_clusters') }}"  role="form">
                             {{ form.csrf_token }}
                             <label><abbr title="Click to show help" href="{{ url_for('help.help_topic', topic='go') }}" data-target="#helpModal">GO</abbr></label>
-                            {{form.go_term(class_="form-control typeahead") }}<br />
+                            {{form.go_term(class_="form-control typeahead update_count") }}<br />
                             <label>Cluster Method</label>
-                            {{form.method(class_="form-control") }}<br />
+                            {{form.method(class_="form-control update_count") }}<br />
                             <div class="checkbox-group">
-                            <label>{{form.check_enrichment(checked=False) }} <span class="title">Enrichment</span> </label><br />
-                            {{form.min_enrichment(class_="form-control") }}<br />
+                            <label>{{form.check_enrichment(checked=False, class_="update_count") }} <span class="title">Enrichment</span> </label><br />
+                            {{form.min_enrichment(class_="form-control update_count") }}<br />
                             </div>
                             <div class="checkbox-group">
-                            <label>{{form.check_p(checked=False) }} <span class="title">p-value</span></label><br />
-                            {{form.max_p(class_="form-control") }}<br />
+                            <label>{{form.check_p(checked=False, class_="update_count") }} <span class="title">p-value</span></label><br />
+                            {{form.max_p(class_="form-control update_count") }}<br />
                             </div>
                             <div class="checkbox-group">
-                            <label>{{form.check_corrected_p(checked=True) }} <span class="title"><abbr title="Click to show help" href="{{ url_for('help.help_topic', topic='fdr') }}" data-target="#helpModal">corrected p-value</abbr></span></label><br />
-                            {{form.max_corrected_p(class_="form-control") }}<br />
+                            <label>{{form.check_corrected_p(checked=True, class_="update_count") }} <span class="title"><abbr title="Click to show help" href="{{ url_for('help.help_topic', topic='fdr') }}" data-target="#helpModal">corrected p-value</abbr></span></label><br />
+                            {{form.max_corrected_p(class_="form-control update_count") }}<br />
                             </div>
                             <div class="pull-right">
                             {% if example and example.go_term %}
                                 <button class="btn btn-default" id="load_example">Load example</button>
                             {% endif %}
-                                <button type="submit" class="btn btn-primary" data-toggle="modal" data-target="#loaderModal">Find clusters</button>
+                                <button class="btn btn-default" id="count_button">Count</button>
+                                <button type="submit" class="btn btn-primary" data-toggle="modal" data-target="#loaderModal" >Show clusters</button>
                             </div>
                         </form>
                     </div>
@@ -111,6 +112,8 @@ <h1>Enriched Clusters</h1>
                             <li>Select the <strong>clusters</strong> to search</li>
                             <li>Set the parameters. Checkboxes enable/disable certain filters. (Recommended: enable corrected p-value and keep this below 0.05)</li>
                             <li>Click <strong>Find clusters</strong></li>
+                            <br />
+                            <li>Using the <strong>Count</strong> button you can check how many clusters meet the current criteria.</li>
                         </ul>
                     </div>
                 </div>
@@ -123,6 +126,45 @@ <h1>Enriched Clusters</h1>
 {% block extrajs %}
 <script src="{{ url_for('static', filename='js/typeahead.bundle.min.js') }}"></script>
 <script src="{{ url_for('static', filename='js/table2CSV.js') }}" > </script>
+{% if form %}
+<script>
+    $(function() {
+        function update_count() {
+            post_data = {
+                        'method': $('#method').val(),
+                        'go_term': $('#go_term').val(),
+                        'condition': $('#conditions').val(),
+
+                        'check_enrichment':  $('#check_enrichment').is(":checked"),
+                        'check_p': $('#check_p').is(":checked"),
+                        'check_corrected_p': $('#check_corrected_p').is(":checked"),
+
+                        'min_enrichment':  $('#min_enrichment').val(),
+                        'max_p': $('#max_p').val(),
+                        'max_corrected_p': $('#max_corrected_p').val()
+                    }
+            console.log(post_data);
+            $.ajax({
+                type: "POST",
+                url: "{{ url_for('search.count_enriched_clusters') }}",
+                contentType: 'application/json;charset=UTF-8',
+                data : JSON.stringify(post_data, null, '\t'),
+                success: function(data) {
+                    $('#count_button').text('Count (' + data.count + ')');
+                }
+            });
+        }
+
+        $("#count_button").click(function( ev) {
+            ev.preventDefault();
+            update_count();
+        });
+
+    });
+</script>
+
+
+{% endif %}
 <script>
 $(function () {
     $('[data-toggle="tooltip"]').tooltip();