generate_analysis_list_per_study to speed up retrival

qiita_db/util.py

@@ -1976,6 +1976,48 @@ def generate_analysis_list(analysis_ids, public_only=False):
     return results
 
 
+def generate_analysis_list_per_study(study_id):
+    """Get study analyses and their preparations
+
+    Parameters
+    ----------
+    study_id : int
+        The study id
+
+    Returns
+    -------
+    list of dict
+        The available analyses and their general information
+    """
+    sql = """
+        SELECT analysis_id, qiita.analysis.name, email, dflt,
+               array_agg(DISTINCT aa.artifact_id) FILTER (
+                    WHERE aa.artifact_id IS NOT NULL) as artifact_ids,
+               array_agg(DISTINCT prep_template_id) as prep_ids,
+               array_agg(DISTINCT visibility) as visibility
+        FROM qiita.analysis_sample analysiss
+        LEFT JOIN qiita.analysis_artifact aa USING (analysis_id)
+        LEFT JOIN qiita.analysis USING (analysis_id)
+        LEFT JOIN qiita.preparation_artifact pa ON (
+            analysiss.artifact_id = pa.artifact_id)
+        LEFT JOIN qiita.artifact a ON (
+            analysiss.artifact_id = a.artifact_id)
+        LEFT JOIN qiita.visibility USING (visibility_id)
+        WHERE sample_id IN (SELECT sample_id
+                            FROM qiita.study_sample
+                            WHERE study_id = %s)
+        GROUP BY analysis_id, qiita.analysis.name, email, dflt
+        ORDER BY analysis_id
+    """
+    results = []
+    with qdb.sql_connection.TRN:
+        qdb.sql_connection.TRN.add(sql, [study_id])
+        for row in qdb.sql_connection.TRN.execute_fetchindex():
+            results.append(dict(row))
+
+    return results
+
+
 def create_nested_path(path):
     """Wraps makedirs() to make it safe to use across multiple concurrent calls.
     Returns successfully if the path was created, or if it already exists.

qiita_pet/handlers/api_proxy/sample_template.py

@@ -10,8 +10,7 @@
 
 from qiita_core.util import execute_as_transaction
 from qiita_core.qiita_settings import r_client
-from qiita_db.study import Study
-from qiita_db.artifact import Artifact
+from qiita_db.util import generate_analysis_list_per_study
 from qiita_db.metadata_template.sample_template import SampleTemplate
 from qiita_db.exceptions import QiitaDBUnknownIDError
 from qiita_db.exceptions import QiitaDBColumnError
@@ -207,10 +206,7 @@ def study_available_analyses(study_id, user_id):
     if access_error:
         return access_error
 
-    values = [(a, sorted(set([Artifact(x).prep_templates[0].id
-                              for x in a.samples.keys()
-                              if Artifact(x).study.id == study_id])))
-              for a in Study(study_id).analyses()]
+    values = generate_analysis_list_per_study(study_id)
 
     return {'status': 'success',
             'message': '',

qiita_pet/handlers/api_proxy/tests/test_sample_template.py

@@ -132,13 +132,19 @@ def test_study_available_analyses(self):
         exp = {'status': 'success', 'message': '', 'values': []}
         self.assertEqual(obs, exp)
 
-        AN = qdb.analysis.Analysis
         obs = study_available_analyses(1, 'test@foo.bar')
         exp = {'status': 'success', 'message': '', 'values': [
-            (AN(1), [1]), (AN(2), [1]), (AN(3), [1])]}
+            {'analysis_id': 1, 'name': 'SomeAnalysis', 'email': 'test@foo.bar',
+             'dflt': False, 'artifact_ids': [8, 9], 'prep_ids': [1],
+             'visibility': ['private']},
+            {'analysis_id': 2, 'name': 'SomeSecondAnalysis',
+             'email': 'admin@foo.bar', 'dflt': False, 'artifact_ids': None,
+             'prep_ids': [1], 'visibility': ['private']},
+            {'analysis_id': 3, 'name': 'test@foo.bar-dflt-1',
+             'email': 'test@foo.bar', 'dflt': True, 'artifact_ids': None,
+             'prep_ids': [1], 'visibility': ['private']}]}
         self.assertEqual(obs, exp)
 
-        AN = qdb.analysis.Analysis
         obs = study_available_analyses(self.new_study.id, 'shared@foo.bar')
         exp = {'status': 'error',
                'message': 'User does not have access to study'}

qiita_pet/templates/study_ajax/study_analyses.html

@@ -5,24 +5,39 @@
   $('#studies-analyses-table').dataTable();
 </script>
 <h3>Analyses that have used this study</h3>
+
+Note that if an analysis doesn't have a link, it means that is a "User default analysis"; which means that the analysis belows to that user but the user has only selected artifacts but hasn't created the actual anlaysis. Please contact the user and ask them to delete that artifact from their analysis creation page.
+<br/><br/>
 <table id="studies-analyses-table" class="display table-bordered table-hover" style="width:100%">
   <thead>
     <tr>
       <th>Analysis</th>
       <th>Owner</th>
       <th>Prep IDs Used</th>
       <th>Is Public?</th>
-      <th>Artifacts</th>
+      <th>Artifacts in Analysis</th>
     </tr>
   </thead>
   <tbody>
-    {% for a, preps in analyses %}
+    {% for a in analyses %}
       <tr>
-        <td><a href="{% raw qiita_config.portal_dir %}/analysis/description/{{a.id}}/" target="_blank">{{a.name}} (ID: {{a.id}})</a></td>
-        <td>{{a.owner.email}}</td>
-        <td>{{','.join(map(str, preps))}}</td>
-        <td>{{a.is_public}}</td>
-        <td>{{len(a.artifacts)}}</td>
+        <td>
+          {% if a['dflt'] %}
+            {{a['name']}} (ID: {{a['analysis_id']}})
+          {% else %}
+            <a href="{% raw qiita_config.portal_dir %}/analysis/description/{{a['analysis_id']}}/" target="_blank">{{a['name']}} (ID: {{a['analysis_id']}})</a>
+          {% end %}
+        </td>
+        <td>{{a['email']}}</td>
+        <td>{{','.join(map(str, a['prep_ids']))}}</td>
+        <td>{{a['visibility'] == ['public']}}</td>
+        <td>
+          {% if a['artifact_ids'] is None %}
+            0
+          {% else %}
+            {{len(a['artifact_ids'])}}
+          {% end %}
+        </td>
       </tr>
     {% end %}
   </tbody>