Merge pull request #2288 from antgonza/redbiom-per-sample

josenavas · web-flow · commit ae3dc0c3213d · 2017-09-18T07:19:01.000-07:00
redbiom now adds per sample studies to analysis
diff --git a/qiita_pet/handlers/qiita_redbiom.py b/qiita_pet/handlers/qiita_redbiom.py
@@ -7,6 +7,7 @@
 # -----------------------------------------------------------------------------
 
 from requests import ConnectionError
+from future.utils import viewitems
 from collections import defaultdict
 import redbiom.summarize
 import redbiom.search
@@ -42,35 +43,38 @@ def _redbiom_metadata_search(self, query, contexts):
                 'Not a valid search: "%s", your query is too small '
                 '(too few letters), try a longer query' % query)
         if not message:
-            sids = set([s.split('.', 1)[0] for s in samples])
-            for s in sids:
-                study_artifacts[s] = [a.id for a in Study(s).artifacts(
-                    artifact_type='BIOM')]
+            study_samples = defaultdict(list)
+            for s in samples:
+                study_samples[s.split('.', 1)[0]].append(s)
+            for sid, samps in viewitems(study_samples):
+                study_artifacts[sid] = {
+                    a.id: samps for a in Study(sid).artifacts(
+                        artifact_type='BIOM')}
 
         return message, study_artifacts
 
     def _redbiom_feature_search(self, query, contexts):
-        study_artifacts = defaultdict(list)
+        study_artifacts = defaultdict(lambda: defaultdict(list))
         query = [f for f in query.split(' ')]
         for ctx in contexts:
             for idx in redbiom.util.ids_from(query, True, 'feature', ctx):
-                aid, sid = idx.split('_', 1)
-                sid = sid.split('.', 1)[0]
-                study_artifacts[sid].append(aid)
+                aid, sample_id = idx.split('_', 1)
+                sid = sample_id.split('.', 1)[0]
+                study_artifacts[sid][aid].append(sample_id)
 
         return '', study_artifacts
 
     def _redbiom_taxon_search(self, query, contexts):
-        study_artifacts = defaultdict(list)
+        study_artifacts = defaultdict(lambda: defaultdict(list))
         for ctx in contexts:
             # find the features with those taxonomies and then search
             # those features in the samples
             features = redbiom.fetch.taxon_descendents(ctx, query)
             for idx in redbiom.util.ids_from(features, True, 'feature',
                                              ctx):
-                aid, sid = idx.split('_', 1)
-                sid = sid.split('.', 1)[0]
-                study_artifacts[sid].append(aid)
+                aid, sample_id = idx.split('_', 1)
+                sid = sample_id.split('.', 1)[0]
+                study_artifacts[sid][aid].append(sample_id)
 
         return '', study_artifacts
 
@@ -98,8 +102,8 @@ def _redbiom_search(self, query, search_on, callback):
                             study_artifacts.keys(), True)
                         # inserting the artifact_biom_ids to the results
                         for i in range(len(results)):
-                            results[i]['artifact_biom_ids'] = list(set(
-                                study_artifacts[str(results[i]['study_id'])]))
+                            results[i]['artifact_biom_ids'] = study_artifacts[
+                                str(results[i]['study_id'])]
                     else:
                         message = "No samples where found! Try again ..."
             else:
diff --git a/qiita_pet/static/js/qiita.js b/qiita_pet/static/js/qiita.js
@@ -127,25 +127,35 @@ function delete_analysis(aname, analysis_id) {
  * Note that we have a list of artifact ids cause the user can select one single
  * artifact to add or all study artifacts
  */
-function send_samples_to_analysis(button, aids) {
+function send_samples_to_analysis(button, aids, samples = null) {
   button.value = 'Adding';
   button.disabled = true;
   $(button).addClass("btn-info");
   bootstrapAlert('We are adding ' + aids.length + ' artifact(s) to the analysis. This ' +
                  'might take some time based on the number of samples on each artifact.', "warning", 10000);
-  $.get('/artifact/samples/', {ids:aids})
-    .done(function ( data ) {
-      if (data['status']=='success') {
-        qiita_websocket.send('sel', data['data']);
-        button.value = 'Added';
-        $(button).removeClass("btn-info");
-      } else {
-        bootstrapAlert('ERROR: ' + data['msg'], "danger");
-        button.value = 'There was an error, scroll up to see it';
-        button.disabled = false;
-        $(button).addClass("btn-danger");
-      }
+  if (samples === null) {
+    $.get('/artifact/samples/', {ids:aids})
+      .done(function ( data ) {
+        if (data['status']=='success') {
+          qiita_websocket.send('sel', data['data']);
+          button.value = 'Added';
+          $(button).removeClass("btn-info");
+        } else {
+          bootstrapAlert('ERROR: ' + data['msg'], "danger");
+          button.value = 'There was an error, scroll up to see it';
+          button.disabled = false;
+          $(button).addClass("btn-danger");
+        }
     });
+  } else {
+    $.each(aids, function(i, aid) {
+      var to_send = {};
+      to_send[aid] = samples.split(',');
+      qiita_websocket.send('sel', to_send);
+    });
+    button.value = 'Added';
+    $(button).removeClass("btn-info");
+  }
 }
 
 /**
@@ -366,25 +376,51 @@ function show_alert(data) {
    $('#dflt-sel-info').css('color', 'rgb(0, 160, 0)');
 }
 
-function format_biom_rows(data, row) {
+function format_biom_rows(data, row, for_study_list = true, samples = null) {
   var proc_data_table = '<table class="table" cellpadding="0" cellspacing="0" border="0" style="padding-left:0px;width:95%">';
   proc_data_table += '<tr>';
+  if (for_study_list) {
+    proc_data_table += '<th></th>';
+  }
   proc_data_table += '<th>Name</th>';
+  if (for_study_list) {
+    proc_data_table += '<th>Data type</th>';
+  }
   proc_data_table += '<th>Processing method</th>';
   proc_data_table += '<th>Parameters</th>';
+  if (for_study_list) {
+    proc_data_table += '<th>Samples in Prep Info</th>';
+  }
   proc_data_table += '<th>Files</th>';
   proc_data_table += '</tr>';
+
   $.each(data, function (idx, info) {
     if (typeof info !== 'string' && !(info instanceof String)) {
       proc_data_table += '<tr>';
+      if (for_study_list) {
+        if (samples === null) {
+          proc_data_table += '<td><input type="button" class="btn btn-sm" value="Add" onclick="send_samples_to_analysis(this, [' + info.artifact_id + '])"></td>';
+        } else {
+          proc_data_table += '<td><input type="button" class="btn btn-sm" value="Add" onclick="send_samples_to_analysis(this, [' + info.artifact_id + "], '" + samples[info.artifact_id].join(',') + "'" + ')"></td>';
+        }
+      }
       proc_data_table += '<td>' + info.name + ' (' + info.artifact_id + ' - ' + info.timestamp.split('.')[0] + ')</td>';
+
+      if (for_study_list) {
+        proc_data_table += '<td>' + info.data_type + ' (' + info.target_subfragment.join(', ') + ')</td>';
+      }
       proc_data_table += '<td>' + info.algorithm + '</td>';
+
       var params = '';
       for (var key in info.parameters) {
         params += '<i>' + key + '</i>: ' + info.parameters[key] + '<br/>';
       }
       proc_data_table += '<td><small>' + params + '</small></td>';
+      if (for_study_list) {
+        proc_data_table += '<td>' + info.prep_samples + '</td>';
+      }
       proc_data_table += '<td><small>' + info.files.join('<br/>')  + '</small></td>';
+
       proc_data_table += '</tr>';
     }
   });
diff --git a/qiita_pet/templates/artifact_ajax/artifact_summary.html b/qiita_pet/templates/artifact_ajax/artifact_summary.html
@@ -108,7 +108,7 @@ <h4>
       {% if editable %}
         <a class="btn btn-default btn-sm" data-toggle="modal" data-target="#update-artifact-name"><span class="glyphicon glyphicon-pencil"></span> Edit</a>
         {% if artifact_type == 'BIOM' %}
-          <a class="btn btn-default btn-sm" onclick="send_samples_to_analysis(this, [{{artifact_id}}]);"> Add to analysis</a>
+          <input type="button" class="btn btn-default btn-sm" value="Add to Analysis" onclick="send_samples_to_analysis(this, [{{artifact_id}}]);">
         {% else %}
           <a class="btn btn-default btn-sm" onclick="load_process_artifact_ui({{artifact_id}});"><span class="glyphicon glyphicon-play"></span> Process</a>
         {% end %}
diff --git a/qiita_pet/templates/list_analyses.html b/qiita_pet/templates/list_analyses.html
@@ -42,7 +42,7 @@
             $.get('/artifact/info/', {ids: JSON.parse(row.data()[0]), only_biom: 'False' })
               .done(function ( data ) {
                 if (data['status']=='success') {
-                  $('td', row.child()).html(format_biom_rows(data.data, row.index())).show();
+                  $('td', row.child()).html(format_biom_rows(data.data, row.index(), for_study_list=false)).show();
                 } else {
                   bootstrapAlert('ERROR: ' + data['msg'], "danger", 10000);
                 }
diff --git a/qiita_pet/templates/list_studies.html b/qiita_pet/templates/list_studies.html
@@ -54,41 +54,6 @@
   $("#search-waiting").hide();
   qiita_websocket.init(window.location.host + '{% raw qiita_config.portal_dir %}/study/list/socket/', error, error);
   qiita_websocket.add_callback('sel', show_alert);
-  function format_biom_rows(data, row) {
-    var proc_data_table = '<table class="table" cellpadding="0" cellspacing="0" border="0" style="padding-left:0px;width:95%">';
-    proc_data_table += '<tr>';
-    proc_data_table += '<th></th>';
-    proc_data_table += '<th>Name</th>';
-    proc_data_table += '<th>Data type</th>';
-    proc_data_table += '<th>Processing method</th>';
-    proc_data_table += '<th>Parameters</th>';
-    proc_data_table += '<th>Samples in Prep Info</th>';
-    proc_data_table += '<th>Files</th>';
-    proc_data_table += '</tr>';
-
-    $.each(data, function (idx, info) {
-      if (typeof info !== 'string' && !(info instanceof String)) {
-        proc_data_table += '<tr>';
-        proc_data_table += '<td><input type="button" class="btn btn-sm" value="Add" onclick="send_samples_to_analysis(this, [' + info.artifact_id + '])"></td>';
-        proc_data_table += '<td>' + info.name + ' (' + info.artifact_id + ' - ' + info.timestamp.split('.')[0] + ')</td>';
-        proc_data_table += '<td>' + info.data_type + ' (' + info.target_subfragment.join(', ') + ')</td>';
-        proc_data_table += '<td>' + info.algorithm + '</td>';
-
-        var params = '';
-        for (var key in info.parameters) {
-          params += '<i>' + key + '</i>: ' + info.parameters[key] + '<br/>';
-        }
-        proc_data_table += '<td><small>' + params + '</small></td>';
-        proc_data_table += '<td>' + info.prep_samples + '</td>';
-        proc_data_table += '<td><small>' + info.files.join('<br/>')  + '</small></td>';
-
-        proc_data_table += '</tr>';
-      }
-    });
-
-    proc_data_table += '</table>';
-    return proc_data_table;
-  }
 
   $('#user-studies-table').dataTable({
       "lengthMenu": [[5, 10, 50, -1], [5, 10, 50, "All"]],
diff --git a/qiita_pet/templates/redbiom.html b/qiita_pet/templates/redbiom.html
@@ -15,42 +15,55 @@
         // adding total features found
 
         var api = this.api(), data;
-        var total_features = api
+        var artifacts_samples = api
           .column(0)
           .data()
-          .reduce( function (a, b) {return a + b.length}, 0);
-
+          .reduce( function (a, b) {
+            var artifacts = 0, samples = 0;
+            $.each( b, function( key, value ) {
+              artifacts += 1;
+              samples += value.length;
+            });
+            return [artifacts, samples]}, [0, 0]);
+        var artifacts = artifacts_samples[0];
+        var samples = artifacts_samples[1];
         $('.footer').addClass("col-md-12 text-right");
-        if (total_features == 0) {
+        if (artifacts == 0) {
           text = '';
         } else {
-            text = 'Found ' + total_features + ' artifacts.';
+            text = 'Found ' + artifacts + ' artifacts with ' + samples + ' samples.';
         }
         $('.footer').html(text)
       },
       "columns": [
-        { "orderable": false,       "width": "15%", "data": "artifact_biom_ids"},
+        { "orderable": false,       "width": "20%", "data": "artifact_biom_ids"},
         { "data": "study_title",    "width": "70%" },
         { "data": "study_abstract", "width": "0%" },
-        { "data": "study_id",       "width": "15%" },
+        { "data": "study_id",       "width": "10%" },
         { "data": "study_alias",    "width": "0%" }],
       columnDefs: [
         // {type:'natural', targets:[2,6,7]},
         {"targets": [ 2, 4 ], "visible": false},
         // render zero
         {"render": function ( data, type, row, meta ) {
-          if (data !== null && data !== undefined && data.length != 0){
-            return '<div class="container" style="max-width: 5em;">'+
-              '<div class="row justify-content-md-center">' +
-                {% if current_user is not None %}
-                  '<div class="col-md-1 text-center details-control">&nbsp;</div>' +
-                {% end %}
-                '<div class="col-md-1 text-center">' + data.length + '</div>' +
-              '</div>' +
-            '</div>';
-          } else {
-            return 'No BIOMs';
+          if (data !== null && data !== undefined){
+            var artifacts = 0, samples = 0;
+            for (var d in data) { if (data.hasOwnProperty(d)) { artifacts++; } }
+            if (artifacts != 0) {
+              return '<div class="container" style="max-width: 15em;">'+
+                '<div class="row justify-content-md-center">' +
+                  {% if current_user is not None %}
+                    '<div class="col-md-12 text-center details-control">&nbsp;</div>' +
+                  {% end %}
+                  '<div class="col-md-12 text-center">' +
+                    'Artifacts: ' + artifacts + ' | ' +
+                    'Samples: ' + artifacts +
+                  '</div>' +
+                '</div>' +
+              '</div>';
+            }
           }
+          return 'No BIOMs';
         }, targets: [0]},
         // render the title cell
         {"render": function ( data, type, row, meta ) {
@@ -85,10 +98,14 @@
         // modified from: https://jsfiddle.net/8rejaL88/2/
         tr.addClass('shown');
         row.child('<p><center><img src="{% raw qiita_config.portal_dir %}/static/img/waiting.gif" style="display:block;margin-left: auto;margin-right: auto"/></center></p>', 'no-padding' ).show();
-        $.get('/artifact/info/', {ids: row.data().artifact_biom_ids})
+
+        var artifact_biom_ids = row.data().artifact_biom_ids;
+        var artifact_biom_ids_keys = []
+        $.each(artifact_biom_ids, function(e){ artifact_biom_ids_keys.push(e) });
+        $.get('/artifact/info/', {ids: artifact_biom_ids_keys })
           .done(function ( data ) {
             if (data['status']=='success') {
-              $('td', row.child()).html(format_biom_rows(data.data, row.index())).show();
+              $('td', row.child()).html(format_biom_rows(data.data, row.index(), true, samples=artifact_biom_ids)).show();
             } else {
               bootstrapAlert('ERROR: ' + data['msg'], "danger", 10000);
             }
diff --git a/qiita_pet/test/test_qiita_redbiom.py b/qiita_pet/test/test_qiita_redbiom.py
@@ -27,7 +27,11 @@ def test_post_metadata(self):
         response = self.post('/redbiom/', post_args)
         self.assertEqual(response.code, 200)
         data = DATA
-        data[0]['artifact_biom_ids'] = [4, 5, 6, 7]
+        samples = ['1.SKD6.640190', '1.SKD9.640182', '1.SKD8.640184',
+                   '1.SKD5.640186', '1.SKD2.640178', '1.SKD4.640185',
+                   '1.SKD1.640179', '1.SKD3.640198', '1.SKD7.640191']
+        data[0]['artifact_biom_ids'] = {
+            '5': samples, '4': samples, '7': samples, '6': samples}
         exp = {'status': 'success', 'message': '', 'data': data}
         self.assertEqual(loads(response.body), exp)
 
@@ -59,7 +63,8 @@ def test_post_features(self):
         }
         response = self.post('/redbiom/', post_args)
         data = DATA
-        data[0]['artifact_biom_ids'] = ['5', '4']
+        data[0]['artifact_biom_ids'] = {
+            '5': ['1.SKM3.640197'], '4': ['1.SKM3.640197']}
         exp = {'status': 'success', 'message': '', 'data': data}
         self.assertEqual(response.code, 200)
         self.assertEqual(loads(response.body), exp)
@@ -80,7 +85,8 @@ def test_post_taxon(self):
             'search_on': 'taxon'
         }
         data = DATA
-        data[0]['artifact_biom_ids'] = ['5', '4']
+        data[0]['artifact_biom_ids'] = {
+            '5': ['1.SKM3.640197'], '4': ['1.SKM3.640197']}
         response = self.post('/redbiom/', post_args)
         exp = {'status': 'success', 'message': '', 'data': data}
         self.assertEqual(response.code, 200)

Original file line number	Diff line number	Diff line change
`@@ -42,7 +42,7 @@`
`42`	`42`	`$.get('/artifact/info/', {ids: JSON.parse(row.data()[0]), only_biom: 'False' })`
`43`	`43`	`.done(function ( data ) {`
`44`	`44`	`if (data['status']=='success') {`
`45`		`- $('td', row.child()).html(format_biom_rows(data.data, row.index())).show();`
	`45`	`+ $('td', row.child()).html(format_biom_rows(data.data, row.index(), for_study_list=false)).show();`
`46`	`46`	`} else {`
`47`	`47`	`bootstrapAlert('ERROR: ' + data['msg'], "danger", 10000);`
`48`	`48`	`}`