From eb294593fd3ccf8f498d38ec709a3fe34b8e27d9 Mon Sep 17 00:00:00 2001
From: Antonio Gonzalez <antgonza@gmail.com>
Date: Tue, 22 Feb 2022 12:28:03 -0700
Subject: [PATCH 1/5] adding how to select metadata for analysis via GUI

---
 qiita_db/analysis.py                          |  4 +-
 .../analysis_handlers/base_handlers.py        |  4 +-
 .../analysis_handlers/listing_handlers.py     | 16 ++-
 qiita_pet/templates/analysis_selected.html    | 99 ++++++++++++++++++-
 qiita_ware/private_plugin.py                  |  4 +-
 5 files changed, 120 insertions(+), 7 deletions(-)

diff --git a/qiita_db/analysis.py b/qiita_db/analysis.py
index 2d465b182..477b43684 100644
--- a/qiita_db/analysis.py
+++ b/qiita_db/analysis.py
@@ -111,7 +111,7 @@ def get_by_status(cls, status):
 
     @classmethod
     def create(cls, owner, name, description, from_default=False,
-               merge_duplicated_sample_ids=False):
+               merge_duplicated_sample_ids=False, categories=None):
         """Creates a new analysis on the database
 
         Parameters
@@ -129,6 +129,8 @@ def create(cls, owner, name, description, from_default=False,
             If the duplicated sample ids in the selected studies should be
             merged or prepended with the artifact ids. False (default) prepends
             the artifact id
+        categories : set of str, optional
+            If not None, use _only_ these categories for the metaanalysis
 
         Returns
         -------
diff --git a/qiita_pet/handlers/analysis_handlers/base_handlers.py b/qiita_pet/handlers/analysis_handlers/base_handlers.py
index 552d9d0de..8000d3884 100644
--- a/qiita_pet/handlers/analysis_handlers/base_handlers.py
+++ b/qiita_pet/handlers/analysis_handlers/base_handlers.py
@@ -26,11 +26,13 @@ def post(self):
         name = self.get_argument('name')
         desc = self.get_argument('description')
         mdsi = self.get_argument('merge_duplicated_sample_ids', False)
+        metadata = self.request.arguments.get('analysis-metadata', None)
+
         if mdsi in (b'on', 'on'):
             mdsi = True
         analysis = Analysis.create(
             self.current_user, name, desc, merge_duplicated_sample_ids=mdsi,
-            from_default=True)
+            from_default=True, categories=metadata)
 
         self.redirect(u"%s/analysis/description/%s/"
                       % (qiita_config.portal_dir, analysis.id))
diff --git a/qiita_pet/handlers/analysis_handlers/listing_handlers.py b/qiita_pet/handlers/analysis_handlers/listing_handlers.py
index c92b3af0c..e2d509136 100644
--- a/qiita_pet/handlers/analysis_handlers/listing_handlers.py
+++ b/qiita_pet/handlers/analysis_handlers/listing_handlers.py
@@ -106,8 +106,8 @@ def get(self):
         # Format sel_data to get study IDs for the processed data
         sel_data = defaultdict(dict)
         proc_data_info = {}
-        sel_samps = self.current_user.default_analysis.samples
-        for aid, samples in sel_samps.items():
+        analysis = self.current_user.default_analysis
+        for aid, samples in analysis.samples.items():
             artifact = Artifact(aid)
             sel_data[artifact.study][aid] = samples
             proc_data_info[aid] = {
@@ -116,5 +116,15 @@ def get(self):
                 'data_type': artifact.data_type
             }
 
+        # finding common metadata fields
+        metadata = analysis.metadata_categories
+        common = []
+        for i, (_, m) in enumerate(metadata.items()):
+            if i == 0:
+                common = {'sample': set(m['sample']), 'prep': set(m['prep'])}
+            else:
+                common['sample'] = common['sample'] & set(m['sample'])
+                common['prep'] = common['prep'] & set(m['prep'])
+
         self.render("analysis_selected.html", sel_data=sel_data,
-                    proc_info=proc_data_info)
+                    proc_info=proc_data_info, metadata=metadata, common=common)
diff --git a/qiita_pet/templates/analysis_selected.html b/qiita_pet/templates/analysis_selected.html
index d6910a97b..0e3e790ef 100644
--- a/qiita_pet/templates/analysis_selected.html
+++ b/qiita_pet/templates/analysis_selected.html
@@ -62,10 +62,84 @@
       qiita_websocket.add_callback('clear', clear_from_html);
       $('#clear-button').on('click', clear);
       {% if sel_data %}$('#no-selected').hide(){% end %}
+
+      var common_sample_fields = {% raw list(common['sample']) %};
+      var common_prep_fields = {% raw list(common['prep']) %};
+
+      $.each($(".chosen-select"), function (_, element){
+        var is_sample = element.id.startsWith('sample-metadata');
+        $.each(element.options, function (_, option){
+          if (is_sample) {
+            if (jQuery.inArray(option.text, common_sample_fields) >= 0) {
+              option.selected=true;
+              $('#analysis-metadata').append(
+                $('<option>', { value: option.value, text: option.text,
+                                selected: true}));
+            }
+          } else {
+            if (jQuery.inArray(option.text, common_prep_fields) >= 0) {
+              option.selected=true;
+              $('#analysis-metadata').append(
+                $('<option>', { value: option.value, text: option.text,
+                                selected: true}));
+            }
+          }
+        });
+      });
+
+      $('#analysis-metadata').chosen({
+        width: "95%"
+      });
+
+      $(".chosen-select").chosen({
+        width: "95%",
+        no_results_text: "Oops, nothing found!",
+        display_disabled_options: false,
+        display_selected_options: false,
+      }).change(function(event, object) {
+        var item = $(this).attr('id');
+        var key = Object.keys(object)[0];
+        var toggle = key == 'selected';
+        var selection = object[key];
+
+        if (toggle) {
+          $('#analysis-metadata').append(
+            $('<option>', { value: selection, text: selection,
+                            selected: true}));
+        } else {
+          $(".analysis-metadata option[value='" + selection + "']").remove();
+        }
+        // we need to update the chosen element AKA this line is needed for
+        // things to work fine
+        $("#analysis-metadata").trigger("chosen:updated");
+
+        if (jQuery.inArray(object[key], common_sample_fields) >= 0) {
+          $.each($(".chosen-select"), function (_, element){
+            if (item != element.id) {
+              $.each(element.options, function (_, option){
+                if (option.text == selection) {
+                  option.selected=toggle;
+                }
+              });
+            }
+          });
+        } else if (jQuery.inArray(object[key], common_sample_fields) >= 0) {
+          $.each($(".chosen-select"), function (_, element){
+            if (item != element.id) {
+              $.each(element.options, function (_, option){
+                if (option.text == selection) {
+                  option.selected=toggle;
+                }
+              });
+            }
+          });
+        }
+      });
     });
 </script>
 {% end %}
 
+
 {% block content %}
 <h1>Selected Samples</h1>
 <span id="ws-error" style="color:red"></span>
@@ -139,6 +213,25 @@ <h4 class="modal-title" id="myModalLabel">Processed Data {{pid}}</h4>
   {% end %}
   {% end %}
   </table>
+  <hr>
+  <h4>Metadata Selection <small>Common fields for all studies are preselected</small></h4>
+  <table border="0" style="width: 100%;">
+    <tr>
+      <td style="width: 50%;">
+        <select data-placeholder="Choose Sample Metadata..." multiple class="chosen-select" id="sample-metadata-{{study.id}}">
+          {% for field in metadata[study.id]['sample'] %}
+             <option value="{{field}}">{{field}}</option>
+          {% end %}
+        </select>
+      </td>
+      <td style="width: 50%;">
+        <select data-placeholder="Choose Preparation Metadata..." multiple class="chosen-select" id="prep-metadata-{{study.id}}">
+          {% for field in metadata[study.id]['prep'] %}
+            <option value="{{field}}">{{field}}</option>
+          {% end %}
+      </td>
+    </tr>
+  </table>
   </div>
 </div>
 {% end %}
@@ -167,10 +260,14 @@ <h4 class="modal-title" id="myModalLabel">Create new analysis</h4>
                   <label for="description">Merge samples with the same name <br/><small>useful when merging multiple preparation artifacts</small></label>
                   <input type="checkbox" class="form-control" id="merge_duplicated_sample_ids" name="merge_duplicated_sample_ids">
                 </div>
+                <div class="form-group">
+                  <label for="description">Metadata selected <small>(to update use the main page)</small></label>
+                  <select name="analysis-metadata" id="analysis-metadata" class="analysis-metadata" multiple disabled></select>
+                </div>
               </div>
             </div>
             <div class="modal-footer">
-              <button type="submit" class="btn btn-primary">Create analysis</button>
+              <button type="submit" onclick="$('#analysis-metadata').removeAttr('disabled');" "class="btn btn-primary">Create analysis</button>
             </div>
           </form>
         </div>
diff --git a/qiita_ware/private_plugin.py b/qiita_ware/private_plugin.py
index af7699499..f050499a1 100644
--- a/qiita_ware/private_plugin.py
+++ b/qiita_ware/private_plugin.py
@@ -34,9 +34,11 @@ def build_analysis_files(job):
     with qdb.sql_connection.TRN:
         params = job.parameters.values
         analysis_id = params['analysis']
+        categories = params['categories']
         merge_duplicated_sample_ids = params['merge_dup_sample_ids']
         analysis = qdb.analysis.Analysis(analysis_id)
-        biom_files = analysis.build_files(merge_duplicated_sample_ids)
+        biom_files = analysis.build_files(
+            merge_duplicated_sample_ids, categories=categories)
 
         cmd = qdb.software.Command.get_validator('BIOM')
         val_jobs = []

From cc98772eadcb34ef22029db57cd21022bb541708 Mon Sep 17 00:00:00 2001
From: Antonio Gonzalez <antgonza@gmail.com>
Date: Tue, 22 Feb 2022 15:26:45 -0700
Subject: [PATCH 2/5] adding sql file

---
 qiita_db/analysis.py                  |  3 ++-
 qiita_db/support_files/patches/85.sql | 12 ++++++++++++
 2 files changed, 14 insertions(+), 1 deletion(-)
 create mode 100644 qiita_db/support_files/patches/85.sql

diff --git a/qiita_db/analysis.py b/qiita_db/analysis.py
index 477b43684..b21f10a1b 100644
--- a/qiita_db/analysis.py
+++ b/qiita_db/analysis.py
@@ -180,7 +180,8 @@ def create(cls, owner, name, description, from_default=False,
             params = qdb.software.Parameters.load(
                 cmd, values_dict={
                     'analysis': a_id,
-                    'merge_dup_sample_ids': merge_duplicated_sample_ids})
+                    'merge_dup_sample_ids': merge_duplicated_sample_ids,
+                    'categories': categories})
             job = qdb.processing_job.ProcessingJob.create(
                 owner, params, True)
             sql = """INSERT INTO qiita.analysis_processing_job
diff --git a/qiita_db/support_files/patches/85.sql b/qiita_db/support_files/patches/85.sql
new file mode 100644
index 000000000..e1692cc0a
--- /dev/null
+++ b/qiita_db/support_files/patches/85.sql
@@ -0,0 +1,12 @@
+-- Feb 22, 2022
+-- adding a new parameter `categories` to build_analysis_files
+
+DO $do$
+DECLARE
+    cmd_id      bigint;
+BEGIN
+    SELECT command_id INTO cmd_id FROM qiita.software_command WHERE name = 'build_analysis_files';
+
+    INSERT INTO qiita.command_parameter (command_id, parameter_name, parameter_type, required, default_value)
+        VALUES (cmd_id, 'categories', 'mchoice', True, NULL);
+END $do$;

From 2cd8044f965b3e7aca318480b3d4c99a8a3f17b5 Mon Sep 17 00:00:00 2001
From: Antonio Gonzalez <antgonza@gmail.com>
Date: Tue, 22 Feb 2022 15:48:36 -0700
Subject: [PATCH 3/5] fix test_build_analysis_files

---
 qiita_ware/test/test_private_plugin.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/qiita_ware/test/test_private_plugin.py b/qiita_ware/test/test_private_plugin.py
index b9a1c7f11..450320829 100644
--- a/qiita_ware/test/test_private_plugin.py
+++ b/qiita_ware/test/test_private_plugin.py
@@ -379,7 +379,7 @@ def test_submit_to_EBI(self):
 
     def test_build_analysis_files(self):
         job = self._create_job('build_analysis_files', {
-            'analysis': 3, 'merge_dup_sample_ids': True})
+            'analysis': 3, 'merge_dup_sample_ids': True, 'categories': None})
 
         # testing shape and get_resource_allocation_info as
         # build_analysis_files is a special case

From 15b286c01d2e3f6f70eaef996cc9f3c064289787 Mon Sep 17 00:00:00 2001
From: Antonio Gonzalez <antgonza@gmail.com>
Date: Tue, 22 Feb 2022 16:12:25 -0700
Subject: [PATCH 4/5] fix test_build_analysis_files v2

---
 qiita_ware/test/test_private_plugin.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/qiita_ware/test/test_private_plugin.py b/qiita_ware/test/test_private_plugin.py
index 450320829..40b329687 100644
--- a/qiita_ware/test/test_private_plugin.py
+++ b/qiita_ware/test/test_private_plugin.py
@@ -407,7 +407,7 @@ def _set_allocation(memory):
 
         # now let's test something that will cause not a number input_size*N
         job = self._create_job('build_analysis_files', {
-            'analysis': 3, 'merge_dup_sample_ids': True})
+            'analysis': 3, 'merge_dup_sample_ids': True, 'categories': None})
         _set_allocation('{input_size}*N')
         self.assertEqual(job.get_resource_allocation_info(), 'Not valid')
         self.assertEqual(job.status, 'error')
@@ -416,7 +416,7 @@ def _set_allocation(memory):
 
         # now let's test something that will return a negative number -samples
         job = self._create_job('build_analysis_files', {
-            'analysis': 3, 'merge_dup_sample_ids': True})
+            'analysis': 3, 'merge_dup_sample_ids': True, 'categories': None})
         _set_allocation('-{samples}')
         self.assertEqual(job.get_resource_allocation_info(), 'Not valid')
         self.assertEqual(job.status, 'error')
@@ -425,7 +425,7 @@ def _set_allocation(memory):
 
         # now let's test a full build_analysis_files job
         job = self._create_job('build_analysis_files', {
-            'analysis': 3, 'merge_dup_sample_ids': True})
+            'analysis': 3, 'merge_dup_sample_ids': True, 'categories': None})
         job._set_status('in_construction')
         job.submit()
 

From bbdf92e536ce524d1c3a0356d2f0ef508980a986 Mon Sep 17 00:00:00 2001
From: Antonio Gonzalez <antgonza@gmail.com>
Date: Thu, 24 Feb 2022 06:54:11 -0700
Subject: [PATCH 5/5] addressing @wasade comment

---
 qiita_pet/templates/analysis_selected.html | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/qiita_pet/templates/analysis_selected.html b/qiita_pet/templates/analysis_selected.html
index 0e3e790ef..a5915a89f 100644
--- a/qiita_pet/templates/analysis_selected.html
+++ b/qiita_pet/templates/analysis_selected.html
@@ -218,15 +218,17 @@ <h4>Metadata Selection <small>Common fields for all studies are preselected</sma
   <table border="0" style="width: 100%;">
     <tr>
       <td style="width: 50%;">
+        Sample Information
         <select data-placeholder="Choose Sample Metadata..." multiple class="chosen-select" id="sample-metadata-{{study.id}}">
-          {% for field in metadata[study.id]['sample'] %}
+          {% for field in sorted(metadata[study.id]['sample']) %}
              <option value="{{field}}">{{field}}</option>
           {% end %}
         </select>
       </td>
       <td style="width: 50%;">
+        Preparation Information
         <select data-placeholder="Choose Preparation Metadata..." multiple class="chosen-select" id="prep-metadata-{{study.id}}">
-          {% for field in metadata[study.id]['prep'] %}
+          {% for field in sorted(metadata[study.id]['prep']) %}
             <option value="{{field}}">{{field}}</option>
           {% end %}
       </td>