Merge pull request #2064 from antgonza/fix-1959

fix #1959

Author: tanaes

qiita_pet/handlers/api_proxy/prep_template.py

@@ -299,7 +299,8 @@ def prep_template_summary_get_req(prep_id, user_id):
         Format {'status': status,
                 'message': message,
                 'num_samples': value,
-                'category': [(val1, count1), (val2, count2), ...], ...}
+                'category': [(val1, count1), (val2, count2), ...],
+                'editable': bool}
     """
     exists = _check_prep_template_exists(int(prep_id))
     if exists['status'] != 'success':
@@ -309,17 +310,21 @@ def prep_template_summary_get_req(prep_id, user_id):
     access_error = check_access(prep.study_id, user_id)
     if access_error:
         return access_error
+
+    editable = Study(prep.study_id).can_edit(User(user_id))
     df = prep.to_dataframe()
     out = {'num_samples': df.shape[0],
-           'summary': {},
+           'summary': [],
            'status': 'success',
-           'message': ''}
+           'message': '',
+           'editable': editable}
 
-    cols = list(df.columns)
+    cols = sorted(list(df.columns))
     for column in cols:
         counts = df[column].value_counts()
-        out['summary'][str(column)] = [(str(key), counts[key])
-                                       for key in natsorted(counts.index)]
+        out['summary'].append(
+            (str(column), [(str(key), counts[key])
+                           for key in natsorted(counts.index)]))
     return out
 
 
@@ -417,10 +422,11 @@ def prep_template_patch_req(user_id, req_op, req_path, req_value=None,
 
     Returns
     -------
-    dict of {str, str}
+    dict of {str, str, str}
         A dictionary with the following keys:
         - status: str, whether if the request is successful or not
         - message: str, if the request is unsuccessful, a human readable error
+        - row_id: str, the row_id that we tried to delete
     """
     req_path = [v for v in req_path.split('/') if v]
     if req_op == 'replace':
@@ -458,13 +464,15 @@ def prep_template_patch_req(user_id, req_op, req_path, req_value=None,
 
         return {'status': status, 'message': msg}
     elif req_op == 'remove':
-        # The structure of the path should be /prep_id/{columns|samples}/name
-        if len(req_path) != 3:
+        # The structure of the path should be:
+        # /prep_id/row_id/{columns|samples}/name
+        if len(req_path) != 4:
             return {'status': 'error',
                     'message': 'Incorrect path parameter'}
         prep_id = int(req_path[0])
-        attribute = req_path[1]
-        attr_id = req_path[2]
+        row_id = req_path[1]
+        attribute = req_path[2]
+        attr_id = req_path[3]
 
         # Check if the user actually has access to the study
         pt = PrepTemplate(prep_id)
@@ -478,12 +486,13 @@ def prep_template_patch_req(user_id, req_op, req_path, req_value=None,
         # Store the job id attaching it to the sample template id
         r_client.set(PREP_TEMPLATE_KEY_FORMAT % prep_id,
                      dumps({'job_id': job_id, 'is_qiita_job': False}))
-        return {'status': 'success', 'message': ''}
+        return {'status': 'success', 'message': '', 'row_id': row_id}
     else:
         return {'status': 'error',
                 'message': 'Operation "%s" not supported. '
                            'Current supported operations: replace, remove'
-                           % req_op}
+                           % req_op,
+                'row_id': '0'}
 
 
 def prep_template_samples_get_req(prep_id, user_id):

qiita_pet/handlers/api_proxy/sample_template.py

@@ -521,13 +521,15 @@ def sample_template_patch_request(user_id, req_op, req_path, req_value=None,
     if req_op == 'remove':
         req_path = [v for v in req_path.split('/') if v]
 
-        if len(req_path) != 3:
+        # format: study_id/row_id/column|sample/attribute_id
+        if len(req_path) != 4:
             return {'status': 'error',
                     'message': 'Incorrect path parameter'}
 
         st_id = req_path[0]
-        attribute = req_path[1]
-        attr_id = req_path[2]
+        row_id = req_path[1]
+        attribute = req_path[2]
+        attr_id = req_path[3]
 
         # Check if the user actually has access to the template
         st = SampleTemplate(st_id)
@@ -542,9 +544,10 @@ def sample_template_patch_request(user_id, req_op, req_path, req_value=None,
         r_client.set(SAMPLE_TEMPLATE_KEY_FORMAT % st_id,
                      dumps({'job_id': job_id}))
 
-        return {'status': 'success', 'message': ''}
+        return {'status': 'success', 'message': '', 'row_id': row_id}
 
     else:
         return {'status': 'error',
                 'message': 'Operation "%s" not supported. '
-                           'Current supported operations: remove' % req_op}
+                           'Current supported operations: remove' % req_op,
+                'row_id': 0}

qiita_pet/handlers/api_proxy/tests/test_prep_template.py

@@ -206,40 +206,9 @@ def test_prep_template_graph_get_req_no_exists(self):
 
     def test_prep_template_summary_get_req(self):
         obs = prep_template_summary_get_req(1, 'test@foo.bar')
-        exp = {'summary': {
-            'experiment_center': [('ANL', 27)],
-            'center_name': [('ANL', 27)],
-            'run_center': [('ANL', 27)],
-            'run_prefix': [('s_G1_L001_sequences', 27)],
-            'primer': [('GTGCCAGCMGCCGCGGTAA', 27)],
-            'target_gene': [('16S rRNA', 27)],
-            'sequencing_meth': [('Sequencing by synthesis', 27)],
-            'run_date': [('8/1/12', 27)],
-            'platform': [('Illumina', 27)],
-            'pcr_primers': [('FWD:GTGCCAGCMGCCGCGGTAA; '
-                             'REV:GGACTACHVGGGTWTCTAAT', 27)],
-            'library_construction_protocol': [(
-                'This analysis was done as in Caporaso et al 2011 Genome '
-                'research. The PCR primers (F515/R806) were developed against '
-                'the V4 region of the 16S rRNA (both bacteria and archaea), '
-                'which we determined would yield optimal community clustering '
-                'with reads of this length using a procedure similar to that '
-                'of ref. 15. [For reference, this primer pair amplifies the '
-                'region 533_786 in the Escherichia coli strain 83972 sequence '
-                '(greengenes accession no. prokMSA_id:470367).] The reverse '
-                'PCR primer is barcoded with a 12-base error-correcting Golay '
-                'code to facilitate multiplexing of up to 1,500 samples per '
-                'lane, and both PCR primers contain sequencer adapter '
-                'regions.', 27)],
-            'experiment_design_description': [(
-                'micro biome of soil and rhizosphere of cannabis plants from '
-                'CA', 27)],
-            'study_center': [('CCME', 27)],
-            'center_project_name': [],
-            'sample_center': [('ANL', 27)],
-            'samp_size': [('.25,g', 27)],
-            'qiita_prep_id': [('1', 27)],
-            'barcode': [
+        exp = {
+            'status': 'success', 'message': '',
+            'summary': [('barcode', [
                 ('AACTCCTGTGGA', 1), ('ACCTCAGTCAAG', 1), ('ACGCACATACAA', 1),
                 ('AGCAGGCACGAA', 1), ('AGCGCTCACATC', 1), ('ATATCGCGATGA', 1),
                 ('ATGGCCTGACTA', 1), ('CATACACGCACC', 1), ('CCACCCAGTAAC', 1),
@@ -248,15 +217,44 @@ def test_prep_template_summary_get_req(self):
                 ('CGTAGAGCTCTC', 1), ('CGTGCACAATTG', 1), ('GATAGCACTCGT', 1),
                 ('GCGGACTATTCA', 1), ('GTCCGCAAGTTA', 1), ('TAATGGTCGTAG', 1),
                 ('TAGCGCGAACTT', 1), ('TCGACCAAACAC', 1), ('TGAGTGGTCTGT', 1),
-                ('TGCTACAGACGT', 1), ('TGGTTATGGCAC', 1), ('TTGCACCGTCGA', 1)],
-            'emp_status': [('EMP', 27)],
-            'illumina_technology': [('MiSeq', 27)],
-            'experiment_title': [('Cannabis Soil Microbiome', 27)],
-            'target_subfragment': [('V4', 27)],
-            'instrument_model': [('Illumina MiSeq', 27)]},
-            'num_samples': 27,
-            'status': 'success',
-            'message': ''}
+                ('TGCTACAGACGT', 1), ('TGGTTATGGCAC', 1), ('TTGCACCGTCGA', 1)
+            ]), ('center_name', [('ANL', 27)]), ('center_project_name', []),
+                ('emp_status', [('EMP', 27)]),
+                ('experiment_center', [('ANL', 27)]),
+                ('experiment_design_description', [
+                    ('micro biome of soil and rhizosphere of cannabis plants '
+                     'from CA', 27)]),
+                ('experiment_title', [('Cannabis Soil Microbiome', 27)]),
+                ('illumina_technology', [('MiSeq', 27)]),
+                ('instrument_model', [('Illumina MiSeq', 27)]),
+                ('library_construction_protocol', [
+                    ('This analysis was done as in Caporaso et al 2011 Genome '
+                     'research. The PCR primers (F515/R806) were developed '
+                     'against the V4 region of the 16S rRNA (both bacteria '
+                     'and archaea), which we determined would yield optimal '
+                     'community clustering with reads of this length using a '
+                     'procedure similar to that of ref. 15. [For reference, '
+                     'this primer pair amplifies the region 533_786 in the '
+                     'Escherichia coli strain 83972 sequence (greengenes '
+                     'accession no. prokMSA_id:470367).] The reverse PCR '
+                     'primer is barcoded with a 12-base error-correcting '
+                     'Golay code to facilitate multiplexing of up to 1,500 '
+                     'samples per lane, and both PCR primers contain '
+                     'sequencer adapter regions.', 27)]),
+                ('pcr_primers', [(
+                    'FWD:GTGCCAGCMGCCGCGGTAA; REV:GGACTACHVGGGTWTCTAAT', 27)]),
+                ('platform', [('Illumina', 27)]),
+                ('primer', [('GTGCCAGCMGCCGCGGTAA', 27)]),
+                ('qiita_prep_id', [('1', 27)]), ('run_center', [('ANL', 27)]),
+                ('run_date', [('8/1/12', 27)]),
+                ('run_prefix', [('s_G1_L001_sequences', 27)]),
+                ('samp_size', [('.25,g', 27)]),
+                ('sample_center', [('ANL', 27)]),
+                ('sequencing_meth', [('Sequencing by synthesis', 27)]),
+                ('study_center', [('CCME', 27)]),
+                ('target_gene', [('16S rRNA', 27)]),
+                ('target_subfragment', [('V4', 27)])],
+            'editable': True, 'num_samples': 27}
         self.assertEqual(obs, exp)
 
     def test_prep_template_summary_get_req_no_access(self):
@@ -476,8 +474,8 @@ def test_prep_template_patch_req(self):
         # Delete a prep template column
         obs = prep_template_patch_req(
             'test@foo.bar', 'remove',
-            '/%s/columns/target_subfragment/' % pt.id)
-        exp = {'status': 'success', 'message': ''}
+            '/%s/10/columns/target_subfragment/' % pt.id)
+        exp = {'status': 'success', 'message': '', 'row_id': '10'}
         self.assertEqual(obs, exp)
         self._wait_for_parallel_job('prep_template_%s' % pt.id)
         self.assertNotIn('target_subfragment', pt.categories())
@@ -489,7 +487,8 @@ def test_prep_template_patch_req(self):
             'Cancer Genomics')
         exp = {'status': 'error',
                'message': 'Operation "add" not supported. '
-                          'Current supported operations: replace, remove'}
+                          'Current supported operations: replace, remove',
+               'row_id': '0'}
         self.assertEqual(obs, exp)
         # Incorrect path parameter
         obs = prep_template_patch_req(

qiita_pet/handlers/api_proxy/tests/test_sample_template.py

@@ -525,28 +525,28 @@ def test_sample_template_meta_cats_get_req_no_template(self):
     def test_sample_template_patch_request(self):
         # Wrong operation operation
         obs = sample_template_patch_request(
-            "test@foo.bar", "add", "/1/columns/season_environment/")
+            "test@foo.bar", "add", "/1/10/columns/season_environment/")
         exp = {'status': 'error',
                'message': 'Operation "add" not supported. '
-                          'Current supported operations: remove'}
+                          'Current supported operations: remove',
+               'row_id': 0}
         self.assertEqual(obs, exp)
         # Wrong path parameter
         obs = sample_template_patch_request(
-            "test@foo.bar", "remove", "/columns/season_environment/")
+            "test@foo.bar", "remove", "10/columns/season_environment/")
         exp = {'status': 'error',
                'message': 'Incorrect path parameter'}
         self.assertEqual(obs, exp)
         # No access
         obs = sample_template_patch_request(
-            "demo@microbio.me", "remove", "/1/columns/season_environment/")
+            "demo@microbio.me", "remove", "/1/10/columns/season_environment/")
         exp = {'status': 'error',
                'message': 'User does not have access to study'}
         self.assertEqual(obs, exp)
         # Success
         obs = sample_template_patch_request(
-            "test@foo.bar", "remove", "/1/columns/season_environment/")
-        exp = {'status': 'success',
-               'message': ''}
+            "test@foo.bar", "remove", "/1/10/columns/season_environment/")
+        exp = {'status': 'success', 'message': '', 'row_id': '10'}
         self.assertEqual(obs, exp)
 
         # This is needed so the clean up works - this is a distributed system

qiita_pet/handlers/study_handlers/prep_template.py

@@ -44,21 +44,26 @@ class PrepTemplateSummaryAJAX(BaseHandler):
     @authenticated
     def get(self):
         prep_id = to_int(self.get_argument('prep_id'))
+
         res = prep_template_summary_get_req(prep_id, self.current_user.id)
+
         self.render('study_ajax/prep_summary_table.html', pid=prep_id,
-                    stats=res['summary'])
+                    stats=res['summary'], editable=res['editable'])
 
 
 class PrepTemplateAJAX(BaseHandler):
     @authenticated
     def get(self):
         """Send formatted summary page of prep template"""
         prep_id = to_int(self.get_argument('prep_id'))
+        row_id = self.get_argument('row_id', '0')
 
         res = prep_template_ajax_get_req(self.current_user.id, prep_id)
         res['prep_id'] = prep_id
+        res['row_id'] = row_id
         # Escape the message just in case javascript breaking characters in it
         res['alert_message'] = url_escape(res['alert_message'])
+
         self.render('study_ajax/prep_summary.html', **res)
 
 

qiita_pet/handlers/study_handlers/sample_template.py

@@ -74,6 +74,8 @@ class SampleTemplateAJAX(BaseHandler):
     def get(self):
         """Send formatted summary page of sample template"""
         study_id = self.get_argument('study_id')
+        row_id = self.get_argument('row_id', '0')
+
         files = [f for _, f in get_files_from_uploads_folders(study_id)
                  if f.endswith(('txt', 'tsv'))]
         data_types = sorted(data_types_get_req()['data_types'])
@@ -95,6 +97,7 @@ def get(self):
         stats['files'] = files
         stats['study_id'] = study_id
         stats['data_types'] = data_types
+        stats['row_id'] = row_id
         # URL encode in case message has javascript-breaking characters in it
         stats['alert_message'] = url_escape(stats['alert_message'])
         self.render('study_ajax/sample_summary.html', **stats)

qiita_pet/templates/study_ajax/prep_summary.html

@@ -181,18 +181,18 @@
    * prep information
    *
    */
-  function delete_prep_column(prep_id, column_name) {
+  function delete_prep_column(prep_id, column_name, row_id) {
     if(confirm("Are you sure you want to delete '" + column_name + "' information?")) {
       $.ajax({
         url: '{% raw qiita_config.portal_dir %}/prep_template/',
         type: 'PATCH',
-        data: {'op': 'remove', 'path': '/' + prep_id + '/columns/' + column_name},
+        data: {'op': 'remove', 'path': '/' + prep_id + '/' + row_id + '/columns/' + column_name},
         success: function(data) {
           if(data.status == 'error') {
             bootstrapAlert(data.message, "danger");
           }
           else {
-            populate_main_div('/study/description/prep_template/', { prep_id: prep_id, study_id: {{study_id}} });
+            populate_main_div('/study/description/prep_template/', { prep_id: prep_id, study_id: {{study_id}}, row_id: row_id });
           }
         }
       });
@@ -329,6 +329,22 @@
     }
   }
 
+  /*
+   * Autoscroll prep info list
+   *
+   * This is a helper function so we can scroll once the prep table is ready
+   */
+  function autoscroll_prep_list() {
+    // taken from: http://stackoverflow.com/a/2906009
+    if ({{row_id}} > 1) {
+      var container = $("html, body"), scrollTo = $("#row_{{row_id}}");
+
+      container.animate({
+          scrollTop: scrollTo.offset().top - container.offset().top + container.scrollTop()
+      });
+    }
+  }
+
   $(document).ready(function () {
     if("{{investigation_type}}" !== "None") {
       // The prep information already has an investigation type
@@ -402,6 +418,8 @@
     {% else %}
       $('#alert-message').alert('close');
     {% end %}
+
+
   });
 </script>
 

qiita_pet/templates/study_ajax/prep_summary_table.html

@@ -1,14 +1,21 @@
+<script type="text/javascript">
+  $(document).ready(function () {
+    autoscroll_prep_list();
+  });
+</script>
+
+
 {% from future.utils import viewitems %}
 <div class="panel panel-default">
   <div class="panel-heading">
     Information summary
   </div>
   <div id="summary-table-div">
     <table class="table">
-      {% for category, summary in viewitems(stats) %}
-        <tr>
+      {% for i, (category, summary) in enumerate(stats, -1) %}
+        <tr id="row_{{i}}">
           <td>
-            <a class="btn btn-danger" onclick="delete_prep_column({{pid}}, '{{category}}');"><span class="glyphicon glyphicon-trash"></span></a>
+              <a class="btn btn-danger" onclick="delete_prep_column({{pid}}, '{{category}}', {{i}});"><span class="glyphicon glyphicon-trash"></span></a>
           </td>
         {% if len(summary) == 1 %}
           <td colspan="2">