fix #2225 and partial #2224

qiita_db/test/test_util.py

@@ -800,36 +800,37 @@ def test_generate_study_list(self):
             qdb.user.User('shared@foo.bar'), 'test_study_1', info=info)
 
         exp_info = [
-            {'status': 'private', 'metadata_complete': True,
-             'study_tags': None, 'publication_doi': [
-                '10.100/123456', '10.100/7891011'],
-             'study_title': ('Identification of the Microbiomes for '
-                             'Cannabis Soils'),
-             'publication_pid': ['123456', '7891011'],
+            {'status': 'private', 'study_title': (
+                'Identification of the Microbiomes for Cannabis Soils'),
+             'metadata_complete': True, 'publication_pid': [
+                '123456', '7891011'], 'artifact_biom_ids': [4, 5, 6, 7],
              'ebi_submission_status': 'submitted', 'study_id': 1,
-             'ebi_study_accession': 'EBI123456-BB',
+             'ebi_study_accession': 'EBI123456-BB', 'owner': 'Dude',
              'shared': [('shared@foo.bar', 'Shared')],
              'study_abstract': (
                 'This is a preliminary study to examine the microbiota '
-                'associated with the Cannabis plant. Soils samples from the '
-                'bulk soil, soil associated with the roots, and the '
-                'rhizosphere were extracted and the DNA sequenced. Roots from '
-                'three independent plants of different strains were examined. '
-                'These roots were obtained November 11, 2011 from plants that '
-                'had been harvested in the summer. Future studies will '
-                'attempt to analyze the soils and rhizospheres from the same '
-                'location at different time points in the plant lifecycle.'),
-             'pi': ('PI_dude@foo.bar', 'PIDude'),
-             'artifact_biom_ids': [4, 5, 6, 7],
+                'associated with the Cannabis plant. Soils samples from '
+                'the bulk soil, soil associated with the roots, and the '
+                'rhizosphere were extracted and the DNA sequenced. Roots '
+                'from three independent plants of different strains were '
+                'examined. These roots were obtained November 11, 2011 from '
+                'plants that had been harvested in the summer. Future studies '
+                'will attempt to analyze the soils and rhizospheres from the '
+                'same location at different time points in the plant '
+                'lifecycle.'), 'pi': ('PI_dude@foo.bar', 'PIDude'),
+             'publication_doi': ['10.100/123456', '10.100/7891011'],
+             'study_alias': 'Cannabis Soils', 'study_tags': None,
              'number_samples_collected': 27},
-            {'status': 'sandbox', 'metadata_complete': True,
-             'study_tags': None, 'publication_doi': [],
-             'study_title': 'test_study_1', 'publication_pid': [],
+            {'status': 'sandbox', 'study_title': 'test_study_1',
+             'metadata_complete': True, 'publication_pid': [],
+             'artifact_biom_ids': None,
              'ebi_submission_status': 'not submitted',
              'study_id': new_study.id, 'ebi_study_accession': None,
-             'shared': [], 'study_abstract': 'Some abstract goes here',
-             'pi': ('lab_dude@foo.bar', 'LabDude'),
-             'artifact_biom_ids': None, 'number_samples_collected': 0}]
+             'owner': 'Shared', 'shared': [],
+             'study_abstract': 'Some abstract goes here',
+             'pi': ('lab_dude@foo.bar', 'LabDude'), 'publication_doi': [],
+             'study_alias': 'TST', 'study_tags': None,
+             'number_samples_collected': 0}]
         obs_info = qdb.util.generate_study_list([1, 2, 3, 4], True)
         self.assertEqual(obs_info, exp_info)
 

qiita_db/util.py

@@ -1205,7 +1205,7 @@ def generate_study_list(study_ids, public_only=False):
     -----
     The main select might look scary but it's pretty simple:
     - We select the requiered fields from qiita.study and qiita.study_person
-        SELECT metadata_complete, study_abstract, study_id,
+        SELECT metadata_complete, study_abstract, study_id, study_alias,
             study_title, ebi_study_accession, ebi_submission_status,
             qiita.study_person.name AS pi_name,
             qiita.study_person.email AS pi_email,
@@ -1235,10 +1235,13 @@ def generate_study_list(study_ids, public_only=False):
     - all study tags
             (SELECT array_agg(study_tag) FROM qiita.per_study_tags
                 WHERE study_id=qiita.study.study_id) AS study_tags
+    - study owner
+            (SELECT name FROM qiita.qiita_user
+                WHERE email=qiita.study.email) AS owner
     """
     with qdb.sql_connection.TRN:
         sql = """
-            SELECT metadata_complete, study_abstract, study_id,
+            SELECT metadata_complete, study_abstract, study_id, study_alias,
                 study_title, ebi_study_accession, ebi_submission_status,
                 qiita.study_person.name AS pi_name,
                 qiita.study_person.email AS pi_email,
@@ -1261,7 +1264,9 @@ def generate_study_list(study_ids, public_only=False):
                     LEFT JOIN qiita.qiita_user USING (email)
                     WHERE study_id=qiita.study.study_id) AS shared_with_email,
                 (SELECT array_agg(study_tag) FROM qiita.per_study_tags
-                    WHERE study_id=qiita.study.study_id) AS study_tags
+                    WHERE study_id=qiita.study.study_id) AS study_tags,
+                (SELECT name FROM qiita.qiita_user
+                    WHERE email=qiita.study.email) AS owner
                 FROM qiita.study
                 LEFT JOIN qiita.study_person ON (
                     study_person_id=principal_investigator_id)
@@ -1303,6 +1308,8 @@ def generate_study_list(study_ids, public_only=False):
             del info["shared_with_email"]
 
             infolist.append({
+                'owner': info['owner'],
+                'study_alias': info['study_alias'],
                 'metadata_complete': info['metadata_complete'],
                 'publication_pid': info['publication_pid'],
                 'ebi_submission_status': info['ebi_submission_status'],

qiita_pet/handlers/api_proxy/tests/test_studies.py

@@ -50,18 +50,16 @@ def test_study_get_req(self):
         obs = study_get_req(1, 'test@foo.bar')
         exp = {
             'status': 'success',
-            'message': '',
             'study_info': {
-                'mixs_compliant': True,
-                'metadata_complete': True,
-                'reprocess': False,
-                'emp_person_id': 2,
-                'number_samples_promised': 27,
-                'funding': None,
-                'vamps_id': None,
+                'mixs_compliant': True, 'metadata_complete': True,
+                'reprocess': False, 'owner': 'test@foo.bar',
+                'emp_person_id': 2, 'number_samples_promised': 27,
+                'funding': None, 'show_biom_download_button': True,
+                'publication_pid': ['123456', '7891011'], 'vamps_id': None,
                 'first_contact': datetime(2014, 5, 19, 16, 10),
-                'timeseries_type_id': 1,
-                'study_abstract':
+                'ebi_submission_status': 'submitted',
+                'show_raw_download_button': True, 'timeseries_type_id': 1,
+                'study_abstract': (
                     'This is a preliminary study to examine the microbiota '
                     'associated with the Cannabis plant. Soils samples from '
                     'the bulk soil, soil associated with the roots, and the '
@@ -71,33 +69,25 @@ def test_study_get_req(self):
                     'from plants that had been harvested in the summer. '
                     'Future studies will attempt to analyze the soils and '
                     'rhizospheres from the same location at different time '
-                    'points in the plant lifecycle.',
-                'status': 'private',
-                'spatial_series': False,
-                'study_description': 'Analysis of the Cannabis Plant '
-                                     'Microbiome',
-                'shared_with': ['shared@foo.bar'],
-                'lab_person': {'affiliation': 'knight lab',
-                               'name': 'LabDude',
-                               'email': 'lab_dude@foo.bar'},
-                'principal_investigator': {'affiliation': 'Wash U',
-                                           'name': 'PIDude',
-                                           'email': 'PI_dude@foo.bar'},
-                'study_alias': 'Cannabis Soils',
-                'study_id': 1,
+                    'points in the plant lifecycle.'),
+                'status': 'private', 'spatial_series': False,
+                'study_description': (
+                    'Analysis of the Cannabis Plant Microbiome'),
+                'shared_with': ['shared@foo.bar'], 'publication_doi': [
+                    '10.100/123456', '10.100/7891011'],
+                'has_access_to_raw_data': True, 'lab_person': {
+                    'affiliation': 'knight lab', 'name': 'LabDude',
+                    'email': 'lab_dude@foo.bar'},
+                'principal_investigator': {
+                    'affiliation': 'Wash U', 'name': 'PIDude',
+                    'email': 'PI_dude@foo.bar'},
+                'study_alias': 'Cannabis Soils', 'study_id': 1,
                 'most_recent_contact': datetime(2014, 5, 19, 16, 11),
-                'publication_doi': ['10.100/123456', '10.100/7891011'],
-                'publication_pid': ['123456', '7891011'],
-                'num_samples': 27,
-                'study_title': 'Identification of the Microbiomes for '
-                               'Cannabis Soils',
-                'number_samples_collected': 27,
-                'owner': 'test@foo.bar',
-                'ebi_submission_status': 'submitted',
-                'has_access_to_raw_data': True,
-                'show_biom_download_button': True,
-                'show_raw_download_button': True,
-                'ebi_study_accession': 'EBI123456-BB'},
+                'ebi_study_accession': 'EBI123456-BB', 'num_samples': 27,
+                'study_title': (
+                    'Identification of the Microbiomes for Cannabis Soils'),
+                'number_samples_collected': 27},
+            'message': '',
             'editable': True}
         self.assertEqual(obs, exp)
 
@@ -139,6 +129,8 @@ def test_study_get_req(self):
                 'study_description': 'DESC',
                 'shared_with': [],
                 'lab_person': None,
+                'study_alias': "FCM",
+                'owner': 'Dude',
                 'principal_investigator': {'affiliation': 'Wash U',
                                            'name': 'PIDude',
                                            'email': 'PI_dude@foo.bar'},

qiita_pet/handlers/study_handlers/tests/test_listing_handlers.py

@@ -32,6 +32,8 @@ def setUp(self):
 
         self.single_exp = {
             'study_id': 1,
+            'owner': 'Dude',
+            'study_alias': 'Cannabis Soils',
             'status': 'private',
             'study_abstract':
                 'This is a preliminary study to examine the microbiota '
@@ -113,8 +115,8 @@ def test_build_study_info_empty_study(self):
             'study_alias': 'alias',
             'study_abstract': 'abstract'}
         Study.create(User('test@foo.bar'), "My study", info=info)
-        obs = _build_study_info(User('test@foo.bar'), 'user')
 
+        obs = _build_study_info(User('test@foo.bar'), 'user')
         self.exp.append({
             'metadata_complete': False,
             'ebi_submission_status':
@@ -126,6 +128,8 @@ def test_build_study_info_empty_study(self):
             'publication_doi': [],
             'study_abstract': 'abstract',
             'study_id': 2,
+            'owner': 'Dude',
+            'study_alias': 'alias',
             'ebi_study_accession': None,
             'study_title': 'My study',
             'study_tags': None,
@@ -260,6 +264,8 @@ def setUp(self):
                 'metadata_complete': True,
                 'ebi_submission_status': 'submitted',
                 'study_id': 1,
+                'study_alias': 'Cannabis Soils',
+                'owner': 'Dude',
                 'ebi_study_accession': 'EBI123456-BB',
                 'shared': ('<a target="_blank" href="mailto:shared@foo.bar">'
                            'Shared</a>'),

qiita_pet/support_files/doc/source/tutorials/sharing.rst

@@ -27,7 +27,7 @@ permissions that the owner of the Study has. These permissions are:
 Sharing a Study
 ---------------
 
-In the “Your Studies (includes shared with you)” section of the Studies List
+In the “Your Studies” section of the Studies List
 you have a “Shared With These Users” column that lists all User names that
 your study is shared with. You can click on the “Modify” button and add/remove
 users. See below.
@@ -47,5 +47,5 @@ will have a link to share it. See below
 
 .. figure::  images/sharing_study.gif
    :align:   center
-   
+
    Analysis sharing example

qiita_pet/templates/list_studies.html

@@ -129,11 +129,11 @@
         { "data": "pi" },
         { "data": "pubs" },
         { "data": "status" },
-        { "data": "ebi_info" }
-      ],
+        { "data": "ebi_info" },
+        { "data": "study_alias" }],
       columnDefs: [
         {type:'natural', targets:[2,6,7]},
-        {"targets": [ 2 ], "visible": false},
+        {"targets": [ 2, 10 ], "visible": false},
         // render zero
         {"render": function ( data, type, row, meta ) {
           if (data !== null && data !== undefined && data.length != 0){
@@ -166,7 +166,10 @@
         {"render": function ( data, type, row, meta ) {
             var glyph = 'remove';
             if(data === true) { glyph = 'ok' }
-            return "<span id='shared_html_"+ row.study_id +"'>"+ data +"</span><br/><a class='btn btn-primary btn-xs' data-toggle='modal' data-target='#share-study-modal-view' onclick='modify_sharing("+ row.study_id +");'>Modify</a>";
+            result = "<a class='btn btn-primary btn-xs' data-toggle='modal' data-target='#share-study-modal-view' onclick='modify_sharing("+ row.study_id +");'>Modify</a><br/>";
+            result += "<b>Owner:</b> " + row.owner + "</br>";
+            result += "<span id='shared_html_"+ row.study_id +"'>"+ data +"</span>";
+            return result;
         }, targets: [5]},
         ],
       "language": {
@@ -408,7 +411,7 @@ <h5 class="gray-msg">
     </h5>
     <select class="js-select2-multiple form-control" id="study_tags_multiple" multiple="multiple" style="width: 100%"></select>
 
-    <h3 class="gray-msg">Your Studies (includes shared with you)</h3>
+    <h3 class="gray-msg">Your Studies</h3>
     <table id="user-studies-table" class="table table-bordered gray-msg">
       <thead>
         <tr>
@@ -422,10 +425,11 @@ <h3 class="gray-msg">Your Studies (includes shared with you)</h3>
           <th>Publications</th>
           <th>Status</th>
           <th>Qiita EBI submission</th>
+          <th>Study Alias</th>
         </tr>
       </thead>
     </table>
-    <h3 class="gray-msg">Other Studies</h3>
+    <h3 class="gray-msg">Public Studies</h3>
     <table id="studies-table" class="table table-bordered gray-msg">
       <thead>
         <tr>