address comments

Author: squirrelo

qiita_db/study.py

@@ -206,21 +206,21 @@ def get_by_status(cls, status):
         return studies
 
     @classmethod
-    def get_info(cls, study_ids, info_cols=None):
+    def get_info(cls, study_ids=None, info_cols=None):
         """Returns study data for a set of study_ids
 
         Parameters
         ----------
-        study_ids : list of ints
-            Studies to get information for.
+        study_ids : list of ints, optional
+            Studies to get information for. Defauls to all studies
         info_cols: list of str, optional
             Information columns to retrieve. Defaults to all study data
 
         Returns
         -------
         list of DictCursor
             Table-like structure of metadata, one study per row. Can be
-            accessed as a list of dictionaries.
+            accessed as a list of dictionaries, keyed on column name.
         """
         if info_cols is None:
             info_cols = cls._info_cols
@@ -236,8 +236,10 @@ def get_info(cls, study_ids, info_cols=None):
             JOIN qiita.portal_type USING (portal_type_id)
             LEFT JOIN (SELECT study_id, array_agg(pmid ORDER BY pmid) as
             pmid FROM qiita.study_pmid GROUP BY study_id) sp USING (study_id)
-            ) WHERE study_id in ({1})""".format(
-            search_cols, ','.join(str(s) for s in study_ids))
+            )""".format(search_cols)
+        if study_ids is not None:
+            sql = "{0} WHERE study_id in ({1})".format(
+                sql, ','.join(str(s) for s in study_ids))
 
         conn_handler = SQLConnectionHandler()
         return conn_handler.execute_fetchall(sql)

qiita_db/support_files/patches/19.sql

@@ -31,4 +31,4 @@ UPDATE qiita.processed_data as pd
 -- We no longer need the status column on the study table
 ALTER TABLE qiita.study DROP CONSTRAINT fk_study_study_status;
 DROP INDEX qiita.idx_study_0;
-ALTER TABLE qiita.study DROP COLUMN study_status_id;
+ALTER TABLE qiita.study DROP COLUMN study_status_id;

qiita_db/support_files/patches/20.sql

@@ -1,6 +1,6 @@
 -- March 19, 2015
 -- Rename columns to be more descriptive and allow easier joins
-ALTER TABLE qiita.processed_data_status RENAME COLUMN description TO status_description;
+ALTER TABLE qiita.processed_data_status RENAME COLUMN description TO processed_data_status_description;
 ALTER TABLE qiita.portal_type RENAME COLUMN description TO portal_description;
 ALTER TABLE qiita.investigation RENAME COLUMN description TO investigation_description;
 ALTER TABLE qiita.investigation RENAME COLUMN name TO investigation_name;

qiita_db/test/test_study.py

@@ -180,6 +180,7 @@ def _change_processed_data_status(self, new_status):
             (id_status,))
 
     def test_get_info(self):
+        # Test get all info for single study
         obs = Study.get_info([1])
         self.assertEqual(len(obs), 1)
         obs = dict(obs[0])
@@ -213,6 +214,7 @@ def test_get_info(self):
             'Soils', 'number_samples_collected': 27}
         self.assertItemsEqual(obs, exp)
 
+        # Test get specific keys for single study
         exp_keys = ['metadata_complete', 'reprocess', 'timeseries_type',
                     'portal_description', 'pmid', 'study_title']
         obs = Study.get_info([1], exp_keys)
@@ -227,6 +229,28 @@ def test_get_info(self):
             'Soils'}
         self.assertItemsEqual(obs, exp)
 
+        # Test get specific keys for all studies
+        info = {
+            'timeseries_type_id': 1,
+            'portal_type_id': 1,
+            'lab_person_id': None,
+            'principal_investigator_id': 3,
+            'metadata_complete': False,
+            'mixs_compliant': True,
+            'study_description': 'desc',
+            'study_alias': 'alias',
+            'study_abstract': 'abstract'}
+        user = User('test@foo.bar')
+
+        Study.create(user, 'test_study_1', efo=[1], info=info)
+        obs = Study.get_info(info_cols=exp_keys)
+        exp = [[True, ['123456', '7891011'], 'EMP portal', False,
+                'Identification of the Microbiomes for Cannabis Soils',
+                'None'],
+                [False, None, 'QIIME portal', False, 'test_study_1', 'None']]
+        self.assertEqual(obs, exp)
+
+
     def test_has_access_public(self):
         self._change_processed_data_status('public')
         self.assertTrue(self.study.has_access(User("demo@microbio.me")))

qiita_pet/handlers/study_handlers/listing_handlers.py

@@ -13,7 +13,6 @@
 from tornado.gen import coroutine, Task
 from pyparsing import ParseException
 
-from qiita_core.exceptions import IncompetentQiitaDeveloperError
 from qiita_db.user import User
 from qiita_db.study import Study, StudyPerson
 from qiita_db.search import QiitaStudySearch
@@ -43,34 +42,29 @@ def _get_shared_links_for_study(study):
     return ", ".join(shared)
 
 
-def _build_study_info(studytype, user, results=None):
-    """builds list of namedtuples for study listings"""
-    if studytype not in {"standard", "shared"}:
-        raise IncompetentQiitaDeveloperError("Must use standard or shared!")
+def _build_study_info(user, results=None):
+    """builds list of dicts for studies table, with all html formatted"""
     # get list of studies for table
-    if studytype == "standard":
-        studylist = user.user_studies.union(Study.get_by_status('public'))
-    elif studytype == "shared":
-        studylist = user.shared_studies
+    study_list = user.user_studies.union(
+        Study.get_by_status('public')).union(user.shared_studies)
     if results is not None:
-        studylist = studylist.intersection(results)
-    if not studylist:
+        study_list = study_list.intersection(results)
+    if not study_list:
         # No studies left so no need to continue
         return []
 
     # get info for the studies
     cols = ['study_id', 'status', 'email', 'principal_investigator_id',
             'pmid', 'study_title', 'metadata_complete',
             'number_samples_collected', 'study_abstract']
-    study_info = Study.get_info(studylist, cols)
+    study_info = Study.get_info(study_list, cols)
 
     infolist = []
     for row, info in enumerate(study_info):
         study = Study(info['study_id'])
         status = study.status
         # Just passing the email address as the name here, since
         # name is not a required field in qiita.qiita_user
-        owner = study_person_linkifier((info['email'], info['email']))
         PI = StudyPerson(info['principal_investigator_id'])
         PI = study_person_linkifier((PI.email, PI.name))
         if info['pmid'] is not None:
@@ -85,12 +79,12 @@ def _build_study_info(studytype, user, results=None):
         # build the HTML elements needed for table cell
         title = ("<a href='#' data-toggle='modal' "
                  "data-target='#study-abstract-modal' "
-                 "onclick='fillAbstract(\"{0}-studies-table\", {1})'>"
+                 "onclick='fillAbstract(\"studies-table\", {0})'>"
                  "<span class='glyphicon glyphicon-file' "
                  "aria-hidden='true'></span></a> | "
-                 "<a href='/study/description/{2}' "
-                 "id='study{1}-title'>{3}</a>").format(
-                     studytype, str(row), str(study.id), info["study_title"])
+                 "<a href='/study/description/{1}' "
+                 "id='study{0}-title'>{2}</a>").format(
+                     str(row), str(study.id), info["study_title"])
         meta_complete = "<span class='glyphicon glyphicon-%s'></span>" % \
             meta_complete_glyph
         if status == 'public':
@@ -112,7 +106,6 @@ def _build_study_info(studytype, user, results=None):
             "num_raw_data": len(study.raw_data()),
             "pi": PI,
             "pmid": pmids,
-            "owner": owner,
             "status": status,
             "abstract": info["study_abstract"]
 
@@ -133,9 +126,9 @@ class ListStudiesHandler(BaseHandler):
     def get(self):
         all_emails_except_current = yield Task(self._get_all_emails)
         all_emails_except_current.remove(self.current_user.id)
-        availmeta = SampleTemplate.metadata_headers() +\
+        avail_meta = SampleTemplate.metadata_headers() +\
             get_table_cols("study")
-        self.render('list_studies.html', availmeta=availmeta,
+        self.render('list_studies.html', availmeta=avail_meta,
                     all_emails_except_current=all_emails_except_current)
 
     def _get_all_emails(self, callback):
@@ -194,13 +187,6 @@ def get(self):
 
 
 class SearchStudiesAJAX(BaseHandler):
-    def _get_standard(self, user, callback):
-        callback(_build_study_info("standard", user))
-
-    def _get_shared(self, user, callback):
-        """builds list of tuples for studies that are shared with user"""
-        callback(_build_study_info("shared", user))
-
     @authenticated
     def get(self, ignore):
         search_type = self.get_argument('type')
@@ -215,7 +201,7 @@ def get(self, ignore):
             # Search for samples matching the query
             search = QiitaStudySearch()
             try:
-                res, meta = search(query, User(user))
+                res, meta = search(query, self.current_user)
             except ParseException:
                 self.clear()
                 self.set_status(400)
@@ -240,8 +226,7 @@ def get(self, ignore):
                 return
             if not res:
                 res = {}
-        info = _build_study_info(search_type, self.current_user,
-                                 results=res)
+        info = _build_study_info(self.current_user, results=res)
         # build the table json
         results = {
             "sEcho": echo,

qiita_pet/templates/list_studies.html

@@ -9,7 +9,7 @@
 var current_study;
 var ajaxURL = "/study/search/?&user={{current_user.id}}&sEcho=" + Math.floor(Math.random()*1001);
 $(document).ready(function() {
-        $('#standard-studies-table').dataTable({
+        $('#studies-table').dataTable({
             "columns": [
               { "data": "checkbox" },
               { "data": "title" },
@@ -23,7 +23,7 @@
               { "data": "pmid" },
               { "data": "status" }
             ],
-            order: [[10, "asc"], [ 1, "asc" ]],
+            order: [[10, "desc"], [ 1, "asc" ]],
             columnDefs: [{type:'natural', targets:[3,4,5,9]}, {"targets": [ 2 ],"visible": false}],
             "oLanguage": {
                 "sSearch": "Narrow search results by column data (Title, abstract, PI, etc):",
@@ -34,35 +34,11 @@
                 "url": ajaxURL + "&type=standard&query=",
                 "error": function(jqXHR, textStatus, ex) {
                     $("#submit-button").prop("disabled",false);
-                    $("#search-error").text(jqXHR.responseText);
+                    if(jqXHR.status === 500) { $("#search-error").text("Internal Server Error, please try again later"); }
+                    else { $("#search-error").text(jqXHR.responseText); }
                 }
             } 
         });
-        $('#shared-studies-table').dataTable({
-          "columns": [
-              { "data": "checkbox" },
-              { "data": "title" },
-              { "data": "abstract" },
-              { "data": "id" },
-              { "data": "owner" },
-              { "data": "meta_complete" },
-              { "data": "num_samples" },
-              { "data": "num_raw_data" },
-              { "data": "pi" },
-              { "data": "pmid" }
-            ],
-            order: [[ 1, "asc" ]],
-            columnDefs: [{type:'natural', targets:[4,5,6]}, {"targets": [ 2 ],"visible": false}],
-            "oLanguage": {
-                "sSearch": "Narrow search results by column data (Title, abstract, PI, etc):",
-                "sLoadingRecords": "Loading table data",
-                "sZeroRecords": "No studies found"
-            },
-            "ajax": {
-                "url": ajaxURL + "&type=shared&query=",
-                "error": function(jqXHR, textStatus, ex) {} 
-            } 
-        });
 
     $('#users_list').chosen({width: "100%"});
     $('#users_list').on('change', function(evt, params) {
@@ -126,8 +102,8 @@ <h1>Metadata Search</h1>
 <!--User Studies-->
 <div class="row">
   <div class="col-sm-12" id="user-studies-div">
-    <h1>Your Studies</h1>
-    <table id="standard-studies-table" class="display table-bordered table-hover">
+    <h1>Available Studies</h1>
+    <table id="studies-table" class="display table-bordered table-hover">
         <thead>
             <tr>
                 <th></th>
@@ -146,29 +122,6 @@ <h1>Your Studies</h1>
         <tbody>
         </tbody>
     </table>
-<!--Shared Studies-->
-<form id="study-sel-form" name="study-sel-form">
-<div class="row">
-  <div class="col-sm-12" id="user-studies-div">
-    <h1>Shared Studies</h1>
-    <table id="shared-studies-table" class="display table-bordered table-hover">
-        <thead>
-            <tr>
-                <th></th>
-                <th>Title</th>
-                <th>Abstract</th>
-                <th>Study ID</th>
-                <th>Owner</th>
-                <th>Metadata Complete</th>
-                <th>Samples</th>
-                <th>Sequence Files</th>
-                <th>Principal Investigator</th>
-                <th>Pubmed ID(s)</th>
-            </tr>
-        </thead>
-        <tbody>
-        </tbody>
-    </table>
 <!--Abstract Modal-->
 <div class="modal fade" tabindex="-1" role="dialog" aria-labelledby="myLargeModalLabel" aria-hidden="true" id="study-abstract-modal">
   <div class="modal-dialog modal-med">