DataTables load using AJAX, Search by metadata on studies page

qiita_db/study.py

@@ -98,12 +98,13 @@
 from __future__ import division
 from future.utils import viewitems
 from copy import deepcopy
+from itertools import chain
 
 from qiita_core.exceptions import IncompetentQiitaDeveloperError
 from .base import QiitaStatusObject, QiitaObject
 from .exceptions import (QiitaDBStatusError, QiitaDBColumnError, QiitaDBError)
 from .util import (check_required_columns, check_table_cols, convert_to_id,
-                   get_environmental_packages)
+                   get_environmental_packages, get_table_cols)
 from .sql_connection import SQLConnectionHandler
 
 
@@ -143,6 +144,11 @@ class Study(QiitaStatusObject):
     _table = "study"
     # The following columns are considered not part of the study info
     _non_info = {"email", "study_status_id", "study_title"}
+    # The following tables are considered part of info
+    _info_cols = frozenset(chain(
+        get_table_cols('study'), get_table_cols('study_status'),
+        get_table_cols('timeseries_type'), get_table_cols('portal_type'),
+        get_table_cols('study_pmid')))
 
     def _lock_non_sandbox(self, conn_handler):
         """Raises QiitaDBStatusError if study is non-sandboxed"""
@@ -175,6 +181,28 @@ def get_by_status(cls, status):
                "ss.status = %s".format(cls._table))
         return {x[0] for x in conn_handler.execute_fetchall(sql, (status, ))}
 
+    @classmethod
+    def get_info(cls, study_ids, info_cols=None):
+        if info_cols is None:
+            info_cols = [s for s in cls._info_cols]
+        else:
+            info_cols = deepcopy(info_cols)
+
+        search_cols = ",".join(sorted(cls._info_cols.intersection(info_cols)))
+
+        sql = """SELECT {0} FROM (
+            qiita.study
+            JOIN qiita.study_status USING (study_status_id)
+            JOIN qiita.timeseries_type  USING (timeseries_type_id)
+            JOIN qiita.portal_type USING (portal_type_id)
+            LEFT JOIN (SELECT study_id, array_agg(pmid ORDER BY study_id) 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))
+
+        conn_handler = SQLConnectionHandler()
+        return conn_handler.execute_fetchall(sql)
+
     @classmethod
     def exists(cls, study_title):
         """Check if a study exists based on study_title, which is unique

qiita_db/support_files/patches/19.sql

@@ -0,0 +1,6 @@
+-- March 19, 2015
+-- Rename columns to be more descirptive and allow easier joins
+ALTER TABLE qiita.study_status RENAME COLUMN description TO 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/support_files/populate_test_db.sql

@@ -49,7 +49,7 @@ INSERT INTO qiita.study_users (study_id, email) VALUES (1, 'shared@foo.bar');
 INSERT INTO qiita.study_pmid (study_id, pmid) VALUES (1, '123456'), (1, '7891011');
 
 -- Insert an investigation
-INSERT INTO qiita.investigation (name, description, contact_person_id) VALUES
+INSERT INTO qiita.investigation (investigation_name, investigation_description, contact_person_id) VALUES
 	('TestInvestigation', 'An investigation for testing purposes', 3);
 
 -- Insert investigation_study (link study 1 with investigation 1)

qiita_db/test/test_study.py

@@ -177,6 +177,49 @@ def _make_sandbox(self):
         # make studies private
         self.conn_handler.execute("UPDATE qiita.study SET study_status_id = 1")
 
+    def test_get_info(self):
+        obs = Study.get_info([1])
+        self.assertEqual(len(obs), 1)
+        exp_keys = ['mixs_compliant', 'metadata_complete', 'reprocess',
+                    'timeseries_type', 'portal_description', 'emp_person_id',
+                    'number_samples_promised', 'funding', 'vamps_id',
+                    'first_contact', 'principal_investigator_id',
+                    'study_status_id', 'timeseries_type_id', 'study_abstract',
+                    'pmid', 'study_alias', 'status', 'spatial_series',
+                    'study_description', 'portal', 'status_description',
+                    'portal_type_id', 'intervention_type', 'email', 'study_id',
+                    'most_recent_contact', 'lab_person_id', 'study_title',
+                    'number_samples_collected']
+        exp_vals = [
+            ['123456', '7891011'], 'test@foo.bar', 2,
+            datetime(2014, 5, 19, 16, 10), None, 'None', 1, True, True,
+            datetime(2014, 5, 19, 16, 11), 27, 27, 'EMP', 'EMP portal', 2, 3,
+            False, False, 'private',
+            'Only owner and shared users can see this study',
+            '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.', 'Cannabis Soils', 'Analysis of the '
+            'Cannabis Plant Microbiome', 1, 3, 'Identification of the '
+            'Microbiomes for Cannabis Soils', 'None', 1, None]
+        self.assertItemsEqual(obs[0].keys(), exp_keys)
+        self.assertItemsEqual(obs[0], exp_vals)
+
+        exp_keys = ['metadata_complete', 'reprocess', 'timeseries_type',
+                    'portal_description', 'pmid', 'study_title']
+        obs = Study.get_info([1], exp_keys)
+        self.assertEqual(len(obs), 1)
+        exp_vals = [
+            True, 'EMP portal', False, 'Identification of the Microbiomes for '
+            'Cannabis Soils', 'None', ['123456', '7891011']]
+        self.assertItemsEqual(obs[0].keys(), exp_keys)
+        self.assertItemsEqual(obs[0], exp_vals)
+
     def test_has_access_public(self):
         self.study.status = 'public'
         self.assertTrue(self.study.has_access(User("demo@microbio.me")))

qiita_pet/handlers/study_handlers/__init__.py

@@ -6,17 +6,16 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
-from .listing_handlers import (PrivateStudiesHandler, PublicStudiesHandler,
-                               StudyApprovalList, ShareStudyAJAX)
+from .listing_handlers import (ListStudiesHandler, StudyApprovalList,
+                               ShareStudyAJAX, SearchStudiesAJAX)
 from .edit_handlers import StudyEditHandler, CreateStudyAJAX
 from .description_handlers import (StudyDescriptionHandler,
                                    PreprocessingSummaryHandler)
 from .ebi_handlers import EBISubmitHandler
 from .metadata_summary_handlers import MetadataSummaryHandler
 from .vamps_handlers import VAMPSHandler
 
-__all__ = ['PrivateStudiesHandler', 'PublicStudiesHandler',
-           'StudyApprovalList', 'ShareStudyAJAX', 'StudyEditHandler',
-           'CreateStudyAJAX', 'StudyDescriptionHandler',
+__all__ = ['ListStudiesHandler', 'StudyApprovalList', 'ShareStudyAJAX',
+           'StudyEditHandler', 'CreateStudyAJAX', 'StudyDescriptionHandler',
            'PreprocessingSummaryHandler', 'EBISubmitHandler',
-           'MetadataSummaryHandler', 'VAMPSHandler']
+           'MetadataSummaryHandler', 'VAMPSHandler', 'SearchStudiesAJAX']