Merge pull request #1006 from squirrelo/cart

DataTables load using AJAX, Search by metadata on studies page

Author: antgonza

qiita_db/study.py

@@ -98,12 +98,14 @@
 from __future__ import division
 from future.utils import viewitems
 from copy import deepcopy
+from itertools import chain
+import warnings
 
 from qiita_core.exceptions import IncompetentQiitaDeveloperError
 from .base import QiitaObject
 from .exceptions import (QiitaDBStatusError, QiitaDBColumnError, QiitaDBError)
 from .util import (check_required_columns, check_table_cols, convert_to_id,
-                   get_environmental_packages, infer_status)
+                   get_environmental_packages, get_table_cols, infer_status)
 from .sql_connection import SQLConnectionHandler
 
 
@@ -142,7 +144,12 @@ class Study(QiitaObject):
     """
     _table = "study"
     # The following columns are considered not part of the study info
-    _non_info = {"email", "study_title"}
+    _non_info = frozenset(["email", "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"""
@@ -198,6 +205,45 @@ def get_by_status(cls, status):
 
         return studies
 
+    @classmethod
+    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, 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, keyed on column name.
+        """
+        if info_cols is None:
+            info_cols = cls._info_cols
+        elif not cls._info_cols.issuperset(info_cols):
+            warnings.warn("Non-info columns passed: %s" % ", ".join(
+                set(info_cols) - cls._info_cols))
+
+        search_cols = ",".join(sorted(cls._info_cols.intersection(info_cols)))
+
+        sql = """SELECT {0} FROM (
+            qiita.study
+            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 pmid) as
+            pmid FROM qiita.study_pmid GROUP BY study_id) sp USING (study_id)
+            )""".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)
+
     @classmethod
     def exists(cls, study_title):
         """Check if a study exists based on study_title, which is unique

qiita_db/support_files/patches/20.sql

@@ -0,0 +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 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/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/support_files/qiita-db.dbs

@@ -518,8 +518,8 @@
 		<table name="investigation" >
 			<comment>Overarching investigation information.An investigation comprises one or more individual studies.</comment>
 			<column name="investigation_id" type="bigserial" jt="-5" mandatory="y" />
-			<column name="name" type="varchar" jt="12" mandatory="y" />
-			<column name="description" type="varchar" jt="12" mandatory="y" >
+			<column name="investigation_name" type="varchar" jt="12" mandatory="y" />
+			<column name="investigation_description" type="varchar" jt="12" mandatory="y" >
 				<comment><![CDATA[Describes the overarching goal of the investigation]]></comment>
 			</column>
 			<column name="contact_person_id" type="bigint" jt="-5" />
@@ -682,7 +682,7 @@
 			<comment>What portals are available to show a study in</comment>
 			<column name="portal_type_id" type="bigserial" jt="-5" mandatory="y" />
 			<column name="portal" type="varchar" jt="12" mandatory="y" />
-			<column name="description" type="varchar" jt="12" mandatory="y" />
+			<column name="portal_description" type="varchar" jt="12" mandatory="y" />
 			<index name="pk_portal_type" unique="PRIMARY_KEY" >
 				<column name="portal_type_id" />
 			</index>
@@ -1000,7 +1000,7 @@
 		<table name="processed_data_status" >
 			<column name="processed_data_status_id" type="bigserial" jt="-5" mandatory="y" />
 			<column name="processed_data_status" type="varchar" jt="12" mandatory="y" />
-			<column name="description" type="varchar" jt="12" mandatory="y" />
+			<column name="processed_data_status_description" type="varchar" jt="12" mandatory="y" />
 			<index name="pk_study_status" unique="PRIMARY_KEY" >
 				<column name="processed_data_status_id" />
 			</index>
@@ -1565,7 +1565,6 @@ Controlled Vocabulary]]></comment>
 	<connector name="PostgreSQL" database="PostgreSQL" driver_class="org.postgresql.Driver" driver_jar="postgresql-9.2-1003.jdbc3.jar" host="localhost" port="5432" instance="qiita_test" user="mcdonadt" schema_mapping="" />
 	<layout id="Layout669806" name="qiita" show_relation_columns="y" >
 		<entity schema="qiita" name="controlled_vocab_values" color="d0def5" x="45" y="1545" />
-		<entity schema="qiita" name="investigation" color="c0d4f3" x="2100" y="255" />
 		<entity schema="qiita" name="investigation_study" color="c0d4f3" x="2100" y="405" />
 		<entity schema="qiita" name="job_results_filepath" color="c0d4f3" x="405" y="855" />
 		<entity schema="qiita" name="analysis_job" color="d0def5" x="285" y="930" />
@@ -1635,10 +1634,11 @@ Controlled Vocabulary]]></comment>
 		<entity schema="qiita" name="analysis" color="d0def5" x="225" y="720" />
 		<entity schema="qiita" name="study_experimental_factor" color="c0d4f3" x="2100" y="495" />
 		<entity schema="qiita" name="study_pmid" color="c0d4f3" x="2145" y="600" />
-		<entity schema="qiita" name="portal_type" color="c0d4f3" x="1995" y="660" />
 		<entity schema="qiita" name="study" color="d0def5" x="1815" y="60" />
 		<entity schema="qiita" name="processed_data" color="d0def5" x="1275" y="960" />
-		<entity schema="qiita" name="processed_data_status" color="c0d4f3" x="1530" y="1050" />
+		<entity schema="qiita" name="investigation" color="c0d4f3" x="2100" y="255" />
+		<entity schema="qiita" name="processed_data_status" color="c0d4f3" x="1500" y="1050" />
+		<entity schema="qiita" name="portal_type" color="c0d4f3" x="1995" y="660" />
 		<group name="Group_analyses" color="c4e0f9" >
 			<comment>analysis tables</comment>
 			<entity schema="qiita" name="analysis" />