Adds analysis.samples, another test analysis

qiita_db/analysis.py

@@ -16,6 +16,7 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 from __future__ import division
+from collections import defaultdict
 
 from .sql_connection import SQLConnectionHandler
 from .base import QiitaStatusObject
@@ -32,6 +33,7 @@ class Analysis(QiitaStatusObject):
     owner
     name
     description
+    samples
     biom_tables
     shared_with
     jobs
@@ -152,6 +154,24 @@ def description(self, description):
                "analysis_id = %s".format(self._table))
         conn_handler.execute(sql, (description, self._id))
 
+    @property
+    def samples(self):
+        """The processed data and samples attached to the analysis
+
+        Returns
+        -------
+        dict
+            Format is {processed_data_id: [sample_id, sample_id, ...]}
+        """
+        conn_handler = SQLConnectionHandler()
+        sql = ("SELECT processed_data_id, sample_id FROM qiita.analysis_sample"
+               " WHERE analysis_id = %s ORDER BY processed_data_id")
+        ret_samples = defaultdict(list)
+        # turn into dict of samples keyed to processed_data_id
+        for pid, sample in conn_handler.execute_fetchall(sql, (self._id, )):
+            ret_samples[pid].append(sample)
+        return ret_samples
+
     @property
     def shared_with(self):
         """The user the analysis is shared with

qiita_db/support_files/initialize.sql

@@ -38,4 +38,4 @@ INSERT INTO qiita.filepath_type (filepath_type) VALUES ('raw_sequences'), ('raw_
 INSERT INTO qiita.checksum_algorithm (name) VALUES ('crc32');
 
 -- Populate commands available
-INSERT INTO qiita.command (name, command) VALUES ('Summarize Taxa', 'summarize_taxa_through_plots.py'), ('Beta Diversity', 'beta_diversity_through_plots.py'), ('Alpha Diversity', 'alpha_diversity_through_plots.py');
+INSERT INTO qiita.command (name, command) VALUES ('Summarize Taxa', 'summarize_taxa_through_plots.py'), ('Beta Diversity', 'beta_diversity_through_plots.py'), ('Alpha Diversity', 'alpha_rarefaction_through_plots.py');

qiita_db/support_files/populate_test_db.sql

@@ -317,19 +317,19 @@ INSERT INTO qiita.processed_filepath (processed_data_id, filepath_id) VALUES (1,
 INSERT INTO qiita.filepath (filepath, filepath_type_id, checksum, checksum_algorithm_id) VALUES ('job1result.txt', 8, '852952723', 1), ('job2tar.tar', 7, '852952723', 1);
 
 -- Insert jobs
-INSERT INTO qiita.job (data_type_id, job_status_id, command_id, options) VALUES (1, 3, 1, '{"option1":true,"option2":12,"option3":"FCM"}'), (1, 3, 2, 'options2');
+INSERT INTO qiita.job (data_type_id, job_status_id, command_id, options) VALUES (1, 1, 1, '{"option1":true,"option2":12,"option3":"FCM"}'), (1, 3, 2, 'options2'), (1, 1, 2, '{"option1":true,"option2":12,"option3":"FCM"}');
 
 -- Insert Analysis
-INSERT INTO qiita.analysis (email, name, description, analysis_status_id, pmid) VALUES ('test@foo.bar', 'SomeAnalysis', 'A test analysis', 4, '121112');
+INSERT INTO qiita.analysis (email, name, description, analysis_status_id, pmid) VALUES ('test@foo.bar', 'SomeAnalysis', 'A test analysis', 4, '121112'), ('test@foo.bar', 'SomeSecondAnalysis', 'Another test analysis', 1, '22221112');
 
 -- Attach jobs to analysis
-INSERT INTO qiita.analysis_job (analysis_id, job_id) VALUES (1, 1), (1, 2);
+INSERT INTO qiita.analysis_job (analysis_id, job_id) VALUES (1, 1), (1, 2), (2, 3);
 
 -- Attach filepath to analysis
 INSERT INTO qiita.analysis_filepath (analysis_id, filepath_id) VALUES (1, 7);
 
 -- Attach samples to analysis
-INSERT INTO qiita.analysis_sample (analysis_id, processed_data_id, sample_id) VALUES (1,1,'SKB8.640193'), (1,1,'SKD8.640184'), (1,1,'SKB7.640196'), (1,1,'SKM9.640192'), (1,1,'SKM4.640180');
+INSERT INTO qiita.analysis_sample (analysis_id, processed_data_id, sample_id) VALUES (1,1,'SKB8.640193'), (1,1,'SKD8.640184'), (1,1,'SKB7.640196'), (1,1,'SKM9.640192'), (1,1,'SKM4.640180'), (2,1,'SKB8.640193'), (2,1,'SKD8.640184'), (2,1,'SKB7.640196');
 
 --Share analysis with shared user
 INSERT INTO qiita.analysis_users (analysis_id, email) VALUES (1, 'shared@foo.bar');

qiita_db/test/test_analysis.py

@@ -35,24 +35,24 @@ def test_lock_public_running(self):
     def test_create(self):
         new = Analysis.create(User("admin@foo.bar"), "newAnalysis",
                               "A New Analysis")
-        self.assertEqual(new.id, 2)
-        sql = "SELECT * FROM qiita.analysis WHERE analysis_id = 2"
+        self.assertEqual(new.id, 3)
+        sql = "SELECT * FROM qiita.analysis WHERE analysis_id = 3"
         obs = self.conn_handler.execute_fetchall(sql)
-        self.assertEqual(obs, [[2, 'admin@foo.bar', 'newAnalysis',
+        self.assertEqual(obs, [[3, 'admin@foo.bar', 'newAnalysis',
                                 'A New Analysis', 1, None]])
 
     def test_create_parent(self):
         new = Analysis.create(User("admin@foo.bar"), "newAnalysis",
                               "A New Analysis", Analysis(1))
-        self.assertEqual(new.id, 2)
-        sql = "SELECT * FROM qiita.analysis WHERE analysis_id = 2"
+        self.assertEqual(new.id, 3)
+        sql = "SELECT * FROM qiita.analysis WHERE analysis_id = 3"
         obs = self.conn_handler.execute_fetchall(sql)
-        self.assertEqual(obs, [[2, 'admin@foo.bar', 'newAnalysis',
+        self.assertEqual(obs, [[3, 'admin@foo.bar', 'newAnalysis',
                                 'A New Analysis', 1, None]])
 
-        sql = "SELECT * FROM qiita.analysis_chain WHERE child_id = 2"
+        sql = "SELECT * FROM qiita.analysis_chain WHERE child_id = 3"
         obs = self.conn_handler.execute_fetchall(sql)
-        self.assertEqual(obs, [[1, 2]])
+        self.assertEqual(obs, [[1, 3]])
 
     def test_retrieve_owner(self):
         self.assertEqual(self.analysis.owner, "test@foo.bar")
@@ -67,6 +67,11 @@ def test_set_description(self):
         self.analysis.description = "New description"
         self.assertEqual(self.analysis.description, "New description")
 
+    def test_retrieve_samples(self):
+        exp = {1: ['SKB8.640193', 'SKD8.640184', 'SKB7.640196',
+                   'SKM9.640192', 'SKM4.640180']}
+        self.assertEqual(self.analysis.samples, exp)
+
     def test_retrieve_shared_with(self):
         self.assertEqual(self.analysis.shared_with, ["shared@foo.bar"])
 

qiita_db/test/test_job.py

@@ -55,35 +55,35 @@ def test_create(self):
         # make first job
         new = Job.create("18S", "Alpha Diversity",
                          self.options, Analysis(1))
-        self.assertEqual(new.id, 3)
+        self.assertEqual(new.id, 4)
         # make sure job inserted correctly
         obs = self.conn_handler.execute_fetchall("SELECT * FROM qiita.job "
-                                                 "WHERE job_id = 3")
-        exp = [[3, 2, 1, 3, '{"option1":false,"option2":25,"option3":"NEW"}',
+                                                 "WHERE job_id = 4")
+        exp = [[4, 2, 1, 3, '{"option1":false,"option2":25,"option3":"NEW"}',
                 None]]
         self.assertEqual(obs, exp)
         # make sure job added to analysis correctly
         obs = self.conn_handler.execute_fetchall("SELECT * FROM "
                                                  "qiita.analysis_job WHERE "
-                                                 "job_id = 3")
-        exp = [[1, 3]]
+                                                 "job_id = 4")
+        exp = [[1, 4]]
         self.assertEqual(obs, exp)
 
         # make second job with diff datatype and command to test column insert
         new = Job.create("16S", "Beta Diversity",
                          self.options, Analysis(1))
-        self.assertEqual(new.id, 4)
+        self.assertEqual(new.id, 5)
         # make sure job inserted correctly
         obs = self.conn_handler.execute_fetchall("SELECT * FROM qiita.job "
-                                                 "WHERE job_id = 4")
-        exp = [[4, 1, 1, 2, '{"option1":false,"option2":25,"option3":"NEW"}',
+                                                 "WHERE job_id = 5")
+        exp = [[5, 1, 1, 2, '{"option1":false,"option2":25,"option3":"NEW"}',
                 None]]
         self.assertEqual(obs, exp)
         # make sure job added to analysis correctly
         obs = self.conn_handler.execute_fetchall("SELECT * FROM "
                                                  "qiita.analysis_job WHERE "
-                                                 "job_id = 4")
-        exp = [[1, 4]]
+                                                 "job_id = 5")
+        exp = [[1, 5]]
         self.assertEqual(obs, exp)
 
     # def test_create_exists(self):

qiita_db/test/test_setup.py

@@ -99,19 +99,19 @@ def test_processed_filepath(self):
         self._check_count("qiita.processed_filepath", 1)
 
     def test_job(self):
-        self._check_count("qiita.job", 2)
+        self._check_count("qiita.job", 3)
 
     def test_analysis(self):
-        self._check_count("qiita.analysis", 1)
+        self._check_count("qiita.analysis", 2)
 
     def test_analysis_job(self):
-        self._check_count("qiita.analysis_job", 2)
+        self._check_count("qiita.analysis_job", 3)
 
     def test_analysis_filepath(self):
         self._check_count("qiita.analysis_filepath", 1)
 
     def test_analysis_sample(self):
-        self._check_count("qiita.analysis_sample", 5)
+        self._check_count("qiita.analysis_sample", 8)
 
     def test_analysis_users(self):
         self._check_count("qiita.analysis_users", 1)