Merge pull request #108 from squirrelo/jobtweaks

tweak job commands

qiita_db/job.py

@@ -58,7 +58,7 @@ def exists(cls, datatype, command, options):
         datatype : str
             Datatype the job is operating on
         command : str
-            The command run on the data
+            The name of the command run on the data
         options : dict
             Options for the command in the format {option: value}
 
@@ -67,12 +67,13 @@ def exists(cls, datatype, command, options):
         bool
             Whether the job exists or not
         """
-        sql = ("SELECT EXISTS(SELECT * FROM  qiita.{0} WHERE data_type_id = %s"
-               " AND command_id = %s AND options = %s)".format(cls._table))
         conn_handler = SQLConnectionHandler()
         datatype_id = convert_to_id(datatype, "data_type", conn_handler)
-        command_id = convert_to_id(command, "command", conn_handler)
+        sql = "SELECT command_id FROM qiita.command WHERE name = %s"
+        command_id = conn_handler.execute_fetchone(sql, (command, ))[0]
         opts_json = dumps(options, sort_keys=True, separators=(',', ':'))
+        sql = ("SELECT EXISTS(SELECT * FROM  qiita.{0} WHERE data_type_id = %s"
+               " AND command_id = %s AND options = %s)".format(cls._table))
         return conn_handler.execute_fetchone(
             sql, (datatype_id, command_id, opts_json))[0]
 
@@ -104,7 +105,8 @@ def create(cls, datatype, command, options, analysis):
         # Get the datatype and command ids from the strings
         conn_handler = SQLConnectionHandler()
         datatype_id = convert_to_id(datatype, "data_type", conn_handler)
-        command_id = convert_to_id(command, "command", conn_handler)
+        sql = "SELECT command_id FROM qiita.command WHERE name = %s"
+        command_id = conn_handler.execute_fetchone(sql, (command, ))[0]
 
         # JSON the options dictionary
         opts_json = dumps(options, sort_keys=True, separators=(',', ':'))
@@ -139,18 +141,18 @@ def datatype(self):
 
     @property
     def command(self):
-        """Returns the command of the job
+        """Returns the command of the job as (name, command)
 
         Returns
         -------
         str
             command run by the job
         """
-        sql = ("SELECT command from qiita.command WHERE command_id = "
+        sql = ("SELECT name, command from qiita.command WHERE command_id = "
                "(SELECT command_id from qiita.{0} WHERE "
                "job_id = %s)".format(self._table))
         conn_handler = SQLConnectionHandler()
-        return conn_handler.execute_fetchone(sql, (self._id, ))[0]
+        return conn_handler.execute_fetchone(sql, (self._id, ))
 
     @property
     def options(self):

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 through plots', 'summarize_taxa_through_plots.py'), ('Beta diversity through plots', 'beta_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_diversity_through_plots.py');

qiita_db/test/test_job.py

@@ -39,20 +39,20 @@ def tearDown(self):
 
     def test_exists(self):
         """tests that existing job returns true"""
-        self.assertTrue(Job.exists("16S", "summarize_taxa_through_plots.py",
+        self.assertTrue(Job.exists("16S", "Summarize Taxa",
                                    {'option1': True, 'option2': 12,
                                     'option3': 'FCM'}))
 
     def test_exists_not_there(self):
         """tests that non-existant job returns false"""
         self.assertFalse(Job.exists("Metabolomic",
-                                    "summarize_taxa_through_plots.py",
+                                    "Summarize Taxa",
                                     {'option1': "Nope", 'option2': 10,
                                      'option3': 'FCM'}))
 
     def test_create(self):
         """Makes sure creation works as expected"""
-        new = Job.create("18S", "beta_diversity_through_plots.py",
+        new = Job.create("18S", "Beta Diversity",
                          self.options, Analysis(1))
         self.assertEqual(new.id, 3)
         # make sure job inserted correctly
@@ -71,7 +71,7 @@ def test_create(self):
     def test_create_exists(self):
         """Makes sure creation doesn't duplicate a job"""
         with self.assertRaises(QiitaDBDuplicateError):
-            Job.create("16S", "summarize_taxa_through_plots.py",
+            Job.create("16S", "Summarize Taxa",
                        {'option1': True, 'option2': 12, 'option3': 'FCM'},
                        Analysis(1))
 
@@ -81,7 +81,8 @@ def test_retrieve_datatype(self):
 
     def test_retrieve_command(self):
         """Makes sure command retriveal is correct"""
-        self.assertEqual(self.job.command, 'summarize_taxa_through_plots.py')
+        self.assertEqual(self.job.command, ['Summarize Taxa',
+                                            'summarize_taxa_through_plots.py'])
 
     def test_retrieve_options(self):
         self.assertEqual(self.job.options, {'option1': True, 'option2': 12,
@@ -97,7 +98,7 @@ def test_retrieve_results(self):
         self.assertTrue(exists(join(get_work_base_dir(), "job1result.txt")))
 
     def test_retrieve_results_blank(self):
-        new = Job.create("18S", "beta_diversity_through_plots.py",
+        new = Job.create("18S", "Beta Diversity",
                          self.options, Analysis(1))
         obs = new.results
         self._delete_path = obs