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qiita-spots · Sep 27, 2016 · c86d37d · c86d37d
1 parent a1df204
commit c86d37d
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Showing 3 changed files with 16 additions and 12 deletions.
diff --git a/qiita_db/handlers/plugin.py b/qiita_db/handlers/plugin.py
@@ -100,15 +100,17 @@ def post(self, name, version):
             cmd_desc = self.get_argument('description')
             req_params = loads(self.get_argument('required_parameters'))
             opt_params = loads(self.get_argument('optional_parameters'))
+            outputs = self.get_argument('outputs', None)
+            if outputs:
+                outputs = loads(outputs)
             dflt_param_set = loads(self.get_argument('default_parameter_sets'))
 
             parameters = req_params
             parameters.update(opt_params)
 
             cmd = qdb.software.Command.create(
-                plugin, cmd_name, cmd_desc, parameters)
+                plugin, cmd_name, cmd_desc, parameters, outputs)
 
-            # params = opt_params
             if dflt_param_set is not None:
                 for name, vals in dflt_param_set.items():
                     qdb.software.DefaultParameters.create(name, cmd, **vals)

diff --git a/qiita_db/handlers/tests/test_plugin.py b/qiita_db/handlers/tests/test_plugin.py
@@ -77,6 +77,7 @@ def test_post(self):
             'optional_parameters': dumps({'param1': ['string', ''],
                                           'param2': ['float', '1.5'],
                                           'param3': ['boolean', 'True']}),
+            'outputs': dumps({'out1': 'BIOM'}),
             'default_parameter_sets': dumps(
                 {'dflt1': {'param1': 'test',
                            'param2': '2.4',

diff --git a/qiita_db/software.py b/qiita_db/software.py
@@ -147,7 +147,7 @@ def exists(cls, software, name):
             return qdb.sql_connection.TRN.execute_fetchlast()
 
     @classmethod
-    def create(cls, software, name, description, parameters, outputs):
+    def create(cls, software, name, description, parameters, outputs=None):
         r"""Creates a new command in the system
 
         The supported types for the parameters are:
@@ -175,7 +175,7 @@ def create(cls, software, name, description, parameters, outputs):
             format is: {parameter_name: (parameter_type, default)},
             where parameter_name, parameter_type and default are strings. If
             default is None.
-        outputs : dict
+        outputs : dict, optional
             The description of the outputs that this command generated. The
             format is: {output_name: artifact_type}
 
@@ -285,14 +285,15 @@ def create(cls, software, name, description, parameters, outputs):
                 qdb.sql_connection.TRN.add(sql_type, sql_params, many=True)
 
             # Add the outputs to the command
-            sql = """INSERT INTO qiita.command_output
-                        (name, command_id, artifact_type_id)
-                     VALUES (%s, %s, %s)"""
-            sql_args = [
-                [pname, c_id, qdb.util.convert_to_id(at, 'artifact_type')]
-                for pname, at in outputs.items()]
-            qdb.sql_connection.TRN.add(sql, sql_args, many=True)
-            qdb.sql_connection.TRN.execute()
+            if outputs:
+                sql = """INSERT INTO qiita.command_output
+                            (name, command_id, artifact_type_id)
+                         VALUES (%s, %s, %s)"""
+                sql_args = [
+                    [pname, c_id, qdb.util.convert_to_id(at, 'artifact_type')]
+                    for pname, at in outputs.items()]
+                qdb.sql_connection.TRN.add(sql, sql_args, many=True)
+                qdb.sql_connection.TRN.execute()
 
         return cls(c_id)