add _helper_update_children

Author: antgonza

qiita_db/processing_job.py

@@ -1311,8 +1311,12 @@ def _complete_artifact_definition(self, artifact_data):
                     data_type=data_type, name=job_params['name'])
                 self._set_status('success')
 
-                if list(self.children):
-                    self._update_and_launch_children({atype: artifact.id})
+                # we need to update the children jobs to replace the input
+                # for the newly created artifact via the validator
+                for c in self.children:
+                    self._helper_update_children({atype: artifact.id})
+
+                    self._update_and_launch_children()
 
     def _complete_artifact_transformation(self, artifacts_data):
         """Performs the needed steps to complete an artifact transformation job
@@ -1682,6 +1686,42 @@ def validator_jobs(self):
             for jid in qdb.sql_connection.TRN.execute_fetchflatten():
                 yield ProcessingJob(jid)
 
+    def _helper_update_children(self, new_map):
+        ready = []
+        sql = """SELECT command_parameters, pending
+                 FROM qiita.processing_job
+                 WHERE processing_job_id = %s"""
+        sql_update = """UPDATE qiita.processing_job
+                        SET command_parameters = %s,
+                            pending = %s
+                        WHERE processing_job_id = %s"""
+        sql_link = """INSERT INTO qiita.artifact_processing_job
+                        (artifact_id, processing_job_id)
+                      VALUES (%s, %s)"""
+
+        for c in self.children:
+            qdb.sql_connection.TRN.add(sql, [c.id])
+            params, pending = qdb.sql_connection.TRN.execute_fetchflatten()
+            for pname, out_name in pending[self.id].items():
+                a_id = new_map[out_name]
+                params[pname] = str(a_id)
+                del pending[self.id]
+                # Link the input artifact with the child job
+                qdb.sql_connection.TRN.add(sql_link, [a_id, c.id])
+
+            # Force to insert a NULL in the DB if pending is empty
+            pending = pending if pending else None
+            qdb.sql_connection.TRN.add(sql_update,
+                                       [dumps(params), pending, c.id])
+            qdb.sql_connection.TRN.execute()
+
+            if pending is None:
+                # The child already has all the parameters
+                # Add it to the ready list
+                ready.append(c)
+
+        return ready
+
     def _update_children(self, mapping):
         """Updates the children of the current job to populate the input params
 
@@ -1695,7 +1735,6 @@ def _update_children(self, mapping):
         list of qiita_db.processing_job.ProcessingJob
             The list of childrens that are ready to be submitted
         """
-        ready = []
         with qdb.sql_connection.TRN:
             sql = """SELECT command_output_id, name
                      FROM qiita.command_output
@@ -1705,37 +1744,7 @@ def _update_children(self, mapping):
             res = qdb.sql_connection.TRN.execute_fetchindex()
             new_map = {name: mapping[oid] for oid, name in res}
 
-            sql = """SELECT command_parameters, pending
-                     FROM qiita.processing_job
-                     WHERE processing_job_id = %s"""
-            sql_update = """UPDATE qiita.processing_job
-                            SET command_parameters = %s,
-                                pending = %s
-                            WHERE processing_job_id = %s"""
-            sql_link = """INSERT INTO qiita.artifact_processing_job
-                            (artifact_id, processing_job_id)
-                          VALUES (%s, %s)"""
-            for c in self.children:
-                qdb.sql_connection.TRN.add(sql, [c.id])
-                params, pending = qdb.sql_connection.TRN.execute_fetchflatten()
-                for pname, out_name in pending[self.id].items():
-                    a_id = new_map[out_name]
-                    params[pname] = str(a_id)
-                    del pending[self.id]
-                    # Link the input artifact with the child job
-                    qdb.sql_connection.TRN.add(sql_link, [a_id, c.id])
-
-                # Force to insert a NULL in the DB if pending is empty
-                pending = pending if pending else None
-                qdb.sql_connection.TRN.add(sql_update,
-                                           [dumps(params), pending, c.id])
-                qdb.sql_connection.TRN.execute()
-
-                if pending is None:
-                    # The child already has all the parameters
-                    # Add it to the ready list
-                    ready.append(c)
-        return ready
+        return self._helper_update_children(new_map)
 
     def _update_and_launch_children(self, mapping):
         """Updates the children of the current job to populate the input params