diff --git a/lib/galaxy/model/mapping.py b/lib/galaxy/model/mapping.py
index 28f986ee61c..151ae354397 100644
--- a/lib/galaxy/model/mapping.py
+++ b/lib/galaxy/model/mapping.py
@@ -920,7 +920,9 @@ model.WorkflowStepInput.table = Table(
     Column("value_from_type", TEXT),
     Column("default_value", JSONType),
     Column("default_value_set", Boolean, default=False),
-    Column("runtime_value", Boolean, default=False))
+    Column("runtime_value", Boolean, default=False),
+    UniqueConstraint("workflow_step_id", "name"),
+)
 
 
 model.WorkflowRequestStepState.table = Table(
@@ -2236,7 +2238,7 @@ mapper(model.WorkflowStepInput, model.WorkflowStepInput.table, properties=dict(
     workflow_step=relation(model.WorkflowStep,
         backref=backref("inputs", uselist=True),
         cascade="all",
-        primaryjoin=(model.WorkflowStep.table.c.id == model.WorkflowStepInput.table.c.workflow_step_id))
+        primaryjoin=(model.WorkflowStepInput.table.c.workflow_step_id == model.WorkflowStep.table.c.id))
 ))
 
 mapper(model.WorkflowOutput, model.WorkflowOutput.table, properties=dict(
diff --git a/lib/galaxy/model/migrate/versions/0145_add_workflow_step_input.py b/lib/galaxy/model/migrate/versions/0145_add_workflow_step_input.py
index e9b5a01c975..d648d4b204c 100644
--- a/lib/galaxy/model/migrate/versions/0145_add_workflow_step_input.py
+++ b/lib/galaxy/model/migrate/versions/0145_add_workflow_step_input.py
@@ -5,7 +5,16 @@ from __future__ import print_function
 
 import logging
 
-from sqlalchemy import Boolean, Column, ForeignKey, Integer, MetaData, Table, TEXT
+from sqlalchemy import (
+    Boolean,
+    Column,
+    ForeignKey,
+    Integer,
+    MetaData,
+    Table,
+    TEXT,
+    UniqueConstraint
+)
 
 from galaxy.model.custom_types import JSONType
 
@@ -13,34 +22,20 @@ log = logging.getLogger(__name__)
 metadata = MetaData()
 
 
-def get_new_tables():
-
-    WorkflowStepInput_table = Table(
-        "workflow_step_input", metadata,
-        Column("id", Integer, primary_key=True),
-        Column("workflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True),
-        Column("name", TEXT),
-        Column("merge_type", TEXT),
-        Column("scatter_type", TEXT),
-        Column("value_from", JSONType),
-        Column("value_from_type", TEXT),
-        Column("default_value", JSONType),
-        Column("default_value_set", Boolean, default=False),
-        Column("runtime_value", Boolean, default=False),
-    )
-
-    WorkflowStepConnection_table = Table(
-        "workflow_step_connection", metadata,
-        Column("id", Integer, primary_key=True),
-        Column("output_step_id", Integer, ForeignKey("workflow_step.id"), index=True),
-        Column("input_step_input_id", Integer, ForeignKey("workflow_step_input.id"), index=True),
-        Column("output_name", TEXT),
-        Column("input_subworkflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True),
-    )
-
-    return [
-        WorkflowStepInput_table, WorkflowStepConnection_table
-    ]
+WorkflowStepInput_table = Table(
+    "workflow_step_input", metadata,
+    Column("id", Integer, primary_key=True),
+    Column("workflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True),
+    Column("name", TEXT),
+    Column("merge_type", TEXT),
+    Column("scatter_type", TEXT),
+    Column("value_from", JSONType),
+    Column("value_from_type", TEXT),
+    Column("default_value", JSONType),
+    Column("default_value_set", Boolean, default=False),
+    Column("runtime_value", Boolean, default=False),
+    UniqueConstraint("workflow_step_id", "name"),
+)
 
 
 def upgrade(migrate_engine):
@@ -48,57 +43,80 @@ def upgrade(migrate_engine):
     print(__doc__)
     metadata.reflect()
 
-    LegacyWorkflowStepConnection_table = Table("workflow_step_connection", metadata, autoload=True)
-    for index in LegacyWorkflowStepConnection_table.indexes:
+    OldWorkflowStepConnection_table = Table("workflow_step_connection", metadata, autoload=True)
+    for index in OldWorkflowStepConnection_table.indexes:
         index.drop()
-    LegacyWorkflowStepConnection_table.rename("workflow_step_connection_premigrate145")
+    OldWorkflowStepConnection_table.rename("workflow_step_connection_preupgrade145")
     # Try to deregister that table to work around some caching problems it seems.
-    LegacyWorkflowStepConnection_table.deregister()
+    OldWorkflowStepConnection_table.deregister()
     metadata._remove_table("workflow_step_connection", metadata.schema)
-
     metadata.reflect()
-    tables = get_new_tables()
-    for table in tables:
-        __create(table)
+
+    NewWorkflowStepConnection_table = Table(
+        "workflow_step_connection", metadata,
+        Column("id", Integer, primary_key=True),
+        Column("output_step_id", Integer, ForeignKey("workflow_step.id"), index=True),
+        Column("input_step_input_id", Integer, ForeignKey("workflow_step_input.id"), index=True),
+        Column("output_name", TEXT),
+        Column("input_subworkflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True),
+    )
+    for table in (WorkflowStepInput_table, NewWorkflowStepConnection_table):
+        _create(table)
 
     insert_step_inputs_cmd = \
         "INSERT INTO workflow_step_input (workflow_step_id, name) " + \
-        "SELECT input_step_id, input_name FROM workflow_step_connection_premigrate145"
-
+        "SELECT input_step_id, input_name FROM workflow_step_connection_preupgrade145"
     migrate_engine.execute(insert_step_inputs_cmd)
 
-    # TODO: verify order here.
     insert_step_connections_cmd = \
         "INSERT INTO workflow_step_connection (output_step_id, input_step_input_id, output_name, input_subworkflow_step_id) " + \
         "SELECT wsc.output_step_id, wsi.id, wsc.output_name, wsc.input_subworkflow_step_id " + \
-        "FROM workflow_step_connection_premigrate145 AS wsc LEFT OUTER JOIN workflow_step_input AS wsi ON wsc.input_step_id = wsi.workflow_step_id AND wsc.input_name = wsi.name ORDER BY wsc.id"
-
+        "FROM workflow_step_connection_preupgrade145 AS wsc JOIN workflow_step_input AS wsi ON wsc.input_step_id = wsi.workflow_step_id AND wsc.input_name = wsi.name ORDER BY wsc.id"
     migrate_engine.execute(insert_step_connections_cmd)
+    _drop(OldWorkflowStepConnection_table)
 
 
 def downgrade(migrate_engine):
     metadata.bind = migrate_engine
 
-    tables = get_new_tables()
-    for table in tables:
-        __drop(table)
-
+    NewWorkflowStepConnection_table = Table("workflow_step_connection", metadata, autoload=True)
+    for index in NewWorkflowStepConnection_table.indexes:
+        index.drop()
+    NewWorkflowStepConnection_table.rename("workflow_step_connection_predowngrade145")
+    # Try to deregister that table to work around some caching problems it seems.
+    NewWorkflowStepConnection_table.deregister()
     metadata._remove_table("workflow_step_connection", metadata.schema)
     metadata.reflect()
 
-    # Drop new workflow invocation step and job association table and restore legacy data.
-    LegacyWorkflowStepConnection_table = Table("workflow_step_connection_premigrate145", metadata, autoload=True)
-    LegacyWorkflowStepConnection_table.rename("workflow_step_connection")
+    OldWorkflowStepConnection_table = Table(
+        "workflow_step_connection", metadata,
+        Column("id", Integer, primary_key=True),
+        Column("output_step_id", Integer, ForeignKey("workflow_step.id"), index=True),
+        Column("input_step_id", Integer, ForeignKey("workflow_step.id"), index=True),
+        Column("output_name", TEXT),
+        Column("input_name", TEXT),
+        Column("input_subworkflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True),
+    )
+    _create(OldWorkflowStepConnection_table)
+
+    insert_step_connections_cmd = \
+        "INSERT INTO workflow_step_connection (output_step_id, input_step_id, output_name, input_name, input_subworkflow_step_id) " + \
+        "SELECT wsc.output_step_id, wsi.workflow_step_id, wsc.output_name, wsi.name, wsc.input_subworkflow_step_id " + \
+        "FROM workflow_step_connection_predowngrade145 AS wsc JOIN workflow_step_input AS wsi ON wsc.input_step_input_id = wsi.id ORDER BY wsc.id"
+    migrate_engine.execute(insert_step_connections_cmd)
+
+    for table in (WorkflowStepInput_table, NewWorkflowStepConnection_table):
+        _drop(table)
 
 
-def __create(table):
+def _create(table):
     try:
         table.create()
     except Exception:
         log.exception("Creating %s table failed.", table.name)
 
 
-def __drop(table):
+def _drop(table):
     try:
         table.drop()
     except Exception: