From 28a28285a7f2c6283be06d0ee5f8c3f83617cb4f Mon Sep 17 00:00:00 2001
From: Tom Close <tom.g.close@gmail.com>
Date: Wed, 15 May 2024 08:33:10 +1000
Subject: [PATCH] fixed duplicate output issue caused by replacement mapping

---
 nipype2pydra/package.py  |  4 ++--
 nipype2pydra/workflow.py | 11 ++++++++++-
 2 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/nipype2pydra/package.py b/nipype2pydra/package.py
index ded7837e..d8344e7c 100644
--- a/nipype2pydra/package.py
+++ b/nipype2pydra/package.py
@@ -365,10 +365,10 @@ def write(self, package_root: Path, to_include: ty.List[str] = None):
 
         nipype_ports = []
 
-        for workflow in tqdm(workflows_to_include, "preparing workflows for writing"):
+        for workflow in tqdm(workflows_to_include, "parsing workflow statements"):
             workflow.prepare()
 
-        for workflow in tqdm(workflows_to_include, "preparing workflow connections"):
+        for workflow in tqdm(workflows_to_include, "processing workflow connections"):
             workflow.prepare_connections()
 
         def collect_intra_pkg_objects(used: UsedSymbols, port_nipype: bool = True):
diff --git a/nipype2pydra/workflow.py b/nipype2pydra/workflow.py
index 29c6efe4..16ad4a9e 100644
--- a/nipype2pydra/workflow.py
+++ b/nipype2pydra/workflow.py
@@ -1056,6 +1056,7 @@ def _parse_statements(self, func_body: str) -> ty.Tuple[
         statements = split_source_into_statements(func_body)
 
         parsed = []
+        outputs = []
         workflow_init = None
         workflow_init_index = None
         assignments = defaultdict(list)
@@ -1104,7 +1105,15 @@ def _parse_statements(self, func_body: str) -> ty.Tuple[
                 conn_stmts = ConnectionStatement.parse(statement, self, assignments)
                 for conn_stmt in conn_stmts:
                     self._unprocessed_connections.append(conn_stmt)
-                    if conn_stmt.wf_out or not conn_stmt.lzouttable:
+                    if conn_stmt.wf_out:
+                        if conn_stmt.conditional:
+                            parsed.append(conn_stmt)
+                        else:
+                            outpt = self.get_output_from_conn(conn_stmt)
+                            if outpt not in outputs:
+                                parsed.append(conn_stmt)
+                                outputs.append(outpt)
+                    elif not conn_stmt.lzouttable:
                         parsed.append(conn_stmt)
                 parsed_stmt = conn_stmts[-1]
             elif ReturnStatement.matches(statement):