From 2211bbd6491d4bfabe4c73aee85abac6834af830 Mon Sep 17 00:00:00 2001
From: Michiel Cottaar <MichielCottaar@protonmail.com>
Date: Fri, 27 Mar 2020 14:06:24 +0000
Subject: [PATCH] REF: set partial_fill to False again
Still using `partial_fill` when creating FileTreeQuery
---
fsl/utils/filetree/filetree.py | 2 +-
fsl/utils/filetree/query.py | 2 ++
tests/test_filetree/test_read.py | 9 ++++++++-
3 files changed, 11 insertions(+), 2 deletions(-)
diff --git a/fsl/utils/filetree/filetree.py b/fsl/utils/filetree/filetree.py
index 3159fefa8..44f2b7b15 100644
--- a/fsl/utils/filetree/filetree.py
+++ b/fsl/utils/filetree/filetree.py
@@ -354,7 +354,7 @@ class FileTree(object):
self.variables = {}
@classmethod
- def read(cls, tree_name: str, directory='.', partial_fill=True, **variables) -> "FileTree":
+ def read(cls, tree_name: str, directory='.', partial_fill=False, **variables) -> "FileTree":
"""
Reads a FileTree from a specific file
diff --git a/fsl/utils/filetree/query.py b/fsl/utils/filetree/query.py
index a2e215c84..d371bcdf3 100644
--- a/fsl/utils/filetree/query.py
+++ b/fsl/utils/filetree/query.py
@@ -89,6 +89,8 @@ class FileTreeQuery(object):
:arg tree: The :class:`.FileTree` object
"""
+ # Hard-code into the templates any pre-defined variables
+ tree = tree.partial_fill()
# Find all files present in the directory
# (as Match objects), and find all variables,
diff --git a/tests/test_filetree/test_read.py b/tests/test_filetree/test_read.py
index 6627969e3..0ceaa5086 100644
--- a/tests/test_filetree/test_read.py
+++ b/tests/test_filetree/test_read.py
@@ -13,14 +13,21 @@ def same_path(p1, p2):
def test_simple_tree():
tree = filetree.FileTree.read('eddy')
- assert 'basename' not in tree.variables
+ assert 'basename' in tree.variables
same_path(tree.get('basename'), './eddy_output')
same_path(tree.get('image'), './eddy_output.nii.gz')
+ same_path(tree.update(basename='eddy').get('image'), './eddy.nii.gz')
tree = filetree.FileTree.read('eddy.tree', basename='out')
+ assert 'basename' in tree.variables
+ same_path(tree.get('basename'), './out')
+ same_path(tree.update(basename='eddy').get('image'), './eddy.nii.gz')
+
+ tree = filetree.FileTree.read('eddy.tree', basename='out', partial_fill=True)
assert 'basename' not in tree.variables
same_path(tree.get('basename'), './out')
+ same_path(tree.update(basename='eddy').get('image'), './out.nii.gz')
with pytest.raises(ValueError):
filetree.FileTree.read('non_existing')
--
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