From 27d4959c1064871e5a58ddbf5542ade43f235e7d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Henrik=20tom=20W=C3=B6rden?= <henrik@trineo.org>
Date: Wed, 21 Jul 2021 07:29:04 +0200
Subject: [PATCH] MAINT: allow default root_name
---
integrationtests/example_hdf5cfood.py | 4 +++-
integrationtests/insert_model.py | 4 ++--
src/caosadvancedtools/cfoods/h5.py | 18 ++++++++++--------
3 files changed, 15 insertions(+), 11 deletions(-)
diff --git a/integrationtests/example_hdf5cfood.py b/integrationtests/example_hdf5cfood.py
index f369f852..5485402d 100644
--- a/integrationtests/example_hdf5cfood.py
+++ b/integrationtests/example_hdf5cfood.py
@@ -34,7 +34,9 @@ from caosadvancedtools.scifolder.generic_pattern import readme_pattern
class ExampleH5CFood(H5CFood):
- root_name = "ExampleH5"
+ def __init__(self, *args, **kwargs):
+ super().__init__(*args, **kwargs)
+ self.root_name = "ExampleH5"
@staticmethod
def get_re():
diff --git a/integrationtests/insert_model.py b/integrationtests/insert_model.py
index f57ea440..ae3dd770 100755
--- a/integrationtests/insert_model.py
+++ b/integrationtests/insert_model.py
@@ -15,8 +15,8 @@ if len(db.execute_query("FIND Property alias")) == 0:
h5model = db.Container()
h5file = h5py.File('extroot/ExperimentalData/2010_TestProject/2019-02-03/hdf5_dummy_file.hdf5', 'r')
-H5CFood.create_structure(h5file, create_recordTypes=True, collection=h5model)
-h5model[0].name = "ExampleH5"
+H5CFood.create_structure(h5file, create_recordTypes=True, collection=h5model,
+ root_name="ExampleH5")
print(h5model)
h5model = DataModel(h5model)
h5model.sync_data_model(noquestion=True)
diff --git a/src/caosadvancedtools/cfoods/h5.py b/src/caosadvancedtools/cfoods/h5.py
index 0e56da71..543ac327 100644
--- a/src/caosadvancedtools/cfoods/h5.py
+++ b/src/caosadvancedtools/cfoods/h5.py
@@ -112,20 +112,17 @@ class H5CFood(AbstractFileCFood):
Attributes
----------
- root_name : str, default "root"
- Type of the root Record (the Record corresponding to the root node in
- the HDF5 file)
h5file : h5py.File, default None
Name of the hdf5-file to read
"""
# to be overwritten by subclasses
- root_name = "root"
def __init__(self, *args, **kwargs):
"""CFood which consumes HDF5 files."""
super().__init__(*args, **kwargs)
self.h5file = None
+ self.root_name = "root"
self.hdf5Container = db.Container()
self.em = EntityMapping()
@@ -152,7 +149,8 @@ class H5CFood(AbstractFileCFood):
"""
# manually create the identifiable root element: self.identifiable_root
self.structure = self.create_structure(self.h5file,
- special_treatment=self.special_treatment)
+ special_treatment=self.special_treatment,
+ root_name=self.root_name)
def update_identifiables(self):
"""Check if the identifiables need to be updated.
@@ -198,7 +196,7 @@ class H5CFood(AbstractFileCFood):
@classmethod
def create_structure(cls, h5obj, create_recordTypes=False, collection=None,
- special_treatment=None):
+ special_treatment=None, root_name="root"):
"""Create Records and Record types from a given hdf5-object for all
items in the tree. Attributes are added as properties, the
values only if the dimension < 2.
@@ -206,7 +204,11 @@ class H5CFood(AbstractFileCFood):
Parameters
----------
h5obj : h5py.File
- a hdf5-file object
+ a hdf5-file object
+
+ root_name : name that is used instead of '/'
+ Type of the root Record (the Record corresponding to
+ the root node in the HDF5 file)
Returns
-------
@@ -223,7 +225,7 @@ class H5CFood(AbstractFileCFood):
def special_treatment(x, y, z): return x, y, z
if h5obj.name == "/":
- name_without_path = cls.root_name
+ name_without_path = root_name
else:
name_without_path = h5obj.name.split("/")[-1]
--
GitLab