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Merged
hannahlanzrath merged 1 commit into from
Jul 29, 2025
Merged

Explicitely set UTF-8 encoding for opening Files #86

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42 changes: 21 additions & 21 deletions cadetrdm/repositories.py
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@


def validate_is_output_repo(path_to_repo):
with open(os.path.join(path_to_repo, ".cadet-rdm-data.json"), "r") as file_handle:
with open(os.path.join(path_to_repo, ".cadet-rdm-data.json"), "r", encoding="utf-8") as file_handle:
rdm_data = json.load(file_handle)
if rdm_data["is_project_repo"]:
raise ValueError("Please use the URL to the output repository.")
Expand Down Expand Up @@ -533,12 +533,12 @@ def __init__(self, path=None, search_parent_directories=True, *args, **kwargs):
self._metadata = self.load_metadata()

def load_metadata(self):
with open(self.data_json_path, "r") as handle:
with open(self.data_json_path, "r", encoding="utf-8") as handle:
metadata = json.load(handle)
if "output_remotes" not in metadata and metadata["is_project_repo"]:
# this enables upgrades from v0.0.23 to v0.0.24.
output_remotes_path = self.path / "output_remotes.json"
with open(output_remotes_path, "r") as handle:
with open(output_remotes_path, "r", encoding="utf-8") as handle:
output_remotes = json.load(handle)
metadata["output_remotes"] = output_remotes
return metadata
Expand Down Expand Up @@ -623,12 +623,12 @@ def add_path_to_gitignore(self, path_to_be_ignored):
:return:
"""
path_to_be_ignored = self.ensure_relative_path(path_to_be_ignored)
with open(self.path / ".gitignore", "r") as file_handle:
with open(self.path / ".gitignore", "r", encoding="utf-8") as file_handle:
gitignore = file_handle.readlines()
gitignore[-1] += "\n" # Sometimes there is no trailing newline
if str(path_to_be_ignored) + "\n" not in gitignore:
gitignore.append(str(path_to_be_ignored) + "\n")
with open(self.path / ".gitignore", "w") as file_handle:
with open(self.path / ".gitignore", "w", encoding="utf-8") as file_handle:
file_handle.writelines(gitignore)

def update_cadet_rdm_cache_json(self, source_repo_location, source_repo_branch, target_repo_location):
Expand All @@ -643,10 +643,10 @@ def update_cadet_rdm_cache_json(self, source_repo_location, source_repo_branch,
Path where to put the repo or data
"""
if not self.cache_json_path.exists():
with open(self.cache_json_path, "w") as file_handle:
with open(self.cache_json_path, "w", encoding="utf-8") as file_handle:
file_handle.writelines("{}")

with open(self.cache_json_path, "r") as file_handle:
with open(self.cache_json_path, "r", encoding="utf-8") as file_handle:
rdm_cache = json.load(file_handle)

repo = GitRepo(target_repo_location)
Expand All @@ -665,7 +665,7 @@ def update_cadet_rdm_cache_json(self, source_repo_location, source_repo_branch,
"commit_hash": commit_hash,
}

with open(self.cache_json_path, "w") as file_handle:
with open(self.cache_json_path, "w", encoding="utf-8") as file_handle:
json.dump(rdm_cache, file_handle, indent=2)

def verify_unchanged_cache(self):
Expand All @@ -677,7 +677,7 @@ def verify_unchanged_cache(self):
:return:
"""

with open(self.cache_json_path, "r") as file_handle:
with open(self.cache_json_path, "r", encoding="utf-8") as file_handle:
rdm_cache = json.load(file_handle)

if "__example/path/to/repo__" in rdm_cache.keys():
Expand Down Expand Up @@ -752,7 +752,7 @@ def add_list_of_remotes_in_readme_file(self, repo_identifier: str, remotes_url_l
f" link to the {repo_identifier}. "
"Can't automatically update the link.")

with open(readme_filepath, "w") as file_handle:
with open(readme_filepath, "w", encoding="utf-8") as file_handle:
file_handle.writelines(filelines)
self.add(readme_filepath)

Expand Down Expand Up @@ -867,17 +867,17 @@ def _update_version(self, metadata, cadetrdm_version):
print(f"Repo version {metadata['cadet_rdm_version']} was outdated. "
f"Current CADET-RDM version is {cadetrdm.__version__}.\n Repo has been updated")
metadata["cadet_rdm_version"] = cadetrdm_version
with open(self.data_json_path, "w") as f:
with open(self.data_json_path, "w", encoding="utf-8") as f:
json.dump(metadata, f, indent=2)
self.add(self.data_json_path)
self.commit("update cadetrdm version", add_all=False)

def fix_gitattributes_log_tsv(self):
file = self.output_path / ".gitattributes"
with open(file) as handle:
with open(file, encoding="utf-8") as handle:
lines = handle.readlines()
lines = [line.replace("rdm-log.tsv", "log.tsv") for line in lines]
with open(file, "w") as handle:
with open(file, "w", encoding="utf-8") as handle:
handle.writelines(lines)
self.output_repo.add(".gitattributes")
self.output_repo.commit("Update gitattributes")
Expand Down Expand Up @@ -973,7 +973,7 @@ def fill_data_from_cadet_rdm_json(self, re_load=False):
:return:
"""

with open(self.cache_json_path, "r") as file_handle:
with open(self.cache_json_path, "r", encoding="utf-8") as file_handle:
rdm_cache = json.load(file_handle)

if "__example/path/to/repo__" in rdm_cache.keys():
Expand Down Expand Up @@ -1007,7 +1007,7 @@ def _expand_tsv_header(self):
if not self.output_log_file.exists():
return

with open(self.output_log_file, "r") as f:
with open(self.output_log_file, "r", encoding="utf-8") as f:
lines = f.readlines()

new_header = [
Expand All @@ -1020,7 +1020,7 @@ def _expand_tsv_header(self):
"Python sys args",
"Tags",
"Options hash", ]
with open(self.output_log_file, "w") as f:
with open(self.output_log_file, "w", encoding="utf-8") as f:
f.writelines(["\t".join(new_header) + "\n"])
f.writelines(lines[1:])

Expand All @@ -1042,12 +1042,12 @@ def _convert_csv_to_tsv_if_necessary(self):
# We have just initialized the repo and neither tsv nor csv exist.
return

with open(csv_filepath) as csv_handle:
with open(csv_filepath, encoding="utf-8") as csv_handle:
csv_lines = csv_handle.readlines()

tsv_lines = [line.replace(",", "\t") for line in csv_lines]

with open(self.output_log_file, "w") as f:
with open(self.output_log_file, "w", encoding="utf-8") as f:
f.writelines(tsv_lines)

write_lines_to_file(path=self.path / ".gitattributes",
Expand Down Expand Up @@ -1092,7 +1092,7 @@ def update_output_main_logs(self, output_dict: dict = None):
**output_dict
)

with open(json_filepath, "w") as f:
with open(json_filepath, "w", encoding="utf-8") as f:
json.dump(entry.to_dict(), f, indent=2)

log = OutputLog(self.output_log_file)
Expand Down Expand Up @@ -1165,13 +1165,13 @@ def update_output_remotes_json(self):
output_repo_remotes = self.output_repo.remote_urls
self.add_list_of_remotes_in_readme_file("Link to Output Repository", output_repo_remotes)

with open(self.data_json_path, "r") as file_handle:
with open(self.data_json_path, "r", encoding="utf-8") as file_handle:
metadata = json.load(file_handle)

remotes_dict = {remote.name: str(remote.url) for remote in self.output_repo.remotes}
metadata["output_remotes"] = {"output_folder_name": self._output_folder, "output_remotes": remotes_dict}

with open(self.data_json_path, "w") as file_handle:
with open(self.data_json_path, "w", encoding="utf-8") as file_handle:
json.dump(metadata, file_handle, indent=2)

self.add(self.data_json_path)
Expand Down
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