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Commit c5a6fddb authored by r.jaepel's avatar r.jaepel
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Remove output_remotes.json

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cadetrdm/initialize_repo.py
+ 9
− 12
View file @ c5a6fddb
......@@ -67,12 +67,13 @@ def initialize_repo(path_to_repo: str | Path, output_folder_name: (str | bool) =
create_readme()
create_environment_yml()
ProjectRepo.add_jupytext_file()
ProjectRepo._add_jupytext_file()
rdm_data = {
"is_project_repo": True, "is_output_repo": False,
"project_uuid": project_repo_uuid, "output_uuid": output_repo_uuid,
"cadet_rdm_version": cadetrdm.__version__
"cadet_rdm_version": cadetrdm.__version__,
"output_remotes": {"output_folder_name": output_folder_name, "output_remotes": {}}
}
with open(".cadet-rdm-data.json", "w") as f:
json.dump(rdm_data, f, indent=2)
......@@ -85,11 +86,6 @@ def initialize_repo(path_to_repo: str | Path, output_folder_name: (str | bool) =
"commit_hash": "6e3c26527999036e9490d2d86251258fe81d46dc"
}}, f, indent=2)
with open("output_remotes.json", "w") as file_handle:
remotes_dict = {}
json_dict = {"output_folder_name": output_folder_name, "output_remotes": remotes_dict}
json.dump(json_dict, file_handle, indent=2)
initialize_output_repo(output_folder_name, project_repo_uuid=project_repo_uuid,
output_repo_uuid=output_repo_uuid, **output_repo_kwargs)
......@@ -103,7 +99,7 @@ def initialize_repo(path_to_repo: str | Path, output_folder_name: (str | bool) =
".gitattributes",
"environment.yml",
"jupytext.yml",
"output_remotes.json"]
]
for file in files:
repo._git.add(file)
......@@ -226,15 +222,16 @@ def clone(project_url, path_to_repo: str = None):
path_to_repo = Path(path_to_repo)
# Clone output repo from remotes
json_path = path_to_repo / "output_remotes.json"
json_path = path_to_repo / ".cadet-rdm-data.json"
with open(json_path, "r") as file_handle:
meta_dict = json.load(file_handle)
output_remotes = meta_dict["output_remotes"]
output_folder_name = path_to_repo / meta_dict["output_folder_name"]
ssh_remotes = list(meta_dict["output_remotes"].values())
output_folder_name = path_to_repo / output_remotes["output_folder_name"]
ssh_remotes = list(output_remotes["output_remotes"].values())
http_remotes = [ssh_url_to_http_url(url) for url in ssh_remotes]
if len(ssh_remotes + http_remotes) == 0:
raise RuntimeError("No output remotes configured in output_remotes.json")
raise RuntimeError("No output remotes configured in .cadet-rdm-data.json")
for output_remote in ssh_remotes + http_remotes:
try:
print(f"Attempting to clone {output_remote} into {output_folder_name}")
......
cadetrdm/repositories.py
+ 46
− 32
View file @ c5a6fddb
......@@ -572,6 +572,7 @@ class BaseRepo:
with open(readme_filepath, "w") as file_handle:
file_handle.writelines(filelines)
self.add(readme_filepath)
class ProjectRepo(BaseRepo):
......@@ -597,32 +598,37 @@ class ProjectRepo(BaseRepo):
"""
super().__init__(repository_path, search_parent_directories=search_parent_directories, *args, **kwargs)
with open(self.path / "output_remotes.json", "r") as handle:
try:
output_remotes = json.load(handle)
except FileNotFoundError:
raise RuntimeError(f"Folder {self.path} does not appear to be a CADET-RDM repository.")
if output_folder is not None:
print("Deprecation Warning. Setting the outputfolder manually during repo instantiation is deprecated"
" and will be removed in a future update.")
self._output_folder = output_remotes["output_folder_name"]
self._output_repo = OutputRepo(self.path / self._output_folder)
if not self.data_json_path.exists():
raise RuntimeError(f"Folder {self.path} does not appear to be a CADET-RDM repository.")
with open(self.data_json_path, "r") as handle:
metadata = json.load(handle)
repo_version = metadata["cadet_rdm_version"]
cadetrdm_version = cadetrdm.__version__
if cadetrdm_version != repo_version:
print(f"Repo version {repo_version} is outdated. Current CADET-RDM version is {cadetrdm_version}\n"
"Updating the repository now.")
self.update_version(repo_version)
metadata["cadet_rdm_version"] = cadetrdm_version
with open(self.data_json_path, "w") as f:
json.dump(metadata, f, indent=2)
self.add(self.data_json_path)
self.commit("update cadetrdm version", add_all=False)
if "output_remotes" not in metadata:
# 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:
output_remotes = json.load(handle)
metadata["output_remotes"] = output_remotes
self._output_folder = metadata["output_remotes"]["output_folder_name"]
self._output_repo = OutputRepo(self.path / self._output_folder)
repo_version = metadata["cadet_rdm_version"]
cadetrdm_version = cadetrdm.__version__
if cadetrdm_version != repo_version:
print(f"Repo version {repo_version} is outdated. Current CADET-RDM version is {cadetrdm_version}\n"
"Updating the repository now.")
self._update_version(repo_version)
metadata["cadet_rdm_version"] = cadetrdm_version
with open(self.data_json_path, "w") as f:
json.dump(metadata, f, indent=2)
self.add(self.data_json_path)
self.commit("update cadetrdm version", add_all=False)
self._on_context_enter_commit_hash = None
self._is_in_context_manager = False
......@@ -634,17 +640,20 @@ class ProjectRepo(BaseRepo):
raise ValueError("The output repo has not been set yet.")
return self._output_repo
def update_version(self, current_version):
def _update_version(self, current_version):
major, minor, patch = [int(x) for x in current_version.split(".")]
version_sum = major * 1000 * 1000 + minor * 1000 + patch
if version_sum < 9:
self.convert_csv_to_tsv_if_necessary()
self.add_jupytext_file(self.path)
self._convert_csv_to_tsv_if_necessary()
self._add_jupytext_file(self.path)
if version_sum < 24:
self.expand_tsv_header()
self._expand_tsv_header()
output_remotes_path = self.path / "output_remotes.json"
delete_path(output_remotes_path)
self.add(output_remotes_path)
@staticmethod
def add_jupytext_file(path_root: str | Path = "."):
def _add_jupytext_file(path_root: str | Path = "."):
jupytext_lines = ['# Pair ipynb notebooks to py:percent text notebooks', 'formats: "ipynb,py:percent"']
write_lines_to_file(Path(path_root) / "jupytext.yml", lines=jupytext_lines, open_type="w")
......@@ -738,7 +747,7 @@ class ProjectRepo(BaseRepo):
def print_results_log(self):
self.output_repo.print_output_log()
def expand_tsv_header(self):
def _expand_tsv_header(self):
if not self.results_log_file.exists():
return
......@@ -762,7 +771,7 @@ class ProjectRepo(BaseRepo):
self.output_repo.add(self.results_log_file)
self.output_repo.commit("Update tsv header", add_all=False)
def convert_csv_to_tsv_if_necessary(self):
def _convert_csv_to_tsv_if_necessary(self):
"""
If not tsv log is found AND a csv log is found, convert the csv to tsv.
......@@ -888,12 +897,17 @@ class ProjectRepo(BaseRepo):
def update_output_remotes_json(self):
output_repo_remotes = self.output_repo.remote_urls
self.add_list_of_remotes_in_readme_file("output_repo", output_repo_remotes)
self.add(self.path / "README.md")
output_json_filepath = self.path / "output_remotes.json"
with open(output_json_filepath, "w") as file_handle:
remotes_dict = {remote.name: str(remote.url) for remote in self.output_repo.remotes}
json_dict = {"output_folder_name": self._output_folder, "output_remotes": remotes_dict}
json.dump(json_dict, file_handle, indent=2)
with open(self.data_json_path, "r") 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:
json.dump(metadata, file_handle, indent=2)
self.add(self.data_json_path)
def download_file(self, url, file_path):
"""
......
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