def update(self) -> None:
"""Method to update the file contents, latex subfile, and metadata file.
Returns:
"""
if self._is_modified():
if self._should_copy_file() is True:
# Copy file if needed
shutil.copyfile(Path(Gigantum.get_project_root(), self.metadata.gigantum_relative_path),
self.data_filename)
# Update commit hash in metadata
kwargs = {"content_hash": self._hash_file(Path(Gigantum.get_project_root(),
self.metadata.gigantum_relative_path).absolute().as_posix()),
"metadata_filename": self.metadata_filename}
self.write_metadata(**kwargs)
# Latex subfile
self.write_subfile()
def _is_modified(self) -> bool:
"""Helper method to check if a file has been modified since the last time you ran .sync()
Returns:
true if the file has changed since the last time you ran .sync(), false if it has not
"""
if self.metadata.content_hash != self._hash_file(Path(Gigantum.get_project_root(),
self.metadata.gigantum_relative_path).absolute().as_posix()):
return True
else:
return False
def write_subfile(self) -> None:
"""Method to write the Latex subfile
Returns:
None
"""
if not isinstance(self.metadata, DataframeFileMetadata):
raise ValueError(
f"Incorrect metadata type loaded: {type(self.metadata)}")
if pandas is None:
raise EnvironmentError(
"Dataframe pickle file support requires pandas. "
"Please run `pip install gigaleaf[pandas]`")
subfile_template = Template(
r"""\documentclass[../../main.tex]{subfiles}
% Subfile autogenerated by gigaleaf
% Gigantum revision: $gigantum_version
% Image content hash: $content_hash
\begin{document}
{$table}
\end{document}
""")
with open(
Path(Gigantum.get_project_root(),
self.metadata.gigantum_relative_path).absolute().as_posix(
), 'rb') as f:
df = pandas.read_pickle(f)
table = df.to_latex(**self.metadata.to_latex_kwargs)
filename = "gigantum/data/" + Path(
self.metadata.gigantum_relative_path).name
subfile_populated = subfile_template.substitute(
filename=filename,
gigantum_version=Gigantum.get_current_revision(),
content_hash=self.metadata.content_hash,
table=table)
Path(self.subfile_filename).write_text(subfile_populated)
def link(cls, relative_path: str, **kwargs: Dict[str, Any]) -> None:
"""Method to link a file output in a Gigantum Project to an Overleaf project
Args:
relative_path: relative path to the file from the current working dir, e.g. `../output/my_fig.png`
**kwargs: args specific to each LinkedFile implementation
Returns:
None
"""
file_path = Path(relative_path).resolve()
if file_path.is_file() is False:
# File provided does not exist
raise ValueError(f"The file {file_path} does not exist. Provide a relative path from the working"
f"directory to your file. In Jupyter, the working directory is the directory containing "
f"your notebook.")
metadata_filename = cls.get_metadata_filename(relative_path)
metadata_abs_filename = Path(Gigantum.get_overleaf_root_directory(),
'project', 'gigantum', 'metadata', metadata_filename)
if metadata_abs_filename.exists() is True:
# This is an update to the link, so get the current content hash for the file.
with open(metadata_abs_filename, 'rt') as mf:
current_metadata: Dict[str, Any] = json.load(mf)
content_hash = current_metadata['content_hash']
else:
# Set content hash to init so it is always detected as "modified" on first link
content_hash = "init"
full_kwargs = {
"gigantum_relative_path": file_path.relative_to(Path(Gigantum.get_project_root()).resolve()).as_posix(),
"gigantum_version": Gigantum.get_current_revision(),
"classname": cls.__name__,
"content_hash": content_hash,
"metadata_filename": metadata_filename}
full_kwargs.update(kwargs)
cls.write_metadata(**full_kwargs)
def test_update_image(self, gigantum_project_fixture):
gigaleaf = Gigaleaf()
assert Path(Gigantum.get_overleaf_root_directory(), 'project',
'gigantum', 'metadata', 'fig1_png.json').is_file() is False
gigaleaf.link_image('../output/fig1.png', width='0.8\\textwidth')
assert Path(Gigantum.get_overleaf_root_directory(), 'project',
'gigantum', 'metadata', 'fig1_png.json').is_file() is True
gigaleaf.sync()
assert Path(Gigantum.get_overleaf_root_directory(), 'project',
'gigantum', 'data', 'fig1.png').is_file() is True
metadata_file = Path(Gigantum.get_overleaf_root_directory(), 'project',
'gigantum', 'metadata', 'fig1_png.json')
with open(metadata_file, 'rt') as mf:
data = json.load(mf)
first_hash = data['content_hash']
test_dir = Path(__file__).parent.absolute()
shutil.copyfile(
Path(test_dir, 'resources', 'fig1.png').as_posix(),
Path(Gigantum.get_project_root(), 'output', 'fig1.png'))
gigaleaf.sync()
metadata_file = Path(Gigantum.get_overleaf_root_directory(), 'project',
'gigantum', 'metadata', 'fig1_png.json')
with open(metadata_file, 'rt') as mf:
data = json.load(mf)
assert first_hash != data['content_hash']