implement lindi.File, drop-in replacement for h5py.File that supports .lindi.json files based on extension (4) #60
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## write-json #60 +/- ##
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+ Coverage 79.95% 81.47% +1.52%
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Files 29 30 +1
Lines 2155 2208 +53
==============================================
+ Hits 1723 1799 +76
+ Misses 432 409 -23 ☔ View full report in Codecov by Sentry. |
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Here we make a lindi.File that can be a drop-in replacement for h5py.File, where it smartly decides whether to use h5py or lindi based on the file extension of the file name. This PR corrects a few small issues/mistakes from previous PRs. |
magland
commented
May 9, 2024
| @@ -52,6 +52,9 @@ def from_lindi_file(url_or_path: str, *, mode: LindiFileMode = "r", staging_area | |||
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| For a description of parameters, see from_reference_file_system(). | |||
| """ | |||
| if local_file_path is None: | |||
| if not url_or_path.startswith("http://") and not url_or_path.startswith("https://"): | |||
| local_file_path = url_or_path | |||
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Set the local file path (the one that can get edited) to be equal to the url_or_path in the case that it is not provided and is not a url
magland
commented
May 9, 2024
| @@ -166,7 +169,7 @@ def from_reference_file_system(rfs: Union[dict, str, None], *, mode: LindiFileMo | |||
| store = LindiReferenceFileSystemStore(rfs, local_cache=local_cache) | |||
| if staging_area: | |||
| store = LindiStagingStore(base_store=store, staging_area=staging_area) | |||
| return LindiH5pyFile.from_zarr_store(store, mode=mode, local_file_path=local_file_path) | |||
| return LindiH5pyFile.from_zarr_store(store, mode=mode, local_file_path=local_file_path, local_cache=local_cache) | |||
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This was accidentally omitted.
magland
commented
May 9, 2024
Comment on lines
+25
to
+45
| def create(*, base_dir: Union[str, None] = None, dir: Union[str, None] = None) -> 'StagingArea': | ||
| """ | ||
| Create a new staging area. | ||
| Create a new staging area. Provide either `base_dir` or `dir`, but not | ||
| both. | ||
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|
||
| Parameters | ||
| ---------- | ||
| base_dir : str | ||
| The base directory where the staging area will be created. The | ||
| staging directory will be a subdirectory of this directory. | ||
| base_dir : str or None | ||
| If provided, the base directory where the staging area will be | ||
| created. The staging directory will be a subdirectory of this | ||
| directory. | ||
| dir : str or None | ||
| If provided, the exact directory where the staging area will be | ||
| created. It is okay if this directory already exists. | ||
| """ | ||
| dir = os.path.join(base_dir, _create_random_id()) | ||
| if base_dir is not None and dir is not None: | ||
| raise ValueError("Provide either base_dir or dir, but not both") | ||
| if base_dir is not None: | ||
| dir = os.path.join(base_dir, _create_random_id()) | ||
| if dir is None: | ||
| raise ValueError("Provide either base_dir or dir") |
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Either supply a dir or a base_dir
magland
changed the title
rly
reviewed
May 9, 2024
…range-error catch chunk byte range error (5)
Add generation metadata to .lindi.json file writing (6)
rly
approved these changes
May 9, 2024
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