From d9144e3bc03b33bdb14a6db85481e09e82c90b96 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Mon, 1 Jul 2024 02:49:49 +0000 Subject: [PATCH] Update documentation --- _modules/kerchunk/hdf.html | 45 ++++++++++++++++++++++++++++++++++---- reference.html | 14 +++++++++--- searchindex.js | 2 +- 3 files changed, 53 insertions(+), 8 deletions(-) diff --git a/_modules/kerchunk/hdf.html b/_modules/kerchunk/hdf.html index 886e135c..7bb5fa1c 100644 --- a/_modules/kerchunk/hdf.html +++ b/_modules/kerchunk/hdf.html @@ -203,7 +203,7 @@

Source code for kerchunk.hdf

 
 

 [docs]
-    def translate(self):
+    def translate(self, preserve_linked_dsets=False):
         """Translate content of one HDF5 file into Zarr storage format.
 
         This method is the main entry point to execute the workflow, and
@@ -211,6 +211,13 @@ 
Source code for kerchunk.hdf
 
         No data is copied out of the HDF5 file.
 
+        Parameters
+        ----------
+        preserve_linked_dsets : bool (optional, default False)
+            If True, translate HDF5 soft and hard links for each `h5py.Dataset`
+            into the reference structure. Requires h5py version 3.11.0 or later.
+            Will not translate external links or links to `h5py.Group` objects.
+
         Returns
         -------
         dict
@@ -218,7 +225,17 @@ 
Source code for kerchunk.hdf
         """
         lggr.debug("Translation begins")
         self._transfer_attrs(self._h5f, self._zroot)
+
         self._h5f.visititems(self._translator)
+
+        if preserve_linked_dsets:
+            if not has_visititems_links():
+                raise RuntimeError(
+                    "'preserve_linked_dsets' kwarg requires h5py 3.11.0 or later "
+                    f"is installed, found {h5py.__version__}"
+                )
+            self._h5f.visititems_links(self._translator)
+
         if self.spec < 1:
             return self.store
         elif isinstance(self.store, LazyReferenceMapper):
@@ -338,10 +355,26 @@ 
Source code for kerchunk.hdf
                 )
         return filters
 
-    def _translator(self, name: str, h5obj: Union[h5py.Dataset, h5py.Group]):
+    def _translator(
+        self,
+        name: str,
+        h5obj: Union[
+            h5py.Dataset, h5py.Group, h5py.SoftLink, h5py.HardLink, h5py.ExternalLink
+        ],
+    ):
         """Produce Zarr metadata for all groups and datasets in the HDF5 file."""
         try:  # method must not raise exception
             kwargs = {}
+
+            if isinstance(h5obj, (h5py.SoftLink, h5py.HardLink)):
+                h5obj = self._h5f[name]
+                if isinstance(h5obj, h5py.Group):
+                    # continues iteration of visititems_links
+                    lggr.debug(
+                        f"Skipping translation of HDF5 linked group: '{h5obj.name}'"
+                    )
+                    return None
+
             if isinstance(h5obj, h5py.Dataset):
                 lggr.debug(f"HDF5 dataset: {h5obj.name}")
                 lggr.debug(f"HDF5 compression: {h5obj.compression}")
@@ -523,7 +556,7 @@ 
Source code for kerchunk.hdf
                         )
 
                 # Create a Zarr array equivalent to this HDF5 dataset...
-                za = self._zroot.create_dataset(
+                za = self._zroot.require_dataset(
                     h5obj.name,
                     shape=h5obj.shape,
                     dtype=dt or h5obj.dtype,
@@ -571,7 +604,7 @@ 
Source code for kerchunk.hdf
 
             elif isinstance(h5obj, h5py.Group):
                 lggr.debug(f"HDF5 group: {h5obj.name}")
-                zgrp = self._zroot.create_group(h5obj.name)
+                zgrp = self._zroot.require_group(h5obj.name)
                 self._transfer_attrs(h5obj, zgrp)
         except Exception as e:
             import traceback
@@ -731,6 +764,10 @@ 
Source code for kerchunk.hdf
 
 def _is_netcdf_variable(dataset: h5py.Dataset):
     return any("_Netcdf4" in _ for _ in dataset.attrs)
+
+
+def has_visititems_links():
+    return hasattr(h5py.Group, "visititems_links")
 

 
            

diff --git a/reference.html b/reference.html
index dc89279b..61c7ba45 100644
--- a/reference.html
+++ b/reference.html
@@ -216,21 +216,29 @@ 
File format backendsMethods

 
-
+

 
translate()
translate([preserve_linked_dsets])

 
Translate content of one HDF5 file into Zarr storage format.

 

 
 

 

 

-translate()[source]

+translate(preserve_linked_dsets=False)[source]
 
Translate content of one HDF5 file into Zarr storage format.

 
This method is the main entry point to execute the workflow, and
 returns a “reference” structure to be used with zarr/kerchunk

 
No data is copied out of the HDF5 file.

 

-
Returns:

+
Parameters:

 

+
preserve_linked_dsetsbool (optional, default False)
If True, translate HDF5 soft and hard links for each h5py.Dataset
+into the reference structure. Requires h5py version 3.11.0 or later.
+Will not translate external links or links to h5py.Group objects.

+

+

+

+
Returns:

+

 
dict
Dictionary containing reference structure.

 

 

diff --git a/searchindex.js b/searchindex.js
index db67e055..aafe8322 100644
--- a/searchindex.js
+++ b/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"alltitles": {".csv/.json": [[6, "csv-json"]], ".tar.zstd": [[6, "tar-zstd"]], "API Reference": [[7, "api-reference"]], "Advanced Topics": [[0, "advanced-topics"]], "Archive Files": [[0, "archive-files"]], "Beyond Python": [[1, "beyond-python"]], "Binary buffers": [[4, "binary-buffers"]], "Bug reports and feature requests": [[3, "bug-reports-and-feature-requests"]], "Case studies": [[2, "case-studies"]], "Codecs": [[7, "codecs"]], "Combine multiple kerchunked datasets into a single logical aggregate dataset": [[10, "combine-multiple-kerchunked-datasets-into-a-single-logical-aggregate-dataset"]], "Combining": [[7, "combining"]], "Contents:": [[5, null]], "Contributing changes": [[3, "contributing-changes"]], "Contributing code": [[3, "contributing-code"]], "Contributing documentation": [[3, "contributing-documentation"]], "Contributing to kerchunk": [[3, "contributing-to-kerchunk"]], "Creating a Fork": [[3, "creating-a-fork"]], "Creating a Python Environment": [[3, "creating-a-python-environment"]], "Creating a branch": [[3, "creating-a-branch"]], "Creating a development environment": [[3, "creating-a-development-environment"]], "Detailed description": [[4, "detailed-description"]], "Example/Tutorial Notebook": [[9, "example-tutorial-notebook"]], "File format backends": [[7, "file-format-backends"]], "HRRR": [[2, "hrrr"]], "Indices and tables": [[5, "indices-and-tables"]], "Introduction": [[5, "introduction"]], "MUR SST": [[2, "mur-sst"]], "Merging variables across jsons": [[10, "merging-variables-across-jsons"]], "Multi-file JSONs": [[9, "multi-file-jsons"]], "National Water Model": [[2, "national-water-model"]], "Non-zarr uses": [[6, "non-zarr-uses"]], "Parquet Storage": [[0, "parquet-storage"]], "Parquet references": [[8, "parquet-references"]], "Postprocessing": [[10, "postprocessing"]], "Preprocessing": [[10, "preprocessing"]], "Quick Start": [[9, "quick-start"]], "References specification": [[8, "references-specification"]], "Running the test suite": [[3, "running-the-test-suite"]], "Sentinel Global coherence": [[2, "sentinel-global-coherence"]], "Setting up pre-commit": [[3, "setting-up-pre-commit"]], "Simple parallel": [[0, "simple-parallel"]], "Single file JSONs": [[9, "single-file-jsons"], [10, "single-file-jsons"]], "Solar Dynamics Observatory": [[2, "solar-dynamics-observatory"]], "Tree reduction": [[0, "tree-reduction"]], "Tutorial": [[10, "tutorial"]], "Using Dask": [[0, "using-dask"]], "Using coo_map": [[10, "using-coo-map"]], "Using the output": [[9, "using-the-output"], [10, "using-the-output"]], "Utilities": [[7, "utilities"]], "Version 0": [[8, "version-0"]], "Version 1": [[8, "version-1"]], "fsspec virtual filesystem": [[4, "fsspec-virtual-filesystem"]], "kerchunk": [[5, "kerchunk"]], "parquet/orc/feather": [[6, "parquet-orc-feather"]], "zarr reader": [[4, "zarr-reader"]]}, "docnames": ["advanced", "beyond", "cases", "contributing", "detail", "index", "nonzarr", "reference", "spec", "test_example", 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false]], "drop() (in module kerchunk.combine)": [[7, "kerchunk.combine.drop", false]], "fillstringscodec (class in kerchunk.codecs)": [[7, "kerchunk.codecs.FillStringsCodec", false]], "generate_coords() (in module kerchunk.tiff)": [[7, "kerchunk.tiff.generate_coords", false]], "gribcodec (class in kerchunk.codecs)": [[7, "kerchunk.codecs.GRIBCodec", false]], "inline_array() (in module kerchunk.utils)": [[7, "kerchunk.utils.inline_array", false]], "merge_vars() (in module kerchunk.combine)": [[7, "kerchunk.combine.merge_vars", false]], "multizarrtozarr (class in kerchunk.combine)": [[7, "kerchunk.combine.MultiZarrToZarr", false]], "netcdf3tozarr (class in kerchunk.netcdf3)": [[7, "kerchunk.netCDF3.NetCDF3ToZarr", false]], "process_file() (in module kerchunk.fits)": [[7, "kerchunk.fits.process_file", false]], "recordarraymember (class in kerchunk.codecs)": [[7, "kerchunk.codecs.RecordArrayMember", false]], "refs_to_dataframe() (in module kerchunk.df)": [[7, 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