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[WIP] Fix relative references when store not in cwd #256

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[WIP] Fix relative references when store not in cwd #256

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23 changes: 14 additions & 9 deletions src/hdmf_zarr/backend.py
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Original file line number Diff line number Diff line change
Expand Up @@ -685,7 +685,7 @@ def write_attributes(self, **kwargs):
raise TypeError(str(e) + " type=" + str(type(value)) + " data=" + str(value)) from e
# Case 2: References
elif isinstance(value, (Builder, ReferenceBuilder)):
refs = self._create_ref(value, self.path)
refs = self._create_ref(value, ref_link_source=self.path)
tmp = {"zarr_dtype": "object", "value": refs}
obj.attrs[key] = tmp
# Case 3: Scalar attributes
Expand Down Expand Up @@ -801,12 +801,13 @@ def resolve_ref(self, zarr_ref):
source_file = str(zarr_ref["path"])
else:
source_file = str(zarr_ref["source"])
# Resolve the path relative to the current file

if not self.is_remote():
if isinstance(self.source, str) and self.source.startswith(("s3://")):
source_file = self.source
else:
source_file = os.path.abspath(source_file)
# Join with source_file to resolve the relative path
source_file = os.path.normpath(os.path.join(self.source, source_file))
else:
# get rid of extra "/" and "./" in the path root and source_file
root_path = str(self.path).rstrip("/")
Expand All @@ -817,7 +818,7 @@ def resolve_ref(self, zarr_ref):
if object_path:
target_name = os.path.basename(object_path)
else:
target_name = ROOT_NAME
target_name = ROOT_NAME

target_zarr_obj = self.__open_file_consolidated(
store=source_file,
Expand Down Expand Up @@ -895,7 +896,7 @@ def _create_ref(self, ref_object, ref_link_source=None):
str_path = self.path.path
else:
str_path = self.path
rel_source = os.path.relpath(os.path.abspath(ref_link_source), os.path.dirname(os.path.abspath(str_path)))
rel_source = os.path.relpath(os.path.abspath(ref_link_source), os.path.abspath(str_path))

# Return the ZarrReference object
ref = ZarrReference(
Expand Down Expand Up @@ -965,7 +966,7 @@ def write_link(self, **kwargs):

name = builder.name
# Get the reference
zarr_ref = self._create_ref(builder, ref_link_source)
zarr_ref = self._create_ref(builder, ref_link_source=ref_link_source)

self.__add_link__(parent, zarr_ref.source, zarr_ref.path, name)
self._written_builders.set_written(builder) # record that the builder has been written
Expand Down Expand Up @@ -1078,9 +1079,13 @@ def write_dataset(self, **kwargs): # noqa: C901
if isinstance(data, Array):
# copy the dataset
data_filename = self.__get_store_path(data.store)
str_path = self.path
if not isinstance(str_path, str): # a store
str_path = self.path.path
rel_data_filename = os.path.relpath(os.path.abspath(data_filename), os.path.abspath(str_path))
if link_data:
if export_source is None: # not exporting
self.__add_link__(parent, data_filename, data.name, name)
self.__add_link__(parent, rel_data_filename, data.name, name)
linked = True
dset = None
else: # exporting
Expand All @@ -1089,7 +1094,7 @@ def write_dataset(self, **kwargs): # noqa: C901
# I have three files, FileA, FileB, FileC. I want to export FileA to FileB. FileA has an
# EXTERNAL link to a dataset in Filec. This case preserves the link to FileC to also be in FileB.
if data_filename != export_source:
self.__add_link__(parent, data_filename, data.name, name)
self.__add_link__(parent, rel_data_filename, data.name, name)
linked = True
dset = None
# Case 2: If the dataset is in the export source and has a DIFFERENT path as the builder,
Expand All @@ -1098,7 +1103,7 @@ def write_dataset(self, **kwargs): # noqa: C901
# INTERNAL link. This case preserves the link to also be in FileB.
###############
elif parent.name != data_parent:
self.__add_link__(parent, self.path, data.name, name)
self.__add_link__(parent, ".", data.name, name)
linked = True
dset = None

Expand Down
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