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new lense clean up
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@mavaylon1
mavaylon1 committed Nov 6, 2024
1 parent 53102f4 commit bcc9283
Showing 1 changed file with 42 additions and 57 deletions.
99 changes: 42 additions & 57 deletions src/hdmf_zarr/backend.py
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Original file line number Diff line number Diff line change
Expand Up @@ -552,33 +552,9 @@ def write_group(self, **kwargs):
# Note: In HDMF, we simply call write_link (within write_group) which contains a similar logic as seen
# below. This is not the case here (until a refactor).
for link_name, sub_builder in links.items():
group_filename = self.__get_store_path(group.store)
if export_source is not None:
if sub_builder.builder.source in (group_filename, export_source):
# Case 1:
# sub_builder.builder.source == export_source
# This means we have a SoftLink for a group and so we want the exported link to
# also point "inwards" in the file being created.
#################################
# Case 2:
# sub_builder.builder.source == group_filename
# This is still a SoftLink; however, it is from adding a link to a group after FileA
# has been read and we are exporting that to FileB. We still want the link to be "inwards".
source = group_filename
else:
# Purpose: Create an ExternalLink to whatever file that has what we are targeting.

# Note: This might change during the refactor, but the idea goes as follows:
# write_link calls _create_ref, which internally has a conditional if the source
# is None. If None, it will use the source from the provided builder.

# In the case the builder is a LinkBuilder or ReferenceBuilder, the source will actually be
# the source of the builder within.
source = None
else:
# Note: Use the export_source to create an ExternalLink to the src_io.source.
source = export_source
self.write_link(group, sub_builder, source)
# Note: sub_builder is a LinkBuilder not the builder within.
# HDMF: h5tools --> 1034
self.write_link(group, sub_builder, export_source)

attributes = builder.attributes
self.write_attributes(group, attributes, export_source=export_source)
Expand Down Expand Up @@ -621,21 +597,8 @@ def write_attributes(self, **kwargs):
# Case 2: References
elif isinstance(value, (Container, Builder, ReferenceBuilder)):
if isinstance(value, (ReferenceBuilder, Container, Builder)):
type_str = 'object'
obj_filename = self.__get_store_path(obj.store)

if not isinstance(value, Builder): # If a ReferenceBuilder
value = value.builder

# Note: The logic is similar to writing links in write_group
# Refer to the notes there.
if value.source in (obj_filename, export_source):
source = obj_filename
else:
source = None

refs = self._create_ref(value, source)
tmp = {'zarr_dtype': type_str, 'value': refs}
refs = self._create_ref(value, self.path)
tmp = {'zarr_dtype': 'object', 'value': refs}
obj.attrs[key] = tmp
# Case 3: Scalar attributes
else:
Expand Down Expand Up @@ -818,20 +781,12 @@ def _create_ref(self, ref_object, ref_link_source=None):
# by checking os.isdir makes sure we have a valid link path to a dir for Zarr. For conversion
# between backends a user should always use export which takes care of creating a clean set of builders.
if ref_link_source is None:
source = (builder.source
ref_link_source = (builder.source
if (builder.source is not None and os.path.isdir(builder.source))
else self.source)
else:
if builder.source == ref_link_source:
# Note: This case comes up when exporting a dataset of references (each point to say a group).
# _create_ref is called on each item (group). We do not support external references, so the source
# maybe an external file, but we need to point inwards because they're actually in the file.
source = self.path
else:
source = ref_link_source

if not isinstance(source, str):
source = source.path
if not isinstance(ref_link_source, str):
ref_link_source = ref_link_source.path

if not isinstance(self.path, str):
str_path = self.path.path
Expand All @@ -846,8 +801,8 @@ def _create_ref(self, ref_object, ref_link_source=None):

# Note2: Don't use just os.path.relpath() with just a single arg, i.e., source. This will make the
# path relative to the working directory. We want it relative to where it lives in the file system.
rel_source = os.path.relpath(os.path.abspath(source), os.path.dirname(os.path.abspath(str_path)))

rel_source = os.path.relpath(os.path.abspath(ref_link_source), os.path.dirname(os.path.abspath(str_path)))
# breakpoint()
# Return the ZarrReference object
ref = ZarrReference(
source=rel_source,
Expand Down Expand Up @@ -886,6 +841,34 @@ def write_link(self, **kwargs):
% (builder.name, parent.name))
return
self.logger.debug("Writing LinkBuilder '%s' to parent group '%s'" % (builder.name, parent.name))

target_builder = builder.builder

group_filename = self.__get_store_path(parent.store)
if ref_link_source is not None:
# HDMF: h5tools 1081
if target_builder.source in (group_filename, ref_link_source):
# Case 1:
# target_builder.source == export_source
# This means we have a SoftLink for a group and so we want the exported link to
# also point "inwards" in the file being created.
#################################
# Case 2:
# target_builder.source == group_filename
# This is still a SoftLink; however, it is from adding a link to a group after FileA
# has been read and we are exporting that to FileB. We still want the link to be "inwards".
ref_link_source = group_filename
else:
# Purpose: Create an ExternalLink to whatever file that has what we are targeting.

# Note: This might change during the refactor, but the idea goes as follows:
# write_link calls _create_ref, which internally has a conditional if the source
# is None. If None, it will use the source from the provided builder.

# In the case the builder is a LinkBuilder or ReferenceBuilder, the source will actually be
# the source of the builder within.
ref_link_source = target_builder.source

name = builder.name
# Get the reference
zarr_ref = self._create_ref(builder, ref_link_source)
Expand Down Expand Up @@ -1117,14 +1100,16 @@ def write_dataset(self, **kwargs): # noqa: C901
dset = self.__list_fill__(parent, name, data, options)
# Write a dataset of references
elif self.__is_ref(options['dtype']):
# Note: ref_link_source is set to self.path because we do not do external references
# We only support external links.
if isinstance(data, ReferenceBuilder):
shape = (1,)
type_str = 'object'
refs = self._create_ref(data.builder, ref_link_source=export_source)
refs = self._create_ref(data, ref_link_source=self.path)
else:
shape = (len(data), )
type_str = 'object'
refs = [self._create_ref(item, ref_link_source=export_source) for item in data]
refs = [self._create_ref(item, ref_link_source=self.path) for item in data]

dset = parent.require_dataset(name,
shape=shape,
Expand Down

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