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When retrieving data from S3, account for chunking #1085

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merged 5 commits into from
May 15, 2023
Merged

When retrieving data from S3, account for chunking #1085

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13cb2be
When retrieving data from S3, account for chunking
horsto May 12, 2023
8d5d6cc
Merge branch 's3_chunked' of https://github.com/horsto/datajoint-pyth…
A-Baji May 12, 2023
2fce9ae
update changelog
A-Baji May 12, 2023
d50fce2
Merge pull request #1 from A-Baji/horst-changelog
horsto May 15, 2023
1a4103a
Merge branch 'master' into s3_chunked
dimitri-yatsenko May 15, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
- Fixed - `.ipynb` output in tutorials is not visible in dark mode ([#1078](https://github.com/datajoint/datajoint-python/issues/1078)) PR [#1080](https://github.com/datajoint/datajoint-python/pull/1080)
- Changed - Readme to update links and include example pipeline image
- Changed - Docs to add landing page and update navigation
- Changed - `.data` method to `.stream` in the `get()` method for S3 (external) objects PR [#1085](https://github.com/datajoint/datajoint-python/pull/1085)
- Fixed - Docs to rename `create_virtual_module` to `VirtualModule`

### 0.14.0 -- Feb 13, 2023
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4 changes: 3 additions & 1 deletion datajoint/s3.py
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Expand Up @@ -68,7 +68,9 @@ def fput(self, local_file, name, metadata=None):
def get(self, name):
logger.debug("get: {}:{}".format(self.bucket, name))
try:
return self.client.get_object(self.bucket, str(name)).data
with self.client.get_object(self.bucket, str(name)) as result:
data = [d for d in result.stream()]
return b"".join(data)
except minio.error.S3Error as e:
if e.code == "NoSuchKey":
raise errors.MissingExternalFile("Missing s3 key %s" % name)
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