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Title: S3+filesystem caching by ixcat · Pull Request #404 · datajoint/datajoint-python · GitHub

Open Graph Title: S3+filesystem caching by ixcat · Pull Request #404 · datajoint/datajoint-python

X Title: S3+filesystem caching by ixcat · Pull Request #404 · datajoint/datajoint-python

Description: Relational Workflows: where database schemas define executable data pipelines. - S3+filesystem caching by ixcat · Pull Request #404 · datajoint/datajoint-python

Open Graph Description: Implementation of an S3 'external' (implements #204) along with a external-blob caching mixin & class definitions for S3 and native to use it. Refactored the external data handling back...

X Description: Implementation of an S3 'external' (implements #204) along with a external-blob caching mixin & class definitions for S3 and native to use it. Refactored the external data h...

Opengraph URL: https://github.com/datajoint/datajoint-python/pull/404

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Nov 28, 2017https://github.com/datajoint/datajoint-python/pull/404#issue-277441859
#204https://github.com/datajoint/datajoint-python/issues/204
Please reload this pagehttps://github.com/datajoint/datajoint-python/pull/404
November 6, 2017 17:11https://github.com/datajoint/datajoint-python/pull/404#commits-pushed-8702187
s3.py: fix header descriptionhttps://github.com/datajoint/datajoint-python/pull/404/commits/8702187ebc8917439e04c60d5adbb858089a3b73
8702187https://github.com/datajoint/datajoint-python/pull/404/commits/8702187ebc8917439e04c60d5adbb858089a3b73
s3: rework existing logic in prep for external ifile merginghttps://github.com/datajoint/datajoint-python/pull/404/commits/40da960fa196c26051e0ae230713cc5a9ae2a410
40da960https://github.com/datajoint/datajoint-python/pull/404/commits/40da960fa196c26051e0ae230713cc5a9ae2a410
rename test_s3.py to test_s3_class.py to match externalhttps://github.com/datajoint/datajoint-python/pull/404/commits/9ce3d968f08e0019bb6bbd89c73dcf739b94ecf0
9ce3d96https://github.com/datajoint/datajoint-python/pull/404/commits/9ce3d968f08e0019bb6bbd89c73dcf739b94ecf0
datajoint/external.py: rework file operations into separate class hei…https://github.com/datajoint/datajoint-python/pull/404/commits/2729fd54508916a907e65f0b8e10613274c2c95a
2729fd5https://github.com/datajoint/datajoint-python/pull/404/commits/2729fd54508916a907e65f0b8e10613274c2c95a
{s3,test_s3_class}.py: use *_fileobj() methods in get/put; add getfil…https://github.com/datajoint/datajoint-python/pull/404/commits/8efa8809f8a92bc191666551105de4606a019450
8efa880https://github.com/datajoint/datajoint-python/pull/404/commits/8efa8809f8a92bc191666551105de4606a019450
datajoint/external.py: add hash_obj to ExternalFileHandlerhttps://github.com/datajoint/datajoint-python/pull/404/commits/dc990b593a0f40b10d067d92e3cb8e87ef9a0072
dc990b5https://github.com/datajoint/datajoint-python/pull/404/commits/dc990b593a0f40b10d067d92e3cb8e87ef9a0072
s3.py: add initial *untested* logic for direct-to-s3 storagehttps://github.com/datajoint/datajoint-python/pull/404/commits/cecad0d205f2de6d4b95a2d1496c3de6b885111e
cecad0dhttps://github.com/datajoint/datajoint-python/pull/404/commits/cecad0d205f2de6d4b95a2d1496c3de6b885111e
external.py: clean put()/insert statement format callhttps://github.com/datajoint/datajoint-python/pull/404/commits/d322a0bf7553aff5ef6954d595946d4337c8f0c8
d322a0bhttps://github.com/datajoint/datajoint-python/pull/404/commits/d322a0bf7553aff5ef6954d595946d4337c8f0c8
s3.py: misc cleanup of unused fn's / out of date comments.https://github.com/datajoint/datajoint-python/pull/404/commits/2d5506561517fe1cb5f1dc7b99b611cf64924012
2d55065https://github.com/datajoint/datajoint-python/pull/404/commits/2d5506561517fe1cb5f1dc7b99b611cf64924012
s3.py: flip get/put to return obj instead of Truehttps://github.com/datajoint/datajoint-python/pull/404/commits/c6ee835a3346bc1ac02018eede647ff583cbb94f
c6ee835https://github.com/datajoint/datajoint-python/pull/404/commits/c6ee835a3346bc1ac02018eede647ff583cbb94f
s3.py: use BytesIO class between put & unpack stageshttps://github.com/datajoint/datajoint-python/pull/404/commits/8eeee652a76636e85c53b139b3883bd4097473a4
8eeee65https://github.com/datajoint/datajoint-python/pull/404/commits/8eeee652a76636e85c53b139b3883bd4097473a4
add tests/{test_s3,schema_s3}.py modeled after test_external.pyhttps://github.com/datajoint/datajoint-python/pull/404/commits/a3d9fe6ec965111bddea51d8e5ab667ed22ce67f
a3d9fe6https://github.com/datajoint/datajoint-python/pull/404/commits/a3d9fe6ec965111bddea51d8e5ab667ed22ce67f
test_s3.py: rename class to DJS3MockTesthttps://github.com/datajoint/datajoint-python/pull/404/commits/1c7c0d65c42badaeefe5ebc425b50a7046128f27
1c7c0d6https://github.com/datajoint/datajoint-python/pull/404/commits/1c7c0d65c42badaeefe5ebc425b50a7046128f27
renamed: tests/test_s3.py -> tests/test_s3_mock.pyhttps://github.com/datajoint/datajoint-python/pull/404/commits/5f3e08d66cb1ceeaf34b0661079f077ef4e8fc56
5f3e08dhttps://github.com/datajoint/datajoint-python/pull/404/commits/5f3e08d66cb1ceeaf34b0661079f077ef4e8fc56
add test_s3_real.py to test real S3 access.https://github.com/datajoint/datajoint-python/pull/404/commits/394924d65e430b27afcc02becc20a6f505094398
394924dhttps://github.com/datajoint/datajoint-python/pull/404/commits/394924d65e430b27afcc02becc20a6f505094398
s3.py: teach S3FileHandler to prevent '/' in bucket from being created.https://github.com/datajoint/datajoint-python/pull/404/commits/680151e13581d57a255fb8dd44e429f73e3b2078
680151ehttps://github.com/datajoint/datajoint-python/pull/404/commits/680151e13581d57a255fb8dd44e429f73e3b2078
{external,s3}.py: add check_required arg checker in ExternalFileHandl…https://github.com/datajoint/datajoint-python/pull/404/commits/50255a3d9ebc982379467257537f9e20bdf3f892
50255a3https://github.com/datajoint/datajoint-python/pull/404/commits/50255a3d9ebc982379467257537f9e20bdf3f892
datajoint/external.py: RawFileHnadler: add new get_folder() utility, …https://github.com/datajoint/datajoint-python/pull/404/commits/469965a2053bdb46138eecc83e1b4dddde2acf29
469965ahttps://github.com/datajoint/datajoint-python/pull/404/commits/469965a2053bdb46138eecc83e1b4dddde2acf29
datajoint/external.py: fix get_folder(): self.location -> self._locationhttps://github.com/datajoint/datajoint-python/pull/404/commits/113af1c5a738b7c7332fa0d0c5779b036a39373a
113af1chttps://github.com/datajoint/datajoint-python/pull/404/commits/113af1c5a738b7c7332fa0d0c5779b036a39373a
datajoint/{external.py,s3.py}: add initial cache implementation; curr…https://github.com/datajoint/datajoint-python/pull/404/commits/91943d0c93b5053cd9eb5ce95435525fe792a21c
91943d0https://github.com/datajoint/datajoint-python/pull/404/commits/91943d0c93b5053cd9eb5ce95435525fe792a21c
Merge remote-tracking branch 'upstream/master' into s3https://github.com/datajoint/datajoint-python/pull/404/commits/633534e62e3b79dbf79a9e3ca9641c9e00f49992
633534ehttps://github.com/datajoint/datajoint-python/pull/404/commits/633534e62e3b79dbf79a9e3ca9641c9e00f49992
external.CacheFileHandler: fix put/get logic, expand/clarify pydocs.https://github.com/datajoint/datajoint-python/pull/404/commits/6d53e0209f41270b8fc96fe1a20293e05dd71293
6d53e02https://github.com/datajoint/datajoint-python/pull/404/commits/6d53e0209f41270b8fc96fe1a20293e05dd71293
external.py: initial fixes/tests for basic caching - tests ok - needs…https://github.com/datajoint/datajoint-python/pull/404/commits/47c209dc7c0f56b308d9509fa955fbd6ce58cfdc
47c209dhttps://github.com/datajoint/datajoint-python/pull/404/commits/47c209dc7c0f56b308d9509fa955fbd6ce58cfdc
{external,s3}.py (&tests): .get()->.get_{blob,obj}(); fix cache to us…https://github.com/datajoint/datajoint-python/pull/404/commits/97b1115c5b5ced619cbda4c6aff8effc92cad0fc
97b1115https://github.com/datajoint/datajoint-python/pull/404/commits/97b1115c5b5ced619cbda4c6aff8effc92cad0fc
test_external_cache_class.py: clarify comment r.e. usefulness.https://github.com/datajoint/datajoint-python/pull/404/commits/3bea011f7f2802b303b9b438aed05502ddaf1b18
3bea011https://github.com/datajoint/datajoint-python/pull/404/commits/3bea011f7f2802b303b9b438aed05502ddaf1b18
test_external_cache_class.py: cleanup imports.https://github.com/datajoint/datajoint-python/pull/404/commits/5309a9676ee11305bd207c410d7c4ed19a15cc84
5309a96https://github.com/datajoint/datajoint-python/pull/404/commits/5309a9676ee11305bd207c410d7c4ed19a15cc84
external.py: fixup check_required exception formatting.https://github.com/datajoint/datajoint-python/pull/404/commits/87e2f0de56d9131b2e284d750dd44035b2d309e9
87e2f0dhttps://github.com/datajoint/datajoint-python/pull/404/commits/87e2f0de56d9131b2e284d750dd44035b2d309e9
datajoint/external.py: make CacheFileHandler use separate config heir…https://github.com/datajoint/datajoint-python/pull/404/commits/a62d3985958c2e520d2dafe631ac68a6ebfc744a
a62d398https://github.com/datajoint/datajoint-python/pull/404/commits/a62d3985958c2e520d2dafe631ac68a6ebfc744a
tests/schema_cache.py: update for separate caching confighttps://github.com/datajoint/datajoint-python/pull/404/commits/c2441b43c149616158a9b6d20e48c6891021949a
c2441b4https://github.com/datajoint/datajoint-python/pull/404/commits/c2441b43c149616158a9b6d20e48c6891021949a
tests/schema_{cache,external,s3}.py: update config to match latesthttps://github.com/datajoint/datajoint-python/pull/404/commits/d45d2ea79fcfd785029662c0180b8a87b835a9fa
d45d2eahttps://github.com/datajoint/datajoint-python/pull/404/commits/d45d2ea79fcfd785029662c0180b8a87b835a9fa
November 27, 2017 18:21https://github.com/datajoint/datajoint-python/pull/404#commits-pushed-bd6f762
tests/test_s3_{mock,real}.py: Add caching version of S3 tests.https://github.com/datajoint/datajoint-python/pull/404/commits/bd6f7628a7144a4d481e11f9cf5da55d89081b20
bd6f762https://github.com/datajoint/datajoint-python/pull/404/commits/bd6f7628a7144a4d481e11f9cf5da55d89081b20
external.py: zap todo note.https://github.com/datajoint/datajoint-python/pull/404/commits/1777615bcdd9071fe576836be29553cf96247da4
1777615https://github.com/datajoint/datajoint-python/pull/404/commits/1777615bcdd9071fe576836be29553cf96247da4
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tests/schema_external.py: fix config syntaxhttps://github.com/datajoint/datajoint-python/pull/404/commits/485a6bc3b1aa982e858aa33c10a587509bd93baf
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