Create dictionaries for NWB export #11

CBroz1 · 2021-11-29T20:30:03Z

Expanding element-lab for nwb export features, see corresponding PR for workflow-animal/session

adding optional foreign keys to support components of nwb export
added lab/project/protocol to dict functions for populating NWB for users with element-lab but not element-session

element_lab/export/nwb.py

element_lab/lab.py

Co-authored-by: Thinh Nguyen <thinhnguyen0405@gmail.com>

element_lab/export/nwb.py

previously, installation would take a while resolving dependency conflicts

CBroz1 · 2021-12-17T15:34:06Z

Ready for review pending resolution of @ttngu207 's comment here

element_lab/__init__.py

Co-authored-by: Kabilar Gunalan <kabilar@datajoint.com>

element_lab/__init__.py

element_lab/lab.py

Co-authored-by: Kabilar Gunalan <kabilar@datajoint.com>

@kabilar

Good catch @kabilar! This was a holdover from my first pass. Now, `element-lab` only has functions for making dicts that feed into a users session-level nwb

element_lab/lab.py

requirements.txt

kabilar · 2022-01-28T05:42:23Z

Also, pending https://github.com/CBroz1/element-lab/pull/1.

Empty strings do not populate the NWBFile

element_lab/export/nwb.py

CHANGELOG.md

element_lab/export/nwb.py

element_lab/lab.py

element_lab/export/nwb.py

Co-authored-by: Kabilar Gunalan <kabilar@datajoint.com>

CHANGELOG.md

element_lab/lab.py

element_lab/export/nwb.py

Co-authored-by: Kabilar Gunalan <kabilar@datajoint.com>

kabilar

Thanks @CBroz1 and all! Great work.

CBroz1 added 2 commits November 22, 2021 12:36

expanding lab tables \for other NWB fields

139fde8

Expand Lab for NWB export

9c56224

dimitri-yatsenko reviewed Nov 29, 2021

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ttngu207 reviewed Nov 29, 2021

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CBroz1 and others added 2 commits November 30, 2021 10:54

Keyword, no default

112005e

Co-authored-by: Thinh Nguyen <thinhnguyen0405@gmail.com>

Pub, no default

b9804c3

Co-authored-by: Thinh Nguyen <thinhnguyen0405@gmail.com>

bendichter reviewed Nov 30, 2021

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CBroz1 and others added 6 commits December 1, 2021 15:26

revise assembly of info for nwb export

5987d93

fix pop empty nwb entries

b600a4a

edit docker users for buildtest

340458a

Add docstrings

1d41a74

quickfix: dependency import

a3c0b75

pynwb version issues w/h5py resolved recently

63bd5f5

previously, installation would take a while resolving dependency conflicts

kabilar reviewed Dec 20, 2021

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Update author dj neuro -> dj

ea71fd5

Co-authored-by: Kabilar Gunalan <kabilar@datajoint.com>

kabilar reviewed Dec 23, 2021

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CBroz1 and others added 4 commits December 23, 2021 16:25

Update element_lab/__init__.py

733d303

Co-authored-by: Kabilar Gunalan <kabilar@datajoint.com>

Remove outdated make_nwb function

ea67c24

Good catch @kabilar! This was a holdover from my first pass. Now, `element-lab` only has functions for making dicts that feed into a users session-level nwb

PEP8 full word funcs. rm equip table

5c4ac32

Deleting tempy.py notes file

e16b95b

kabilar reviewed Jan 9, 2022

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CBroz1 marked this pull request as ready for review January 13, 2022 18:40

pass Nones intead of empty strings. These do not populate the NWBFile

0d393cd

kabilar reviewed Jan 27, 2022

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Pin pynwb to 1.4.0

33288d5

kabilar self-assigned this Jan 28, 2022

Merge from bendichter: pass Nones instead of empty strings

8c0373c

Empty strings do not populate the NWBFile