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Id restructure #19

Merged
merged 32 commits into from
Mar 25, 2024
Merged

Id restructure #19

merged 32 commits into from
Mar 25, 2024

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seankim658
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Restructured ID assignment process around the canonical/second level ID structure.

seankim658 added 30 commits March 18, 2024 17:11
@seankim658
moving id assignment process files
8ef9d2e
@seankim658
updating id structure/handling process
5c83bf8
@seankim658
update docs
15b7e82
@seankim658
typo fix
9a46fdc
@seankim658
add new collections
6d4a57e
@seankim658
typo/formatting fix
55245cd
@seankim658
id backend layer
06df473
@seankim658
control flow changes
6fc63b7
@seankim658
add no collision logic
65e16c1
@seankim658
refactor public facing id assign script
165e6cd
@seankim658
move id assign process docs
a6d1175
@seankim658
update links
adb3d17
@seankim658
add dump id collection
63a749c
@seankim658
add dump id collection logic
ff5dfea
@seankim658
add connection string builder and id collection dump
d0f6dca
@seankim658
reworked collision logic and load id collection in prod logic
332d388
@seankim658
fixed relative imports in helpers module
712b7e2
@seankim658
moved logger setup to capture potential mongo handle failure
e74da48
@seankim658
deep diff to json for serialization
46428c2
@seankim658
fixed output formatting f string formatting
8aef6db
@seankim658
added file sorting to increase reproduceability and consistency
f83ecaa
@seankim658
fix deepdiff serialization formatting
a94dd4d
@seankim658
fix mongodb connection string
87924ab
@seankim658
add debug information for dumping id collection to disk
ec4b04d
@seankim658
add debug information for loading id collection to prod database
c6cd38f
@seankim658
ignore load map in glob loops
fec635d
@seankim658
fix config file pathing
7f191ea
@seankim658
ignore load map during load map configuration
f8c0308
@seankim658
change data collection index to biomarker_id field instead of canonical
c4ad64b
@seankim658
refactored error handling
301240b
@seankim658 seankim658 added documentation Improvements or additions to documentation enhancement New feature or request labels Mar 25, 2024
@seankim658 seankim658 self-assigned this Mar 25, 2024
@seankim658 seankim658 linked an issue Mar 25, 2024 that may be closed by this pull request
Restructuring the ID process #17
Closed
@seankim658 seankim658 merged commit caed71e into main Mar 25, 2024
@seankim658 seankim658 deleted the id_restructure branch March 25, 2024 22:59
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Restructuring the ID process
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