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Id restructure #19

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merged 32 commits into from
Mar 25, 2024
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8ef9d2e
moving id assignment process files
seankim658 Mar 18, 2024
5c83bf8
updating id structure/handling process
seankim658 Mar 18, 2024
15b7e82
update docs
seankim658 Mar 18, 2024
9a46fdc
typo fix
seankim658 Mar 18, 2024
6d4a57e
add new collections
seankim658 Mar 19, 2024
55245cd
typo/formatting fix
seankim658 Mar 19, 2024
06df473
id backend layer
seankim658 Mar 19, 2024
6fc63b7
control flow changes
seankim658 Mar 19, 2024
65e16c1
add no collision logic
seankim658 Mar 19, 2024
165e6cd
refactor public facing id assign script
seankim658 Mar 19, 2024
a6d1175
move id assign process docs
seankim658 Mar 21, 2024
adb3d17
update links
seankim658 Mar 21, 2024
63a749c
add dump id collection
seankim658 Mar 21, 2024
ff5dfea
add dump id collection logic
seankim658 Mar 21, 2024
d0f6dca
add connection string builder and id collection dump
seankim658 Mar 21, 2024
332d388
reworked collision logic and load id collection in prod logic
seankim658 Mar 21, 2024
712b7e2
fixed relative imports in helpers module
seankim658 Mar 22, 2024
e74da48
moved logger setup to capture potential mongo handle failure
seankim658 Mar 22, 2024
46428c2
deep diff to json for serialization
seankim658 Mar 22, 2024
8aef6db
fixed output formatting f string formatting
seankim658 Mar 22, 2024
f83ecaa
added file sorting to increase reproduceability and consistency
seankim658 Mar 22, 2024
a94dd4d
fix deepdiff serialization formatting
seankim658 Mar 23, 2024
87924ab
fix mongodb connection string
seankim658 Mar 23, 2024
ec4b04d
add debug information for dumping id collection to disk
seankim658 Mar 23, 2024
c6cd38f
add debug information for loading id collection to prod database
seankim658 Mar 23, 2024
fec635d
ignore load map in glob loops
seankim658 Mar 24, 2024
7f191ea
fix config file pathing
seankim658 Mar 24, 2024
f8c0308
ignore load map during load map configuration
seankim658 Mar 24, 2024
c4ad64b
change data collection index to biomarker_id field instead of canonical
seankim658 Mar 24, 2024
301240b
refactored error handling
seankim658 Mar 24, 2024
687872f
fix logging when there are id collisions within the same data load ve…
seankim658 Mar 24, 2024
19bbd21
fix documentation for load_map.json file
seankim658 Mar 25, 2024
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4 changes: 3 additions & 1 deletion README.md
Original file line number Diff line number Diff line change
@@ -1,8 +1,10 @@
# Biomarker Backend API

This repository handles the backend API for the Biomarker-Partnership project and handles the data ID assignment process.

Usage Guides:
- [Initial Server Setup](/docs/initial_setup.md)
- [Biomarker ID Assignment Process](/docs/id_assign_process.md)
- [Biomarker ID Assignment Process](/id/README.md)
- [ID Backend Implementation Documentation](/docs/id_implementation.md)
- [Config File Definitions](/docs/config_file.md)

Expand Down
7 changes: 4 additions & 3 deletions api/config.json
Original file line number Diff line number Diff line change
Expand Up @@ -24,10 +24,11 @@
"biomarkerdb_api":{
"db":"biomarkerdb_api",
"collection": "biomarker_collection",
"id_collection": "id_map_collection",
"collision_collection": "collision_collection",
"canonical_id_map": "canonical_id_map_collection",
"second_level_id_map": "second_id_map_collection",
"unreviewed_collection": "unreviewed_collection",
"user":"biomarkeradmin",
"password":"biomarkerpass"
}
}
}
}
240 changes: 0 additions & 240 deletions api/id.py

This file was deleted.

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