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post-voting env triad value set serialization #280

Merged
merged 50 commits into from
Dec 18, 2024
Merged

post-voting env triad value set serialization #280

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3e982c5
recaptitulate_soil_env_broad_scale_voting_sheet
turbomam Nov 14, 2024
a32b504
ignore database fiels and gzip
turbomam Nov 14, 2024
6c04e9b
regen
turbomam Nov 14, 2024
f7feeb0
include nmdc ebs counts
turbomam Nov 14, 2024
a4caa53
nmdc soil biosmaples with two ebs classes
turbomam Nov 14, 2024
73c6b91
oops tsv
turbomam Nov 14, 2024
90cabc4
abstracted out env/ext but not contextual level
turbomam Nov 15, 2024
0b75eb1
water ebs voting sheet
turbomam Nov 15, 2024
06d3fab
sediment ebs
turbomam Nov 15, 2024
effec0c
up to plant associated
turbomam Nov 15, 2024
832d074
generic generation of voting sheets
turbomam Nov 20, 2024
86cf565
Add goldData.xlsx to .gitignore
turbomam Nov 21, 2024
74eeae1
latest voting sheets but no gold xlsx
turbomam Nov 21, 2024
0fd4452
cleanup
turbomam Nov 21, 2024
c481088
continued cleanup
turbomam Nov 21, 2024
dae13d9
use voting sheet for file names
turbomam Nov 21, 2024
0f815d5
re-checked env_medium sheets
turbomam Nov 21, 2024
973e64f
draft voting sheet documentation
turbomam Nov 22, 2024
3cbe498
clearer settings inc. reference enum
turbomam Dec 4, 2024
eea06e3
improved code. generate fresh sheets.
turbomam Dec 6, 2024
7783eda
soil ebs
turbomam Dec 6, 2024
cd41b0d
for hackathon
turbomam Dec 6, 2024
4930acd
almost done
turbomam Dec 6, 2024
ee835b5
soil/water booleans
turbomam Dec 6, 2024
07fbc10
fixed water ice boolean column
turbomam Dec 6, 2024
3401006
plant associated medium
turbomam Dec 6, 2024
943a042
double checked env_mediums
turbomam Dec 6, 2024
e122050
pre-load gold mappings dont merge
turbomam Dec 6, 2024
10fc762
multi-pass-duckdb
turbomam Dec 9, 2024
b9834e2
single-pass
turbomam Dec 9, 2024
94e6dc2
Detect Mark's bias in SELS
turbomam Dec 9, 2024
e0804ff
non-abp ancestors
turbomam Dec 9, 2024
4589f5d
compare biosample/bioproject retreiveals
turbomam Dec 9, 2024
2f02968
EMP500 lacks biosample/bioproject links
turbomam Dec 9, 2024
638a2ed
fixed code fences
turbomam Dec 9, 2024
2b23ee5
looser constraints mining goldterms mappings
turbomam Dec 10, 2024
4639695
flow and documentation
turbomam Dec 10, 2024
8459325
12 voting sheets; broad use of GOLDTERMS; NCBI BioProject counts
turbomam Dec 11, 2024
141e145
infer sediment env_package
turbomam Dec 11, 2024
229c0fb
with nlcd
turbomam Dec 11, 2024
1c31f3d
sed els
turbomam Dec 11, 2024
cb00cda
more caching inc lexical index
turbomam Dec 12, 2024
c316dfb
included cache files
turbomam Dec 12, 2024
da995a6
2024-12-12T12:40EDT
turbomam Dec 12, 2024
827aa35
dev dependencies
turbomam Dec 12, 2024
f194cba
sediment overrides again
turbomam Dec 12, 2024
fd0776a
do'nt settle for one longest annotation
turbomam Dec 13, 2024
03c470f
regen post missing NMDC plant and sediment counts
turbomam Dec 13, 2024
f5b453e
labelled plant associated goldterms mappings
turbomam Dec 13, 2024
7303d7d
remove voting sheet gen; better notebook comments
turbomam Dec 17, 2024
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5 changes: 5 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
@@ -1,9 +1,14 @@
local
*.db
*.duckdb
*.gz
.idea
.~*#
.DS_Store
sub_schema_dh/

notebooks/environmental_context_value_sets/goldData.xlsx

/docs/
/project/docs/
/tmp/
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58 changes: 0 additions & 58 deletions notebooks/environmental_context_value_sets/README.md
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15 changes: 0 additions & 15 deletions notebooks/environmental_context_value_sets/environmental_context_value_sets.Makefile
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