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Add eFP/ePlant gene ID validation, microarray probeset support, and m… #324

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aa56b67
Add eFP/ePlant gene ID validation, microarray probeset support, and m…
rmobmina Jun 25, 2026
a577ee3
Integrate Vincent's regex registry, fix master JSON species, refactor…
rmobmina Jul 17, 2026
afd8c63
Remove scratch CSVs, MDs, and one-off analysis files from repo root
rmobmina Jul 17, 2026
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4 changes: 2 additions & 2 deletions api/models/efp_schemas.py
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Original file line number Diff line number Diff line change
Expand Up @@ -105,7 +105,7 @@ def _schema(species: str, charset: str = "latin1") -> DatabaseSpec:
("grape_developmental", "grape"),
("guard_cell", "guard cell"),
("gynoecium", "gynoecium"),
("heterodera_schachtii", "heterodera"),
("heterodera_schachtii", "arabidopsis"),
("hnahal", "hnahal"),
("human_body_map_2", "human"),
("human_developmental", "human"),
Expand Down Expand Up @@ -181,7 +181,7 @@ def _schema(species: str, charset: str = "latin1") -> DatabaseSpec:
("root_Schaefer_lab", "root Schaefer lab"),
("rpatel", "rpatel"),
("seed_db", "seed db"),
("seedcoat", "oat"),
("seedcoat", "arabidopsis seedcoat"),
("selaginella", "selaginella"),
("shoot_apex", "arabidopsis"),
("silique", "arabidopsis"),
Expand Down
242 changes: 242 additions & 0 deletions api/random_rows_json/actinidia_bud_development_test_data.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,242 @@
[
{
"db": "actinidia_bud_development",
"proj_id": "1",
"sample_id": 7,
"data_probeset_id": "Acc23558.1",
"data_signal": 0.0593103,
"data_bot_id": "Jul"
},
{
"db": "actinidia_bud_development",
"proj_id": "1",
"sample_id": 12,
"data_probeset_id": "Acc27556.1",
"data_signal": 0.0,
"data_bot_id": "Nov"
},
{
"db": "actinidia_bud_development",
"proj_id": "1",
"sample_id": 4,
"data_probeset_id": "Acc13569.1",
"data_signal": 1.50114,
"data_bot_id": "Feb"
},
{
"db": "actinidia_bud_development",
"proj_id": "1",
"sample_id": 6,
"data_probeset_id": "Acc24157.1",
"data_signal": 0.0,
"data_bot_id": "Jan_TB"
},
{
"db": "actinidia_bud_development",
"proj_id": "1",
"sample_id": 6,
"data_probeset_id": "Acc27341.1",
"data_signal": 7.36061,
"data_bot_id": "Jan_TB"
},
{
"db": "actinidia_bud_development",
"proj_id": "1",
"sample_id": 2,
"data_probeset_id": "Acc15429.1",
"data_signal": 2.44246,
"data_bot_id": "Aug"
},
{
"db": "actinidia_bud_development",
"proj_id": "1",
"sample_id": 5,
"data_probeset_id": "Acc32753.1",
"data_signal": 1.78871,
"data_bot_id": "Jan"
},
{
"db": "actinidia_bud_development",
"proj_id": "1",
"sample_id": 8,
"data_probeset_id": "Acc12083.1",
"data_signal": 0.117258,
"data_bot_id": "Jun"
},
{
"db": "actinidia_bud_development",
"proj_id": "1",
"sample_id": 1,
"data_probeset_id": "Acc24253.1",
"data_signal": 0.0526919,
"data_bot_id": "Apr"
},
{
"db": "actinidia_bud_development",
"proj_id": "1",
"sample_id": 3,
"data_probeset_id": "Acc24221.1",
"data_signal": 3.63306,
"data_bot_id": "Dec"
},
{
"db": "actinidia_bud_development",
"proj_id": "1",
"sample_id": 5,
"data_probeset_id": "Acc21077.1",
"data_signal": 1.36209,
"data_bot_id": "Jan"
},
{
"db": "actinidia_bud_development",
"proj_id": "1",
"sample_id": 8,
"data_probeset_id": "Acc16361.1",
"data_signal": 10.9285,
"data_bot_id": "Jun"
},
{
"db": "actinidia_bud_development",
"proj_id": "1",
"sample_id": 10,
"data_probeset_id": "Acc30784.1",
"data_signal": 1.30967,
"data_bot_id": "Mar_TB"
},
{
"db": "actinidia_bud_development",
"proj_id": "1",
"sample_id": 5,
"data_probeset_id": "Acc05038.1",
"data_signal": 1.61503,
"data_bot_id": "Jan"
},
{
"db": "actinidia_bud_development",
"proj_id": "1",
"sample_id": 7,
"data_probeset_id": "Acc09894.1",
"data_signal": 0.184609,
"data_bot_id": "Jul"
},
{
"db": "actinidia_bud_development",
"proj_id": "1",
"sample_id": 4,
"data_probeset_id": "Acc31729.1",
"data_signal": 4.49147,
"data_bot_id": "Feb"
},
{
"db": "actinidia_bud_development",
"proj_id": "1",
"sample_id": 1,
"data_probeset_id": "Acc18094.1",
"data_signal": 1.21865,
"data_bot_id": "Apr"
},
{
"db": "actinidia_bud_development",
"proj_id": "1",
"sample_id": 10,
"data_probeset_id": "Acc17305.1",
"data_signal": 4.03641,
"data_bot_id": "Mar_TB"
},
{
"db": "actinidia_bud_development",
"proj_id": "1",
"sample_id": 5,
"data_probeset_id": "Acc24053.1",
"data_signal": 2.99612,
"data_bot_id": "Jan"
},
{
"db": "actinidia_bud_development",
"proj_id": "1",
"sample_id": 12,
"data_probeset_id": "Acc19198.1",
"data_signal": 1.28844,
"data_bot_id": "Nov"
},
{
"db": "actinidia_bud_development",
"proj_id": "1",
"sample_id": 1,
"data_probeset_id": "Acc06107.1",
"data_signal": 0.428198,
"data_bot_id": "Apr"
},
{
"db": "actinidia_bud_development",
"proj_id": "1",
"sample_id": 4,
"data_probeset_id": "Acc18350.1",
"data_signal": 4.16934,
"data_bot_id": "Feb"
},
{
"db": "actinidia_bud_development",
"proj_id": "1",
"sample_id": 8,
"data_probeset_id": "Acc33448.1",
"data_signal": 1.79429,
"data_bot_id": "Jun"
},
{
"db": "actinidia_bud_development",
"proj_id": "1",
"sample_id": 1,
"data_probeset_id": "Acc08927.1",
"data_signal": 2.33835,
"data_bot_id": "Apr"
},
{
"db": "actinidia_bud_development",
"proj_id": "1",
"sample_id": 13,
"data_probeset_id": "Acc18447.1",
"data_signal": 0.0179441,
"data_bot_id": "Nov_TB"
},
{
"db": "actinidia_bud_development",
"proj_id": "1",
"sample_id": 12,
"data_probeset_id": "Acc24973.1",
"data_signal": 3.48936,
"data_bot_id": "Nov"
},
{
"db": "actinidia_bud_development",
"proj_id": "1",
"sample_id": 11,
"data_probeset_id": "Acc09777.1",
"data_signal": 0.0298628,
"data_bot_id": "May"
},
{
"db": "actinidia_bud_development",
"proj_id": "1",
"sample_id": 11,
"data_probeset_id": "Acc09117.1",
"data_signal": 0.612542,
"data_bot_id": "May"
},
{
"db": "actinidia_bud_development",
"proj_id": "1",
"sample_id": 7,
"data_probeset_id": "Acc02018.1",
"data_signal": 3.17797,
"data_bot_id": "Jul"
},
{
"db": "actinidia_bud_development",
"proj_id": "1",
"sample_id": 8,
"data_probeset_id": "Acc14238.1",
"data_signal": 6.29684,
"data_bot_id": "Jun"
}
]
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