Implement OTF (On-The-Fly) expression call propagation and remove Affymetrix/EST datatypes - #252

Draft

jwollbrett wants to merge 121 commits into

updated_implement_otf

Commits on Dec 1, 2025

first attempt of removing ESTs and Affymetrix datatypes
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4672a1d
manage devOntologyXRef information for each species
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dfc6454
cache condition graph for OTF propagation
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9c2dd09
insert propagated conditions for OTF propagation
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0444628
commented code that will not be used anymore
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36f3bc3
updated dao-api to manage OTF propagation
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cf24f67
updated dao-sql to manage OTF propagation
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c2bce30
started to implement bgee-core for OTF propagation
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5e20c9c
continued update of bgee-core for OTF propagation
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855e9c9
solve last errors from bgee-core after removing affymetrix and ESTs
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b3ad729
solve misc errors in bgee-pipeline after removing affymetrix and ESTs
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303fd3f
solved errors related to affy and ESTs removal for bgee-webapp
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8dc63a5

Commits on Jan 16, 2026

remove unused classes
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d826b97
convert raw data sex & strain to sex & strain
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b59ed4f
high level cleaning
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1b9a4ce
update insertion of global condition by the pipeline
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6cf9d72
rename some database columns
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ffed2f5
store score rather than score in the expression table
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d35eb88
messy commit about OTF propagation
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5d40723

Commits on Mar 26, 2026

adapt API to new field species.hiddenSpecies
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0a5f8af

Commits on Apr 2, 2026

Commits on Apr 16, 2026

Commits on Apr 30, 2026

Commits on Jun 9, 2026

fasten retrieval of single cell experiment info
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302b689

Commits on Jun 25, 2026

add log for timing of OTF propagation
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6283af7
add possibility to load condition graph on demand
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1cffeef
solve bug excluding annotated dev stage during condition propagation
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c7bd0f8
fasten generation of the condition graph for condition propagation
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af65328
added fixme comment
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a15f149
improve speed of slow raw data SQL queries
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7d088ca
update exclusion reasons
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608051c
consider only expression values with observation for selected datatypes
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b7ffdfc
update insertion of propagated conditions
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7216b46
update exclusion reason in bgee-core
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a525744
add logs to detect slowest parts of the OTF propagation
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07d0b9e
do not retrieve maxRanksPerSpecies for OTF propagation
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2b9e5de
precise that descendant values are only direct descendant
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4bc0a44
format pvalue
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97393ee
reminder to remove unused max ranks
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a62d446
sort calls per decreasing score
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76564ce
misc modifictations on OTF propagation
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b5a2898
continue updating CommandData to use OTF propagation
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f5355f3
first version of gene page API call compatible with OTF propagation
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3cb17cd

Commits on Jun 30, 2026

Commits on Jul 1, 2026

Commits on Jul 2, 2026

solved wrong management of excluded terms
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b6018f0
throw an error if conditionId present in the expression table is not present in raw to global condition
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f9d13cf
removed code not used anymore
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deea193
add FIXME comment to remember functionalities not yet implemented
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745df76
better formatting of JSON output for condition part
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ed2f28d
update TODO comment
jwollbrett
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88f3e83

Commits on Jul 3, 2026

Commits on Jul 10, 2026

fix p-value formatting when value is 0 in OTFExpressionCall
jwollbrett
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e4142e9

Commits on Jul 12, 2026

add missing import
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0c6a0f9
Merge branch 'implement_otf' into updated_implement_otf
jwollbrett
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affe0ec

Commits on Aug 18, 2026

Commits on Aug 27, 2026

Commits on Sep 2, 2026

Commits on Sep 10, 2026

Commits on Sep 11, 2026

generate XRefs expression info with OTF propagation, as on the gene page
jwollbrett
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fa62853

Commits on Sep 15, 2026

Commits on Sep 16, 2026

Commits on Sep 17, 2026

Commits on Sep 25, 2026