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New template system for pathfinder #202

Merged
merged 63 commits into from
Aug 30, 2024
Merged

New template system for pathfinder #202

merged 63 commits into from
Aug 30, 2024

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rjawesome
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colleenXu and others added 30 commits March 20, 2024 23:19
@colleenXu
feat: add pathfinder templateGroups, templates for drug-disease
7ec573a
@tokebe @colleenXu
feat: allow inferred explain-type queries
8deeada
@colleenXu
Merge branch 'main' into pathfinder-templates
f52c0f8
@rjawesome
identify pathfinder queries. identify templates
52bc25d
@rjawesome
create pathfinder intermediate aux graphs & results
60dc949
@rjawesome
add kg edges to pathfinder
f8fe4e2
@rjawesome
score pathfinder results
9e1e0f7
@rjawesome
implementation of creative limit for pathfinder
bd77b6d
@rjawesome
Merge branch 'pathfinder-templates' into pathfinder
d12742e
@rjawesome
add debug statements
24eb56f
@rjawesome
code reorganization for pathfinder
f2832f0
@rjawesome
logs & telemetry
286dd47
@rjawesome
bugfix for couting ids
aa26be6
@rjawesome
testing / function reorganization
c94cdb5
@rjawesome
remove unnecessary types; creative mode bugfix
a1619c3
@rjawesome
use guard clauses for easier code readibility
7ff4daa
@rjawesome
variable names, cleaning up more loops
e4e1a3a
@colleenXu
Merge branch 'main' into pathfinder-templates
97092c3
@colleenXu
feat: add pathfinder templates for chem-gene
dd27a9d
@colleenXu
chore: remove extra predicate from pathfinder template
c9c9e8c
@colleenXu
feat: add pathfinder templates for disease-disease
6f84108
@rjawesome
Merge branch 'main' of https://github.com/biothings/bte_trapi_query_g…
b6aed6f 
…raph_handler into pathfinder
@rjawesome
Merge branch 'pathfinder-templates' of https://github.com/biothings/b…
3cd3b90 
…te_trapi_query_graph_handler into pathfinder
@rjawesome
fix pathfinder improt
fd7bd75
@rjawesome
fix push call
080de45
@rjawesome
implement pruning for pathfinder
4a119a2
@rjawesome
fix aux graph for main edge
fbd4558
@colleenXu
feat: add pathfinder gene-disease templates
2fc3fda
@colleenXu
Merge branch 'pathfinder-templates' into pathfinder
1faf114
@rjawesome
fix node in PF edge
be78fec
tokebe and others added 29 commits April 17, 2024 13:10
@tokebe
Merge branch 'main' of https://github.com/biothings/bte_trapi_query_g…
78c0c84 
…raph_handler into pathfinder
@rjawesome
make aux graphs more efficient
e1ab149
@rjawesome
Analyze aux graphs individually
715c1c9
@rjawesome
fix: support graph suffixes
88bad1e
@rjawesome
add pruning test
894bbb0
@colleenXu
feat: add initial tables for pathfinder refactor
7c33fc0
@rjawesome
load pf tables & generate templates
5e572de
@rjawesome
merge predicates/categories for each template
88900c9
@rjawesome
use related_to for empty rpedicate
ed7f41b
@rjawesome
run templates from pf template generator
5c8c670
@colleenXu
feat: change format of predicates table
78afb32
@rjawesome
Merge branch 'pathfinder-newsystem' of https://github.com/biothings/b…
1445076 
…te_trapi_query_graph_handler into pathfinder-newsystem
@rjawesome
update for new predicate table format
6d5a38f
@rjawesome
filter pf results by category
b405a25
@rjawesome
bugfix for adding related_to for missing predicates
a951463
@rjawesome
remove debug console.log
921642c
@rjawesome
delete predicates if not present
e54bb73
@rjawesome
add agent type/knowledge level to pathfinder
915598b
@rjawesome
add test for pathfinder template creator
67f6d62
@rjawesome
add more test cases for pf template generator
8055fa9
@rjawesome
Merge remote-tracking branch 'origin/main' into pathfinder-newsystem
2ff3a8b
@tokebe
fix: template qualifiers
567f392
@tokebe
Merge branch 'main' of https://github.com/biothings/bte_trapi_query_g…
034d01f 
…raph_handler into pathfinder-newsystem
@tokebe
fix: reset totalRecords between templates
3bd1de2
@tokebe
fix: add fallback ancestors in pathfinder queries
7e34f68
@tokebe
fix: gene/protein conflation should work both ways
a2c8a5b
@tokebe
Merge branch 'main' of https://github.com/biothings/bte_trapi_query_g…
3797d03 
…raph_handler into pathfinder-newsystem
@tokebe
fix: fallback ancestor handling, add logs
e76cd73
@tokebe
fix: ensure conflation is used in expandedCategories
3d58df4
@tokebe tokebe merged commit 265360d into main Aug 30, 2024
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3 participants
@rjawesome @tokebe @colleenXu