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Pathfinder #191

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merged 39 commits into from
Aug 30, 2024
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7ec573a
feat: add pathfinder templateGroups, templates for drug-disease
colleenXu Mar 21, 2024
8deeada
feat: allow inferred explain-type queries
tokebe Dec 20, 2023
f52c0f8
Merge branch 'main' into pathfinder-templates
colleenXu Mar 22, 2024
52bc25d
identify pathfinder queries. identify templates
rjawesome Mar 23, 2024
60dc949
create pathfinder intermediate aux graphs & results
rjawesome Mar 26, 2024
f8fe4e2
add kg edges to pathfinder
rjawesome Mar 26, 2024
9e1e0f7
score pathfinder results
rjawesome Mar 27, 2024
bd77b6d
implementation of creative limit for pathfinder
rjawesome Mar 28, 2024
d12742e
Merge branch 'pathfinder-templates' into pathfinder
rjawesome Mar 28, 2024
24eb56f
add debug statements
rjawesome Mar 28, 2024
f2832f0
code reorganization for pathfinder
rjawesome Mar 29, 2024
286dd47
logs & telemetry
rjawesome Mar 30, 2024
aa26be6
bugfix for couting ids
rjawesome Apr 2, 2024
c94cdb5
testing / function reorganization
rjawesome Apr 2, 2024
a1619c3
remove unnecessary types; creative mode bugfix
rjawesome Apr 2, 2024
7ff4daa
use guard clauses for easier code readibility
rjawesome Apr 2, 2024
e4e1a3a
variable names, cleaning up more loops
rjawesome Apr 2, 2024
97092c3
Merge branch 'main' into pathfinder-templates
colleenXu Apr 3, 2024
dd27a9d
feat: add pathfinder templates for chem-gene
colleenXu Apr 3, 2024
c9c9e8c
chore: remove extra predicate from pathfinder template
colleenXu Apr 3, 2024
6f84108
feat: add pathfinder templates for disease-disease
colleenXu Apr 3, 2024
b6aed6f
Merge branch 'main' of https://github.com/biothings/bte_trapi_query_g…
rjawesome Apr 4, 2024
3cd3b90
Merge branch 'pathfinder-templates' of https://github.com/biothings/b…
rjawesome Apr 4, 2024
fd7bd75
fix pathfinder improt
rjawesome Apr 4, 2024
080de45
fix push call
rjawesome Apr 4, 2024
4a119a2
implement pruning for pathfinder
rjawesome Apr 5, 2024
fbd4558
fix aux graph for main edge
rjawesome Apr 5, 2024
2fc3fda
feat: add pathfinder gene-disease templates
colleenXu Apr 5, 2024
1faf114
Merge branch 'pathfinder-templates' into pathfinder
colleenXu Apr 5, 2024
be78fec
fix node in PF edge
rjawesome Apr 6, 2024
576721e
more pathfinder testing
rjawesome Apr 6, 2024
79a66d6
Merge branch 'pathfinder' of https://github.com/biothings/bte_trapi_q…
rjawesome Apr 6, 2024
f861412
chore: fix error with missing pathfinder flag for one group
colleenXu Apr 11, 2024
82bd2d6
fix aux graph while loop
rjawesome Apr 17, 2024
78c0c84
Merge branch 'main' of https://github.com/biothings/bte_trapi_query_g…
tokebe Apr 17, 2024
e1ab149
make aux graphs more efficient
rjawesome Apr 18, 2024
715c1c9
Analyze aux graphs individually
rjawesome Apr 19, 2024
88bad1e
fix: support graph suffixes
rjawesome May 3, 2024
894bbb0
add pruning test
rjawesome May 11, 2024
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50 changes: 50 additions & 0 deletions __test__/data/chemical_to_disease_pathfinder.json
Original file line number Diff line number Diff line change
@@ -0,0 +1,50 @@
{
"message": {
"query_graph": {
"nodes": {
"n0": {
"ids": [
"PUBCHEM.COMPOUND:5291"
],
"categories": ["biolink:Drug"]
},
"un": {
"categories": [
"biolink:NamedThing"
]
},
"n2": {
"ids": [
"MONDO:0004979"
]
}
},
"edges": {
"e0": {
"subject": "n0",
"object": "un",
"predicates": [
"biolink:related_to"
],
"knowledge_type": "inferred"
},
"e1": {
"subject": "un",
"object": "n2",
"predicates": [
"biolink:related_to"
],
"knowledge_type": "inferred"
},
"e2": {
"subject": "n0",
"object": "n2",
"predicates": [
"biolink:related_to"
],
"knowledge_type": "inferred"
}
}
}
}
}
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