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Issue1818 #1859

Merged
merged 48 commits into from
Jul 4, 2022
Merged

Issue1818 #1859

merged 48 commits into from
Jul 4, 2022

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dkoslicki
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Converted to a PR as tests are passing. Requesting additional testing for #1818
I'll be adding more tests to this PR likely later as well

finnagin and others added 30 commits April 10, 2022 23:21
@finnagin
#1818, added arax infer
ade0556
@finnagin
#1818, add dtd predictions
fc17ad3
@finnagin
#1818, add n_paths parameter
0862d0b
@finnagin
#1818, added logic to add paths to knowledge graph and fill results
02d0322
@finnagin
#1818, added example pickle files
b969275
@finnagin
#1818, added creative DTD scripts
d3c7b30
@finnagin
Merge branch 'master' into issue1818
08ca66a
@finnagin
#1818, added csv of saved top drugs response to allow for pandas back…
0eca43a 
…wards compatibility
@finnagin
#1818, update infer code to expand one path at a time
b3be691
@finnagin
Merge branch 'master' into issue1818
530051d
@finnagin
merge master into issue1818
ee166ad
@finnagin
#1818, sped up TRAPI generation step
5ca3d9a
@finnagin
#1818, added test
f1f3261
@finnagin
merge master into issue1818
352df51
@finnagin
#1818, breakout subgraph generation into infer utilities
e4083bf
@finnagin
#1818, added bug fix
c456de8
@finnagin
#1818, update dockerfile to checkout issue1818
014e6e0
@dkoslicki
update doc string
e628594
@dkoslicki
update comments
cab8378
@finnagin
#1818, regen documantation
4392890
@finnagin
#1818, regen documantation with infer added
dd1a93f
@chunyuma
#1818 add pre-computation database
37b256c
@dkoslicki
update database manager for XDTD and issue #1818
b7107c3
@dkoslicki
also add version and path #1818
229ae78
@dkoslicki
Made a note of an unresolved reference #1818
6e33cc1
@dkoslicki
fix odd logging issue and fix unresolved reference
578b15b
@dkoslicki
remove fixme comment
192a50a
@dkoslicki
use the database manager to download the database for #1818
7e21156
@dkoslicki
Merge remote-tracking branch 'origin/master' into issue1818
dabe8de 
for issue #1818
@dkoslicki
add test script for json queries and eventual testing of inferred mode …
246dbb2 
…#1818
dkoslicki and others added 9 commits July 1, 2022 15:02
@dkoslicki
add tests towards #1818
6218405
@dkoslicki
add another test to see if it matches the right template #1857
511166c
@amykglen
Make Expand use XDTD for one-hop inferred treats queries #1818
cbe90bf
@dkoslicki
remove debug statement
87c2144
@dkoslicki
much closer to a solution to #1818 issue, but this is all I have time…
e855a26 
… for today. Run test_ARAX_infer -k test_with_qg to see what's wrong
@dkoslicki
fixed the test_ARAX_infer test, next on to the expand one
27b2112
@dkoslicki
add comment about calling resultify in the infer utilities
3c44fa8
@dkoslicki
works now save for the after query testing (needed to not inject a ne…
de0c2ce 
…w probably_treats edge when a treats edge already exists in the QG) #1818
@dkoslicki
final test passes when I nuke the category of the drug node (or more …
65a6a2c 
…precisely, replace it with biolink:NamedThing) since the model can return quite the variety of categories, and does not respect the biolink traversal up the heirarchy #1818
@dkoslicki dkoslicki requested a review from amykglen July 3, 2022 03:03
@dkoslicki
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@amykglen I added a test for mixed inferred and lookup (test_xdtd_with_other_edges), but did see the warning Expand does not yet know how to answer multi-qedge query graphs when one or more of the qedges has knowledge_type == inferred. Will answer using the normal 'fill' strategy (not creative mode), so I will mark this one as should fail (as it does fail)

@dkoslicki dkoslicki merged commit 46462aa into master Jul 4, 2022
@dkoslicki dkoslicki deleted the issue1818 branch October 20, 2023 17:39
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@amykglen amykglen Awaiting requested review from amykglen

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4 participants
@dkoslicki @finnagin @chunyuma @amykglen