-
Notifications
You must be signed in to change notification settings - Fork 6
81 lines (68 loc) · 2.35 KB
/
uberon-integration.yml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
name: Uberon integration
on:
# Manual triggering only
workflow_dispatch:
jobs:
uberon_integration:
runs-on: ubuntu-latest
container: obolibrary/odkfull:v1.5
steps:
- name: Checkout current FBbt
uses: actions/checkout@v4
with:
path: fbbt
- name: Checkout current Uberon
uses: actions/checkout@v4
with:
repository: obophenotype/uberon
path: uberon
- name: Checkout current CL
uses: actions/checkout@v4
with:
repository: obophenotype/cell-ontology
path: cl
- name: Build FBbt
run: |
cd fbbt/src/ontology
make fbbt.owl ../mappings/fbbt.sssom.tsv MIR=false IMP=false PAT=false
- name: Build Uberon
run: |
cd uberon/src/ontology
make uberon.owl MIR=false IMP=false PAT=false BRI=false GH_ACTION=true
- name: Build CL
run: |
cd cl/src/ontology
make cl.owl MIR=false IMP=false PAT=false
- name: Merge all ontologies together
env:
ROBOT_PLUGINS_DIRECTORY: uberon/src/ontology/tmp/plugins
run: |
robot merge -i fbbt/src/ontology/fbbt.owl \
-i uberon/src/ontology/uberon.owl \
-i cl/src/ontology/cl.owl \
sssom:inject --sssom fbbt/src/mappings/fbbt.sssom.tsv \
--ruleset fbbt/src/scripts/bridging.rules \
annotate --ontology-iri http://purl.obolibrary.org/obo/fbbt/fbbt-uberon-cl-merge.owl \
--output fbbt-uberon-cl-merge.owl \
reason --reasoner ELK | tee merge.log
- name: Upload merged ontology
uses: actions/upload-artifact@v4
with:
name: merged-ontology
path: fbbt-uberon-cl-merge.owl
- name: Check and explain unsats
run: |
if grep -q unsat merge.log ; then
robot explain -i fbbt-uberon-cl-merge.owl \
--reasoner ELK \
--mode unsatisfiability \
--unsatisfiable all \
--explanation unsats.md
exit 1
fi
- name: Upload explanations
if: ${{ failure() }}
uses: actions/upload-artifact@v4
with:
name: explanations
path: unsats.md