-
Notifications
You must be signed in to change notification settings - Fork 119
79 lines (70 loc) · 2.73 KB
/
preview_new_data.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
on:
pull_request:
branches:
- "*"
jobs:
changed_files:
runs-on: ubuntu-latest
outputs:
new_study_dir: ${{ steps.new-dir.outputs.NEW_DIR_LOCATION }}
new_study_name: ${{ steps.new-study.outputs.NEW_STUDY_NAME }}
steps:
- name: Get New Directories Added
id: changed-files-dir-names
uses: tj-actions/changed-files@v38
with:
dir_names: "true"
- name: Extract Directory Name of New Study
id: new-dir
shell: bash
run: |
echo "NEW_DIR_LOCATION=$( echo ${{ steps.changed-files-dir-names.outputs.added_files }} | awk '{print $1}' )" >> $GITHUB_OUTPUT
- name: Extract New Study Name
id: new-study
shell: bash
run: |
echo "NEW_STUDY_NAME=$( cut -d "/" -f2- <<< ${{ steps.new-dir.outputs.NEW_DIR_LOCATION }} )" >> $GITHUB_OUTPUT
preview:
needs: changed_files
runs-on: ubuntu-latest
container: docker.io/okteto/okteto:2.19.1
steps:
- name: Checkout Datahub Repository
uses: actions/checkout@v3
- name: Copy Files to Study Directory
shell: bash
run: |
# mkdir -p study/${{ needs.changed_files.outputs.new_study_name }}
cp -v -R ${{ needs.changed_files.outputs.new_study_dir }} preview_infrastructure/cbioportal-docker-compose/study/${{ needs.changed_files.outputs.new_study_name }}
- name: Context
uses: okteto/context@latest
with:
url: ${{secrets.OKTETO_URL}}
token: ${{ secrets.OKTETO_TOKEN }}
- name: Okteto Build to Import Studies
working-directory: preview_infrastructure/cbioportal-docker-compose
run: |
okteto build --no-cache -t okteto.dev/datahub-cbioportal:okteto-with-volume-mounts cbioportal
- name: Deploy preview environment
uses: okteto/deploy-preview@latest
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
with:
name: pr-${{ github.event.number }}-averyniceday
file: preview_infrastructure/cbioportal-docker-compose/okteto.yml
timeout: 15m
- name: Wait For Response
uses: nev7n/[email protected]
with:
url: 'https://cbioportal-pr-${{ github.event.number }}-averyniceday.cloud.okteto.net/'
responseCode: 200
timeout: 600000 # 10 minutes
interval: 30000 # 30 seconds
- name: "Activate Namespace"
uses: okteto/namespace@latest
with:
namespace: pr-${{github.event.number}}-averyniceday
- name: Kubectl test
run: |
okteto kubeconfig
kubectl exec -it deployment/cbioportal -- metaImport.py -u http://localhost:8080 -s study/${{needs.changed_files.outputs.new_study_name}}/ -o