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cicd: update elastic beanstalk commands #280

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merged 51 commits into from
Mar 28, 2024
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eea8917
feat!: update database to reflect schema changes (#264)
korikuzma Dec 20, 2023
f49e5ed
fix: bugs in database code (#267)
korikuzma Dec 20, 2023
7c32e37
feat: include type in nodes representing VRS objects (#268)
korikuzma Jan 2, 2024
bc8e3af
fix: db should include gene aliases (#275)
korikuzma Jan 3, 2024
537a219
merge update-test-data
korikuzma Jan 3, 2024
09ae1b3
wip: store progress
korikuzma Jan 3, 2024
3eba709
add more tests
korikuzma Jan 4, 2024
8b1c22e
resolve deprecation warning for event loop redefined
korikuzma Jan 4, 2024
70e5099
cleanup
korikuzma Jan 4, 2024
5350f73
handle some exceptions
korikuzma Jan 4, 2024
1f286e0
add tests for combo / sub therapies
korikuzma Jan 4, 2024
c7f80e2
more cleanup
korikuzma Jan 4, 2024
6d7f02e
chore: update elastic beanstalk commands
korikuzma Jan 8, 2024
3064881
tests: update civic + moa test data (#276) (#281)
korikuzma Jan 8, 2024
9c26cc8
allow querying based on has_members rel + has_defining_context rel
korikuzma Jan 9, 2024
85eb3e1
Merge branch 'issue-273' into issue-238
korikuzma Jan 9, 2024
9824a0b
Merge branch 'epic-231' into epic-231-db
korikuzma Mar 15, 2024
5a50cfa
test: update database to reflect normalizer_data in extensions
korikuzma Mar 15, 2024
992e4ff
revert
korikuzma Mar 22, 2024
c720ac7
Merge branch 'epic-231-db' into issue-273
korikuzma Mar 22, 2024
8c82551
update tests to reflect cdm changes
korikuzma Mar 25, 2024
6e18fb6
Merge branch 'issue-273' into issue-238
korikuzma Mar 25, 2024
2ce74cd
update deps + digests
korikuzma Mar 25, 2024
a92c350
Merge branch 'update-deps' into epic-231-db
korikuzma Mar 25, 2024
cb5a7d1
update digests
korikuzma Mar 25, 2024
18b512e
Merge branch 'epic-231-db' into issue-273
korikuzma Mar 25, 2024
f08e8f0
Merge branch 'epic-231' into epic-231-db
korikuzma Mar 25, 2024
ce499fa
Merge branch 'epic-231-db' into issue-273
korikuzma Mar 25, 2024
0be32ae
update api to dump response
korikuzma Mar 25, 2024
98847c6
udpate LOC KEYS to incl digest
korikuzma Mar 25, 2024
58d49b5
Merge branch 'epic-231-db' into issue-273
korikuzma Mar 25, 2024
22cb4e5
udpate digests
korikuzma Mar 25, 2024
b64c64d
fix tests
korikuzma Mar 25, 2024
c38a794
Merge branch 'epic-231-db' into issue-273
korikuzma Mar 25, 2024
09862de
test: update civicpy cache data
korikuzma Mar 25, 2024
a06d013
Merge branch 'update-civicpy-cache' into epic-231-db
korikuzma Mar 25, 2024
7b6af79
Merge branch 'epic-231-db' into issue-273
korikuzma Mar 25, 2024
b2e8256
Merge branch 'issue-273' into issue-238
korikuzma Mar 25, 2024
21987ab
Merge branch 'epic-231' into epic-231-db
korikuzma Mar 26, 2024
577b95b
cleanup
korikuzma Mar 26, 2024
ef44c6c
cleanup secret
korikuzma Mar 26, 2024
abcc149
better name for catvar key
korikuzma Mar 26, 2024
29e42a8
format
korikuzma Mar 26, 2024
2314201
Merge branch 'epic-231-db' into issue-273
korikuzma Mar 26, 2024
077d29b
cleanup
korikuzma Mar 27, 2024
7333d30
Merge branch 'epic-231' into issue-273
korikuzma Mar 27, 2024
a93252e
fix: creating location parameterized query string
korikuzma Mar 27, 2024
c1ed28f
Merge branch 'fix-db-keys' into issue-273
korikuzma Mar 27, 2024
5518bb0
StrEnum -> str, Enum
korikuzma Mar 27, 2024
1acadbc
Merge branch 'issue-273' into issue-238
korikuzma Mar 27, 2024
a22b2c9
Merge branch 'epic-231' into issue-238
korikuzma Mar 28, 2024
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Original file line number Diff line number Diff line change
Expand Up @@ -3,25 +3,25 @@ commands:
command: "yum install -y python-devel postgresql-devel"
02_install_aws_cli:
command: "yum install -y awscli"
03_install_unzip:
command: "yum install -y unzip"
03_install_p7zip:
command: "yum install -y p7zip"
04_eb_packages:
command: "/var/app/venv/staging-LQM1lest/bin/pip install uvloop websockets httptools typing-extensions"
05_export_eb_env_var:
command: "export $(cat /opt/elasticbeanstalk/deployment/env | xargs)"

container_commands:
01_uta_permissions:
test: test -d "/var/app/venv/staging-LQM1lest/lib/python3.8/site-packages/uta_tools"
command: "chmod -R 777 /var/app/venv/staging-LQM1lest/lib/python3.8/site-packages/uta_tools/data"
01_cool_seq_tool_permissions:
test: test -d "/var/app/venv/staging-LQM1lest/lib/python3.11/site-packages/cool_seq_tool"
command: "chmod -R 777 /var/app/venv/staging-LQM1lest/lib/python3.11/site-packages/cool_seq_tool/data"

02_s3_download:
test: test ! -d "/usr/local/share/seqrepo"
command: "aws s3 cp s3://${AWS_BUCKET_NAME}/${AWS_SEQREPO_OBJECT} /usr/local/share/seqrepo.zip --region us-east-2"

03_unzip_seqrepo:
03_p7zip_seqrepo:
test: test -f "/usr/local/share/seqrepo.zip"
command: "unzip /usr/local/share/seqrepo.zip -d /usr/local/share"
command: "7za x /usr/local/share/seqrepo.zip -o/usr/local/share -y"
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04_seqrepo_permission:
test: test -d "/usr/local/share/seqrepo"
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