Skip to content

Commit

Permalink
Merge pull request #227 from cancervariants/issue-226
Browse files Browse the repository at this point in the history 
Issue 226: psycopg2-binary + postgresql-devel
  • Loading branch information
@korikuzma
korikuzma authored Jan 27, 2022
2 parents 8797c5b + 5c77848 commit 09955ae
Show file tree
Hide file tree
Showing 5 changed files with 69 additions and 61 deletions.
35 changes: 17 additions & 18 deletions .ebextensions/01_download_data.config
View file
Original file line number Diff line number Diff line change
@@ -1,51 +1,50 @@
container_commands:
01_export_eb_env_var:
test: test ! -d "/usr/local/share/seqrepo"
command: "export $(cat /opt/elasticbeanstalk/deployment/env | xargs)"

02_install_awscli:
commands:
01_install_postgresql_devel:
command: "yum install -y python-devel postgresql-devel"
02_install_aws_cli:
command: "yum install -y awscli"

03_install_unzip:
test: test ! -d "/usr/local/share/seqrepo"
command: "yum install -y unzip"
04_export_eb_env_var:
command: "export $(cat /opt/elasticbeanstalk/deployment/env | xargs)"

05_refseq_gene_symbol_download:
container_commands:
01_refseq_gene_symbol_download:
test: test ! -f "./variation/data/refseq_gene_symbols.txt"
command: "aws s3 cp s3://${AWS_BUCKET_NAME}/variation/refseq_gene_symbols.txt ./variation/data/refseq_gene_symbols.txt --region us-east-2"

06_mane_grch38_refseq_download:
02_mane_grch38_refseq_download:
test: test ! -f "./variation/data/MANE.GRCh38.v0.93.summary.txt"
command: "aws s3 cp s3://${AWS_BUCKET_NAME}/variation/MANE.GRCh38.v0.93.summary.txt ./variation/data/MANE.GRCh38.v0.93.summary.txt --region us-east-2"

07_s3_download:
03_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"

08_unzip_seqrepo:
04_unzip_seqrepo:
test: test -f "/usr/local/share/seqrepo.zip"
command: "unzip /usr/local/share/seqrepo.zip -d /usr/local/share"

09_seqrepo_permission:
05_seqrepo_permission:
test: test -d "/usr/local/share/seqrepo"
command: "chmod -R 777 /usr/local/share/seqrepo"

10_macosx_permission:
06_macosx_permission:
test: test -d "/usr/local/share/__MACOSX"
command: "chmod -R +wr /usr/local/share/__MACOSX"

11_seqrepo_zip_permission:
07_seqrepo_zip_permission:
test: test -f "/usr/local/share/seqrepo.zip"
command: "chmod +wr /usr/local/share/seqrepo.zip"

12_remove_macosx:
08_remove_macosx:
test: test -d "/usr/local/share/__MACOSX"
command: "rm -R /usr/local/share/__MACOSX"

13_remove_seqrepo_zip:
09_remove_seqrepo_zip:
test: test -f "/usr/local/share/seqrepo.zip"
command: "rm /usr/local/share/seqrepo.zip"

14_data_permission:
10_data_permission:
test: test -d "/usr/local/share/seqrepo"
command: "chmod -R +wrx /usr/local/share/seqrepo"
1 change: 1 addition & 0 deletions Pipfile
View file
Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@ jupyter = "*"
ipykernel = "*"
twine = "*"
matplotlib = "*"
psycopg2-binary = "*"

[packages]
hgvs = "*"
Expand Down
45 changes: 23 additions & 22 deletions requirements-dev.txt
View file
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@
anyio==3.5.0; python_full_version >= '3.6.2'
appdirs==1.4.4
appnope==0.1.2; sys_platform == 'darwin'
argcomplete==2.0.0; python_version >= '3.6'
argcomplete==2.0.0; python_full_version >= '3.6.0'
argh==0.26.2
argon2-cffi-bindings==21.2.0; python_version >= '3.6'
argon2-cffi==21.3.0; python_version >= '3.6'
Expand All @@ -24,21 +24,21 @@ babel==2.9.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2,
backcall==0.2.0
beautifulsoup4==4.10.0; python_version >= '3.1'
biocommons.seqrepo==0.6.5
bioutils==0.5.5; python_version >= '3.6'
bioutils==0.5.5; python_full_version >= '3.6.0'
black==21.12b0; python_full_version >= '3.6.2'
bleach==4.1.0; python_version >= '3.6'
boto3==1.20.44
botocore==1.23.44; python_version >= '3.6'
botocore==1.23.44; python_full_version >= '3.6.0'
bs4==0.0.1
canonicaljson==1.5.0; python_version ~= '3.5'
certifi==2021.10.8
cffi==1.15.0
cfgv==3.3.1; python_full_version >= '3.6.1'
charset-normalizer==2.0.10; python_version >= '3'
click==8.0.3; python_version >= '3.6'
click==8.0.3; python_full_version >= '3.6.0'
colorama==0.4.4; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
coloredlogs==15.0.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
configparser==5.2.0; python_version >= '3.6'
configparser==5.2.0; python_full_version >= '3.6.0'
coverage==6.3
coveralls==3.3.1
cssselect==1.1.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
Expand All @@ -57,13 +57,13 @@ filelock==3.4.2; python_version >= '3.7'
flake8-docstrings==1.6.0
flake8==4.0.1
fonttools==4.29.0; python_version >= '3.7'
frozendict==2.2.0; python_version >= '3.6'
frozendict==2.2.1; python_full_version >= '3.6.0'
ga4gh.vrs[extras]==0.7.2
ga4gh.vrsatile.pydantic==0.0.6
gene-normalizer==0.1.24
gffutils==0.10.1
greenlet==1.1.2; python_version >= '3' and platform_machine == 'aarch64' or (platform_machine == 'ppc64le' or (platform_machine == 'x86_64' or (platform_machine == 'amd64' or (platform_machine == 'AMD64' or (platform_machine == 'win32' or platform_machine == 'WIN32')))))
h11==0.13.0; python_version >= '3.6'
h11==0.13.0; python_full_version >= '3.6.0'
hgvs==1.5.2
httptools==0.3.0
humanfriendly==10.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
Expand All @@ -76,7 +76,7 @@ ipykernel==6.7.0
ipython-genutils==0.2.0
ipython==8.0.1; python_version >= '3.8'
ipywidgets==7.6.5
jedi==0.18.1; python_version >= '3.6'
jedi==0.18.1; python_full_version >= '3.6.0'
jinja2==3.0.3; python_version >= '3.6'
jmespath==0.10.0; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'
json5==0.9.6
Expand All @@ -93,7 +93,7 @@ jupyterlab==3.2.8
keyring==23.5.0; python_version >= '3.7'
kiwisolver==1.3.2; python_version >= '3.7'
lxml==4.7.1
markdown==3.3.6; python_version >= '3.6'
markdown==3.3.6; python_full_version >= '3.6.0'
markupsafe==2.0.1; python_version >= '3.6'
matplotlib-inline==0.1.3; python_version >= '3.5'
matplotlib==3.5.1
Expand All @@ -107,13 +107,13 @@ nbformat==5.1.3; python_version >= '3.5'
nest-asyncio==1.5.4; python_version >= '3.5'
nodeenv==1.6.0
notebook==6.4.8; python_version >= '3.6'
numpy==1.22.1; python_version < '3.10' and platform_machine != 'aarch64' and platform_machine != 'arm64'
numpy==1.22.1; python_version >= '3.8'
packaging==21.3; python_version >= '3.6'
pandas==1.4.0
pandocfilters==1.5.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
parse==1.19.0
parsley==1.3
parso==0.8.3; python_version >= '3.6'
parso==0.8.3; python_full_version >= '3.6.0'
pathspec==0.9.0
pexpect==4.8.0; sys_platform != 'win32'
pickleshare==0.7.5
Expand All @@ -123,8 +123,9 @@ platformdirs==2.4.1; python_version >= '3.7'
pluggy==1.0.0; python_version >= '3.6'
pre-commit==2.17.0
prometheus-client==0.13.0; python_version >= '3.6'
prompt-toolkit==3.0.24; python_full_version >= '3.6.2'
psycopg2==2.9.3; python_version >= '3.6'
prompt-toolkit==3.0.25; python_full_version >= '3.6.2'
psycopg2-binary==2.9.3
psycopg2==2.9.3; python_full_version >= '3.6.0'
ptyprocess==0.7.0
pure-eval==0.2.2
py==1.11.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
Expand All @@ -138,7 +139,7 @@ pyflakes==2.4.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.
pygments==2.11.2; python_version >= '3.5'
pyliftover==0.4
pyparsing==3.0.7; python_version >= '3.6'
pyppeteer==1.0.2; python_version >= '3.7' and python_version < '4.0'
pyppeteer==1.0.2; python_version >= '3.7' and python_version < '4'
pyquery==1.4.3
pyrsistent==0.18.1; python_version >= '3.7'
pysam==0.18.0
Expand All @@ -147,38 +148,38 @@ pytest==6.2.5
python-dateutil==2.8.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
python-jsonschema-objects==0.4.1
pytz==2021.3
pyyaml==6.0; python_version >= '3.6'
pyyaml==6.0; python_full_version >= '3.6.0'
pyzmq==22.3.0; python_version >= '3.6'
qtconsole==5.2.2; python_version >= '3.6'
qtpy==2.0.0; python_version >= '3.6'
readme-renderer==32.0; python_version >= '3.6'
requests-html==0.10.0; python_version >= '3.6'
requests-html==0.10.0; python_full_version >= '3.6.0'
requests-toolbelt==0.9.1
requests==2.27.1
rfc3986==2.0.0; python_version >= '3.7'
s3transfer==0.5.0; python_version >= '3.6'
s3transfer==0.5.0; python_full_version >= '3.6.0'
send2trash==1.8.0
setuptools==60.5.0; python_version >= '3.7'
simplejson==3.17.6; python_version >= '2.5' and python_version not in '3.0, 3.1, 3.2, 3.3'
six==1.16.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
sniffio==1.2.0; python_version >= '3.5'
snowballstemmer==2.2.0
soupsieve==2.3.1; python_version >= '3.6'
soupsieve==2.3.1; python_full_version >= '3.6.0'
sqlalchemy==1.4.31
sqlparse==0.4.2; python_version >= '3.5'
stack-data==0.1.4
starlette==0.17.1; python_version >= '3.6'
starlette==0.17.1; python_full_version >= '3.6.0'
tabulate==0.8.9
terminado==0.12.1; python_version >= '3.6'
terminado==0.13.0; python_version >= '3.6'
testpath==0.5.0; python_version >= '3.5'
toml==0.10.2; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'
tomli==1.2.3; python_version >= '3.6'
tomli==1.2.3; python_full_version >= '3.6.0'
tornado==6.1; python_version >= '3.5'
tqdm==4.62.3; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
traitlets==5.1.1; python_version >= '3.7'
twine==3.7.1
typing-extensions==4.0.1
urllib3==1.26.8; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4.0'
urllib3==1.26.8; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4'
uvicorn==0.17.0.post1
uvloop==0.16.0
virtualenv==20.13.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
Expand Down
42 changes: 21 additions & 21 deletions requirements.txt
View file
Original file line number Diff line number Diff line change
Expand Up @@ -9,95 +9,95 @@
anyio==3.5.0; python_full_version >= '3.6.2'
appdirs==1.4.4
appnope==0.1.2; sys_platform == 'darwin'
argcomplete==2.0.0; python_version >= '3.6'
argcomplete==2.0.0; python_full_version >= '3.6.0'
argh==0.26.2
asgiref==3.5.0; python_version >= '3.7'
asttokens==2.0.5
attrs==21.4.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
backcall==0.2.0
beautifulsoup4==4.10.0; python_version >= '3.1'
biocommons.seqrepo==0.6.5
bioutils==0.5.5; python_version >= '3.6'
bioutils==0.5.5; python_full_version >= '3.6.0'
black==21.12b0; python_full_version >= '3.6.2'
boto3==1.20.44
botocore==1.23.44; python_version >= '3.6'
botocore==1.23.44; python_full_version >= '3.6.0'
bs4==0.0.1
canonicaljson==1.5.0; python_version ~= '3.5'
certifi==2021.10.8
charset-normalizer==2.0.10; python_version >= '3'
click==8.0.3; python_version >= '3.6'
click==8.0.3; python_full_version >= '3.6.0'
coloredlogs==15.0.1; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
configparser==5.2.0; python_version >= '3.6'
configparser==5.2.0; python_full_version >= '3.6.0'
cssselect==1.1.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
decorator==5.1.1; python_version >= '3.5'
executing==0.8.2
fake-useragent==0.1.11
fastapi==0.73.0
frozendict==2.2.0; python_version >= '3.6'
frozendict==2.2.1; python_full_version >= '3.6.0'
ga4gh.vrs[extras]==0.7.2
ga4gh.vrsatile.pydantic==0.0.6
gene-normalizer==0.1.24
gffutils==0.10.1
greenlet==1.1.2; python_version >= '3' and platform_machine == 'aarch64' or (platform_machine == 'ppc64le' or (platform_machine == 'x86_64' or (platform_machine == 'amd64' or (platform_machine == 'AMD64' or (platform_machine == 'win32' or platform_machine == 'WIN32')))))
h11==0.13.0; python_version >= '3.6'
h11==0.13.0; python_full_version >= '3.6.0'
hgvs==1.5.2
httptools==0.3.0
humanfriendly==10.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4'
idna==3.3; python_version >= '3'
importlib-metadata==4.10.1; python_version < '3.10'
inflection==0.5.1; python_version >= '3.5'
ipython==8.0.1; python_version >= '3.8'
jedi==0.18.1; python_version >= '3.6'
jedi==0.18.1; python_full_version >= '3.6.0'
jmespath==0.10.0; python_version >= '2.6' and python_version not in '3.0, 3.1, 3.2, 3.3'
jsonschema==3.2.0
lxml==4.7.1
markdown==3.3.6; python_version >= '3.6'
markdown==3.3.6; python_full_version >= '3.6.0'
matplotlib-inline==0.1.3; python_version >= '3.5'
mypy-extensions==0.4.3
numpy==1.22.1; python_version < '3.10' and platform_machine != 'aarch64' and platform_machine != 'arm64'
numpy==1.22.1; python_version >= '3.8'
pandas==1.4.0
parse==1.19.0
parsley==1.3
parso==0.8.3; python_version >= '3.6'
parso==0.8.3; python_full_version >= '3.6.0'
pathspec==0.9.0
pexpect==4.8.0; sys_platform != 'win32'
pickleshare==0.7.5
platformdirs==2.4.1; python_version >= '3.7'
prompt-toolkit==3.0.24; python_full_version >= '3.6.2'
psycopg2==2.9.3; python_version >= '3.6'
prompt-toolkit==3.0.25; python_full_version >= '3.6.2'
psycopg2==2.9.3; python_full_version >= '3.6.0'
ptyprocess==0.7.0
pure-eval==0.2.2
pydantic==1.9.0
pyee==8.2.2
pyfaidx==0.6.3.1
pygments==2.11.2; python_version >= '3.5'
pyliftover==0.4
pyppeteer==1.0.2; python_version >= '3.7' and python_version < '4.0'
pyppeteer==1.0.2; python_version >= '3.7' and python_version < '4'
pyquery==1.4.3
pyrsistent==0.18.1; python_version >= '3.7'
pysam==0.18.0
python-dateutil==2.8.2; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
python-jsonschema-objects==0.4.1
pytz==2021.3
pyyaml==6.0; python_version >= '3.6'
requests-html==0.10.0; python_version >= '3.6'
pyyaml==6.0; python_full_version >= '3.6.0'
requests-html==0.10.0; python_full_version >= '3.6.0'
requests==2.27.1
s3transfer==0.5.0; python_version >= '3.6'
s3transfer==0.5.0; python_full_version >= '3.6.0'
setuptools==60.5.0; python_version >= '3.7'
simplejson==3.17.6; python_version >= '2.5' and python_version not in '3.0, 3.1, 3.2, 3.3'
six==1.16.0; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
sniffio==1.2.0; python_version >= '3.5'
soupsieve==2.3.1; python_version >= '3.6'
soupsieve==2.3.1; python_full_version >= '3.6.0'
sqlalchemy==1.4.31
sqlparse==0.4.2; python_version >= '3.5'
stack-data==0.1.4
starlette==0.17.1; python_version >= '3.6'
starlette==0.17.1; python_full_version >= '3.6.0'
tabulate==0.8.9
tomli==1.2.3; python_version >= '3.6'
tomli==1.2.3; python_full_version >= '3.6.0'
tqdm==4.62.3; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3'
traitlets==5.1.1; python_version >= '3.7'
typing-extensions==4.0.1
urllib3==1.26.8; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4.0'
urllib3==1.26.8; python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4'
uvicorn==0.17.0.post1
uvloop==0.16.0
w3lib==1.22.0
Expand Down
7 changes: 7 additions & 0 deletions setup.cfg
View file
Original file line number Diff line number Diff line change
Expand Up @@ -50,5 +50,12 @@ variation =
data/transcript_mapping.tsv


[options.extras_require]
dev =
pytest
pytest-cov
pyyaml
psycopg2-binary

[tool:pytest]
addopts = --ignore setup.py --doctest-modules --cov-report term-missing --cov .

0 comments on commit 09955ae

Please sign in to comment.