diff --git a/.coveragerc b/.coveragerc index e7a7bd52..bd8953c9 100644 --- a/.coveragerc +++ b/.coveragerc @@ -4,4 +4,4 @@ source = tests/ omit = setup.py - docs/* \ No newline at end of file + docs/* diff --git a/Dockerfile b/Dockerfile index e3207f12..9f3a8192 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,6 +1,6 @@ # A simple container for gene-service. # Runs service on port 80. -# Healthchecks service up every 5m. +# Healthchecks service up every 5m. FROM python:3.7 RUN pip install pipenv uvicorn[standard] diff --git a/docs/make.bat b/docs/make.bat index 747ffb7b..dc1312ab 100644 --- a/docs/make.bat +++ b/docs/make.bat @@ -1,35 +1,35 @@ -@ECHO OFF - -pushd %~dp0 - -REM Command file for Sphinx documentation - -if "%SPHINXBUILD%" == "" ( - set SPHINXBUILD=sphinx-build -) -set SOURCEDIR=source -set BUILDDIR=build - -%SPHINXBUILD% >NUL 2>NUL -if errorlevel 9009 ( - echo. - echo.The 'sphinx-build' command was not found. Make sure you have Sphinx - echo.installed, then set the SPHINXBUILD environment variable to point - echo.to the full path of the 'sphinx-build' executable. Alternatively you - echo.may add the Sphinx directory to PATH. - echo. - echo.If you don't have Sphinx installed, grab it from - echo.https://www.sphinx-doc.org/ - exit /b 1 -) - -if "%1" == "" goto help - -%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% -goto end - -:help -%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% - -:end -popd +@ECHO OFF + +pushd %~dp0 + +REM Command file for Sphinx documentation + +if "%SPHINXBUILD%" == "" ( + set SPHINXBUILD=sphinx-build +) +set SOURCEDIR=source +set BUILDDIR=build + +%SPHINXBUILD% >NUL 2>NUL +if errorlevel 9009 ( + echo. + echo.The 'sphinx-build' command was not found. Make sure you have Sphinx + echo.installed, then set the SPHINXBUILD environment variable to point + echo.to the full path of the 'sphinx-build' executable. Alternatively you + echo.may add the Sphinx directory to PATH. + echo. + echo.If you don't have Sphinx installed, grab it from + echo.https://www.sphinx-doc.org/ + exit /b 1 +) + +if "%1" == "" goto help + +%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% +goto end + +:help +%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% + +:end +popd diff --git a/docs/source/managing_data/index.rst b/docs/source/managing_data/index.rst index a340b645..85c9824f 100644 --- a/docs/source/managing_data/index.rst +++ b/docs/source/managing_data/index.rst @@ -8,4 +8,3 @@ The current iteration of the Gene Normalizer stores millions of symbols, names, Loading and updating data DynamoDB storage backend PostgreSQL storage backend - diff --git a/tests/unit/data/etl_data/ncbi_history_20210813.tsv b/tests/unit/data/etl_data/ncbi_history_20210813.tsv index b7559bc0..76026be3 100644 --- a/tests/unit/data/etl_data/ncbi_history_20210813.tsv +++ b/tests/unit/data/etl_data/ncbi_history_20210813.tsv @@ -16,4 +16,4 @@ 9606 7637 100287429 LOC100287429 20110803 9606 - 103344718 HOTS 20200620 9606 - 544580 AASTH23 20190503 -9606 10036 107985297 LOC107985297 20220408 \ No newline at end of file +9606 10036 107985297 LOC107985297 20220408 diff --git a/tests/unit/dynamodb_build.bash b/tests/unit/dynamodb_build.bash index 98f84cce..a476be6f 100644 --- a/tests/unit/dynamodb_build.bash +++ b/tests/unit/dynamodb_build.bash @@ -3,4 +3,4 @@ mkdir ./tests/unit/dynamodb_local cd ./tests/unit/dynamodb_local curl -O "https://s3-us-west-2.amazonaws.com/dynamodb-local/dynamodb_local_latest.tar.gz" tar -xvzf dynamodb_local_latest.tar.gz; rm dynamodb_local_latest.tar.gz -java -jar DynamoDBLocal.jar & \ No newline at end of file +java -jar DynamoDBLocal.jar &