diff --git a/.ebextensions/00_metakb_log.config b/.ebextensions/00_metakb_log.config index c6986363..aa4bc1b4 100644 --- a/.ebextensions/00_metakb_log.config +++ b/.ebextensions/00_metakb_log.config @@ -5,4 +5,4 @@ files: "/opt/elasticbeanstalk/tasks/taillogs.d/metakb.conf": content: | - /tmp/metakb.log \ No newline at end of file + /tmp/metakb.log diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index d0ef1cc3..e26a6b60 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -8,7 +8,7 @@ * If you're unable to find an open issue addressing the problem, [open a new one](https://github.com/cancervariants/metakb/issues/new). Be sure to include a **title and clear description**, as much relevant information as possible, and a **code sample** or an **executable test case** demonstrating the expected behavior that is not occurring. -* If possible, use the relevant bug report templates to create the issue. Simply copy the content of the appropriate template into a .rb file, make the necessary changes to demonstrate the issue, and **paste the content into the issue description**: +* If possible, use the relevant bug report templates to create the issue. Simply copy the content of the appropriate template into a .rb file, make the necessary changes to demonstrate the issue, and **paste the content into the issue description**: #### **Did you write a patch that fixes a bug?** diff --git a/docs/make.bat b/docs/make.bat index 7d65db30..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 +@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/reference/api/metakb.harvesters.base.rst b/docs/source/reference/api/metakb.harvesters.base.rst index 0c33d706..82d90ed0 100644 --- a/docs/source/reference/api/metakb.harvesters.base.rst +++ b/docs/source/reference/api/metakb.harvesters.base.rst @@ -5,4 +5,4 @@ :members: :undoc-members: :special-members: __init__ - :exclude-members: model_fields, model_config, model_computed_fields \ No newline at end of file + :exclude-members: model_fields, model_config, model_computed_fields diff --git a/docs/source/reference/api/metakb.harvesters.civic.rst b/docs/source/reference/api/metakb.harvesters.civic.rst index 09d18af8..6ee58f16 100644 --- a/docs/source/reference/api/metakb.harvesters.civic.rst +++ b/docs/source/reference/api/metakb.harvesters.civic.rst @@ -5,4 +5,4 @@ :members: :undoc-members: :special-members: __init__ - :exclude-members: model_fields, model_config, model_computed_fields \ No newline at end of file + :exclude-members: model_fields, model_config, model_computed_fields diff --git a/docs/source/reference/api/metakb.harvesters.moa.rst b/docs/source/reference/api/metakb.harvesters.moa.rst index a7543663..248d9279 100644 --- a/docs/source/reference/api/metakb.harvesters.moa.rst +++ b/docs/source/reference/api/metakb.harvesters.moa.rst @@ -5,4 +5,4 @@ :members: :undoc-members: :special-members: __init__ - :exclude-members: model_fields, model_config, model_computed_fields \ No newline at end of file + :exclude-members: model_fields, model_config, model_computed_fields diff --git a/docs/source/reference/api/metakb.normalizers.rst b/docs/source/reference/api/metakb.normalizers.rst index 123246c1..41fbdae6 100644 --- a/docs/source/reference/api/metakb.normalizers.rst +++ b/docs/source/reference/api/metakb.normalizers.rst @@ -5,4 +5,4 @@ :members: :undoc-members: :special-members: __init__ - :exclude-members: model_fields, model_config, model_computed_fields \ No newline at end of file + :exclude-members: model_fields, model_config, model_computed_fields diff --git a/docs/source/reference/api/metakb.query.rst b/docs/source/reference/api/metakb.query.rst index 385d0627..5f15fc7b 100644 --- a/docs/source/reference/api/metakb.query.rst +++ b/docs/source/reference/api/metakb.query.rst @@ -5,4 +5,4 @@ :members: :undoc-members: :special-members: __init__ - :exclude-members: model_fields, model_config, model_computed_fields \ No newline at end of file + :exclude-members: model_fields, model_config, model_computed_fields diff --git a/docs/source/reference/api/metakb.schemas.annotation.rst b/docs/source/reference/api/metakb.schemas.annotation.rst index a3e2d7cf..8a2c97f0 100644 --- a/docs/source/reference/api/metakb.schemas.annotation.rst +++ b/docs/source/reference/api/metakb.schemas.annotation.rst @@ -5,4 +5,4 @@ :members: :undoc-members: :special-members: __init__ - :exclude-members: model_fields, model_config, model_computed_fields \ No newline at end of file + :exclude-members: model_fields, model_config, model_computed_fields diff --git a/docs/source/reference/api/metakb.schemas.api.rst b/docs/source/reference/api/metakb.schemas.api.rst index daefb625..49454b40 100644 --- a/docs/source/reference/api/metakb.schemas.api.rst +++ b/docs/source/reference/api/metakb.schemas.api.rst @@ -5,4 +5,4 @@ :members: :undoc-members: :special-members: __init__ - :exclude-members: model_fields, model_config, model_computed_fields \ No newline at end of file + :exclude-members: model_fields, model_config, model_computed_fields diff --git a/docs/source/reference/api/metakb.schemas.app.rst b/docs/source/reference/api/metakb.schemas.app.rst index 21a97083..487c77a8 100644 --- a/docs/source/reference/api/metakb.schemas.app.rst +++ b/docs/source/reference/api/metakb.schemas.app.rst @@ -5,4 +5,4 @@ :members: :undoc-members: :special-members: __init__ - :exclude-members: model_fields, model_config, model_computed_fields \ No newline at end of file + :exclude-members: model_fields, model_config, model_computed_fields diff --git a/docs/source/reference/api/metakb.schemas.categorical_variation.rst b/docs/source/reference/api/metakb.schemas.categorical_variation.rst index e19603c8..22c60672 100644 --- a/docs/source/reference/api/metakb.schemas.categorical_variation.rst +++ b/docs/source/reference/api/metakb.schemas.categorical_variation.rst @@ -5,4 +5,4 @@ :members: :undoc-members: :special-members: __init__ - :exclude-members: model_fields, model_config, model_computed_fields \ No newline at end of file + :exclude-members: model_fields, model_config, model_computed_fields diff --git a/docs/source/reference/api/metakb.schemas.variation_statement.rst b/docs/source/reference/api/metakb.schemas.variation_statement.rst index 3f85e34e..57d72a36 100644 --- a/docs/source/reference/api/metakb.schemas.variation_statement.rst +++ b/docs/source/reference/api/metakb.schemas.variation_statement.rst @@ -5,4 +5,4 @@ :members: :undoc-members: :special-members: __init__ - :exclude-members: model_fields, model_config, model_computed_fields \ No newline at end of file + :exclude-members: model_fields, model_config, model_computed_fields diff --git a/tests/data/harvesters/civic/civic_variant_12.json b/tests/data/harvesters/civic/civic_variant_12.json index 5de88311..540aeae0 100644 --- a/tests/data/harvesters/civic/civic_variant_12.json +++ b/tests/data/harvesters/civic/civic_variant_12.json @@ -48,4 +48,4 @@ "V640E", "VAL640GLU" ] -} \ No newline at end of file +} diff --git a/tests/data/harvesters/moa/assertions.json b/tests/data/harvesters/moa/assertions.json index 960aef85..3d85b011 100644 --- a/tests/data/harvesters/moa/assertions.json +++ b/tests/data/harvesters/moa/assertions.json @@ -103,4 +103,4 @@ "therapy_type": "Combination therapy", "validated": true } -] \ No newline at end of file +] diff --git a/tests/data/harvesters/moa/variants.json b/tests/data/harvesters/moa/variants.json index 7aefa381..8d688fb7 100644 --- a/tests/data/harvesters/moa/variants.json +++ b/tests/data/harvesters/moa/variants.json @@ -19,4 +19,4 @@ "feature_id": 145, "feature_type": "somatic_variant" } -] \ No newline at end of file +]