format

.ebextensions/00_metakb_log.config

@@ -5,4 +5,4 @@ files:
 
   "/opt/elasticbeanstalk/tasks/taillogs.d/metakb.conf":
     content: |
-      /tmp/metakb.log
+      /tmp/metakb.log

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?**

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

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
+   :exclude-members: model_fields, model_config, model_computed_fields

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
+   :exclude-members: model_fields, model_config, model_computed_fields

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
+   :exclude-members: model_fields, model_config, model_computed_fields

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
+   :exclude-members: model_fields, model_config, model_computed_fields

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
+   :exclude-members: model_fields, model_config, model_computed_fields

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
+   :exclude-members: model_fields, model_config, model_computed_fields

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
+   :exclude-members: model_fields, model_config, model_computed_fields

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
+   :exclude-members: model_fields, model_config, model_computed_fields

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
+   :exclude-members: model_fields, model_config, model_computed_fields

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
+   :exclude-members: model_fields, model_config, model_computed_fields

tests/data/harvesters/civic/civic_variant_12.json

@@ -48,4 +48,4 @@
     "V640E",
     "VAL640GLU"
   ]
-}
+}

tests/data/harvesters/moa/assertions.json

@@ -103,4 +103,4 @@
 		"therapy_type": "Combination therapy",
 		"validated": true
 	}
-]
+]

tests/data/harvesters/moa/variants.json

@@ -19,4 +19,4 @@
 		"feature_id": 145,
 		"feature_type": "somatic_variant"
 	}
-]
+]