<?xml version="1.0"?>
<!DOCTYPE module PUBLIC
  "-//Checkstyle//DTD Checkstyle Configuration 1.3//EN"
  "https://checkstyle.org/dtds/configuration_1_3.dtd">

<!--
    Checkstyle configuration that checks the Google coding conventions from Google Java Style
    that can be found at https://google.github.io/styleguide/javaguide.html

    Checkstyle is very configurable. Be sure to read the documentation at
    http://checkstyle.org (or in your downloaded distribution).

    To completely disable a check, just comment it out or delete it from the file.
    To suppress certain violations please review suppression filters.

    Authors: Max Vetrenko, Ruslan Diachenko, Roman Ivanov.
 -->

<module name = "Checker">
    <property name="charset" value="UTF-8"/>

    <!-- Dockstore override, warning to error -->
    <property name="severity" value="error"/>

    <property name="fileExtensions" value="java, properties, xml"/>
    <!-- Excludes all 'module-info.java' files              -->
    <!-- See https://checkstyle.org/config_filefilters.html -->
    <module name="BeforeExecutionExclusionFileFilter">
        <property name="fileNamePattern" value="module\-info\.java$"/>
    </module>
    <!-- https://checkstyle.org/config_filters.html#SuppressionFilter -->
    <module name="SuppressionFilter">
        <property name="file" value="${org.checkstyle.google.suppressionfilter.config}"
          default="checkstyle-suppressions.xml" />
        <property name="optional" value="true"/>
    </module>

    <!-- Checks for whitespace                               -->
    <!-- See http://checkstyle.org/config_whitespace.html -->
    <module name="FileTabCharacter">
        <property name="eachLine" value="true"/>
    </module>

    <module name="LineLength">
        <property name="fileExtensions" value="java"/>
        <!-- Dockstore override, addition -->
        <property name="severity" value="warning"/>
        <!-- Dockstore override, 100 to 200 -->
        <property name="max" value="200"/>
        <property name="ignorePattern" value="^package.*|^import.*|a href|href|http://|https://|ftp://"/>
    </module>
    <!-- Dockstore override, addition -->
    <module name="SuppressWarningsFilter"/>
    <module name="TreeWalker">
        <!-- Dockstore override, addition -->
        <module name="SuppressWarningsHolder"/>
        <module name="OuterTypeFilename"/>
        <module name="IllegalTokenText">
            <property name="tokens" value="STRING_LITERAL, CHAR_LITERAL"/>
            <property name="format"
              value="\\u00(09|0(a|A)|0(c|C)|0(d|D)|22|27|5(C|c))|\\(0(10|11|12|14|15|42|47)|134)"/>
            <property name="message"
              value="Consider using special escape sequence instead of octal value or Unicode escaped value."/>
        </module>
        <module name="AvoidEscapedUnicodeCharacters">
            <property name="allowEscapesForControlCharacters" value="true"/>
            <property name="allowByTailComment" value="true"/>
            <property name="allowNonPrintableEscapes" value="true"/>
        </module>
        <module name="AvoidStarImport"/>
        <module name="OneTopLevelClass"/>
        <module name="NoLineWrap">
            <property name="tokens" value="PACKAGE_DEF, IMPORT, STATIC_IMPORT"/>
        </module>
        <module name="EmptyBlock">
            <property name="option" value="TEXT"/>
            <property name="tokens"
              value="LITERAL_TRY, LITERAL_FINALLY, LITERAL_IF, LITERAL_ELSE, LITERAL_SWITCH"/>
        </module>
        <module name="NeedBraces">
            <property name="tokens"
              value="LITERAL_DO, LITERAL_ELSE, LITERAL_FOR, LITERAL_IF, LITERAL_WHILE"/>
        </module>
        <module name="LeftCurly">
            <property name="tokens"
              value="ANNOTATION_DEF, CLASS_DEF, CTOR_DEF, ENUM_CONSTANT_DEF, ENUM_DEF,
                    INTERFACE_DEF, LAMBDA, LITERAL_CASE, LITERAL_CATCH, LITERAL_DEFAULT,
                    LITERAL_DO, LITERAL_ELSE, LITERAL_FINALLY, LITERAL_FOR, LITERAL_IF,
                    LITERAL_SWITCH, LITERAL_SYNCHRONIZED, LITERAL_TRY, LITERAL_WHILE, METHOD_DEF,
                    OBJBLOCK, STATIC_INIT"/>
        </module>
        <module name="RightCurly">
            <property name="id" value="RightCurlySame"/>
            <property name="tokens"
              value="LITERAL_TRY, LITERAL_CATCH, LITERAL_FINALLY, LITERAL_IF, LITERAL_ELSE,
                    LITERAL_DO"/>
        </module>
        <module name="RightCurly">
            <property name="id" value="RightCurlyAlone"/>
            <property name="option" value="alone"/>
            <property name="tokens"
              value="CLASS_DEF, METHOD_DEF, CTOR_DEF, LITERAL_FOR, LITERAL_WHILE, STATIC_INIT,
                    INSTANCE_INIT, ANNOTATION_DEF, ENUM_DEF, INTERFACE_DEF"/>
        </module>
        <module name="SuppressionXpathSingleFilter">
            <!-- suppresion is required till https://github.com/checkstyle/checkstyle/issues/7541 -->
            <property name="id" value="RightCurlyAlone"/>
            <property name="query" value="//RCURLY[parent::SLIST[count(./*)=1]
                                                 or preceding-sibling::*[last()][self::LCURLY]]"/>
        </module>
        <module name="WhitespaceAfter">
            <!-- Dockstore override, see comment, 200+ errors with TYPECAST added back in-->
            <property name="tokens"
              value="COMMA, SEMI, LITERAL_IF, LITERAL_ELSE,
                    LITERAL_WHILE, LITERAL_DO, LITERAL_FOR, DO_WHILE"/>
<!--            <property name="tokens"-->
<!--              value="COMMA, SEMI, TYPECAST, LITERAL_IF, LITERAL_ELSE,-->
<!--                    LITERAL_WHILE, LITERAL_DO, LITERAL_FOR, DO_WHILE"/>-->
        </module>
        <module name="WhitespaceAround">
            <property name="allowEmptyConstructors" value="true"/>
            <property name="allowEmptyLambdas" value="true"/>
            <property name="allowEmptyMethods" value="true"/>
            <property name="allowEmptyTypes" value="true"/>
            <property name="allowEmptyLoops" value="true"/>
            <property name="tokens"
              value="ASSIGN, BAND, BAND_ASSIGN, BOR, BOR_ASSIGN, BSR, BSR_ASSIGN, BXOR,
                    BXOR_ASSIGN, COLON, DIV, DIV_ASSIGN, DO_WHILE, EQUAL, GE, GT, LAMBDA, LAND,
                    LCURLY, LE, LITERAL_CATCH, LITERAL_DO, LITERAL_ELSE, LITERAL_FINALLY,
                    LITERAL_FOR, LITERAL_IF, LITERAL_RETURN, LITERAL_SWITCH, LITERAL_SYNCHRONIZED,
                     LITERAL_TRY, LITERAL_WHILE, LOR, LT, MINUS, MINUS_ASSIGN, MOD, MOD_ASSIGN,
                     NOT_EQUAL, PLUS, PLUS_ASSIGN, QUESTION, RCURLY, SL, SLIST, SL_ASSIGN, SR,
                     SR_ASSIGN, STAR, STAR_ASSIGN, LITERAL_ASSERT, TYPE_EXTENSION_AND"/>
            <message key="ws.notFollowed"
              value="WhitespaceAround: ''{0}'' is not followed by whitespace. Empty blocks may only be represented as '{}' when not part of a multi-block statement (4.1.3)"/>
            <message key="ws.notPreceded"
              value="WhitespaceAround: ''{0}'' is not preceded with whitespace."/>
        </module>
        <module name="OneStatementPerLine"/>
        <module name="MultipleVariableDeclarations"/>
        <module name="ArrayTypeStyle"/>
        <module name="MissingSwitchDefault"/>
        <module name="FallThrough"/>
        <module name="UpperEll"/>
        <module name="ModifierOrder"/>

        <module name="EmptyLineSeparator">
            <!-- Dockstore override, see comment -->
            <property name="tokens"
              value="IMPORT, STATIC_IMPORT, INTERFACE_DEF, ENUM_DEF,
                    STATIC_INIT, INSTANCE_INIT, CTOR_DEF, VARIABLE_DEF"/>
            <!--            <property name="tokens"-->
            <!--              value="PACKAGE_DEF, IMPORT, STATIC_IMPORT, CLASS_DEF, INTERFACE_DEF, ENUM_DEF,-->
            <!--                    STATIC_INIT, INSTANCE_INIT, METHOD_DEF, CTOR_DEF, VARIABLE_DEF"/>-->
            <property name="allowNoEmptyLineBetweenFields" value="true"/>
        </module>
        <module name="SeparatorWrap">
            <property name="id" value="SeparatorWrapDot"/>
            <property name="tokens" value="DOT"/>
            <property name="option" value="nl"/>
        </module>
        <module name="SeparatorWrap">
            <property name="id" value="SeparatorWrapComma"/>
            <property name="tokens" value="COMMA"/>
            <property name="option" value="EOL"/>
        </module>
        <module name="SeparatorWrap">
            <!-- ELLIPSIS is EOL until https://github.com/google/styleguide/issues/258 -->
            <property name="id" value="SeparatorWrapEllipsis"/>
            <property name="tokens" value="ELLIPSIS"/>
            <property name="option" value="EOL"/>
        </module>
        <module name="SeparatorWrap">
            <!-- ARRAY_DECLARATOR is EOL until https://github.com/google/styleguide/issues/259 -->
            <property name="id" value="SeparatorWrapArrayDeclarator"/>
            <property name="tokens" value="ARRAY_DECLARATOR"/>
            <property name="option" value="EOL"/>
        </module>
        <module name="SeparatorWrap">
            <property name="id" value="SeparatorWrapMethodRef"/>
            <property name="tokens" value="METHOD_REF"/>
            <property name="option" value="nl"/>
        </module>
        <module name="PackageName">
            <!-- Dockstore override, addition -->
            <property name="severity" value="warning"/>
            <property name="format" value="^[a-z]+(\.[a-z][a-z0-9]*)*$"/>
            <message key="name.invalidPattern"
              value="Package name ''{0}'' must match pattern ''{1}''."/>
        </module>
        <module name="TypeName">
            <property name="tokens" value="CLASS_DEF, INTERFACE_DEF, ENUM_DEF, ANNOTATION_DEF"/>
            <message key="name.invalidPattern"
              value="Type name ''{0}'' must match pattern ''{1}''."/>
        </module>
        <module name="MemberName">
            <!-- Dockstore override, removal -->
<!--            <property name="format" value="^[a-z][a-z0-9][a-zA-Z0-9]*$"/>-->
            <message key="name.invalidPattern"
              value="Member name ''{0}'' must match pattern ''{1}''."/>
        </module>
        <module name="ParameterName">
            <!-- Dockstore override, removal -->
<!--            <property name="format" value="^[a-z]([a-z0-9][a-zA-Z0-9]*)?$"/>-->
            <message key="name.invalidPattern"
              value="Parameter name ''{0}'' must match pattern ''{1}''."/>
        </module>
        <module name="LambdaParameterName">
            <property name="format" value="^[a-z]([a-z0-9][a-zA-Z0-9]*)?$"/>
            <message key="name.invalidPattern"
              value="Lambda parameter name ''{0}'' must match pattern ''{1}''."/>
        </module>
        <module name="CatchParameterName">
            <property name="format" value="^[a-z]([a-z0-9][a-zA-Z0-9]*)?$"/>
            <message key="name.invalidPattern"
              value="Catch parameter name ''{0}'' must match pattern ''{1}''."/>
        </module>
        <module name="LocalVariableName">
            <!-- Dockstore override, removal -->
<!--            <property name="format" value="^[a-z]([a-z0-9][a-zA-Z0-9]*)?$"/>-->
            <message key="name.invalidPattern"
              value="Local variable name ''{0}'' must match pattern ''{1}''."/>
        </module>
        <module name="ClassTypeParameterName">
            <property name="format" value="(^[A-Z][0-9]?)$|([A-Z][a-zA-Z0-9]*[T]$)"/>
            <message key="name.invalidPattern"
              value="Class type name ''{0}'' must match pattern ''{1}''."/>
        </module>
        <module name="MethodTypeParameterName">
            <property name="format" value="(^[A-Z][0-9]?)$|([A-Z][a-zA-Z0-9]*[T]$)"/>
            <message key="name.invalidPattern"
              value="Method type name ''{0}'' must match pattern ''{1}''."/>
        </module>
        <module name="InterfaceTypeParameterName">
            <property name="format" value="(^[A-Z][0-9]?)$|([A-Z][a-zA-Z0-9]*[T]$)"/>
            <message key="name.invalidPattern"
              value="Interface type name ''{0}'' must match pattern ''{1}''."/>
        </module>
        <module name="NoFinalizer"/>
        <module name="GenericWhitespace">
            <message key="ws.followed"
              value="GenericWhitespace ''{0}'' is followed by whitespace."/>
            <message key="ws.preceded"
              value="GenericWhitespace ''{0}'' is preceded with whitespace."/>
            <message key="ws.illegalFollow"
              value="GenericWhitespace ''{0}'' should followed by whitespace."/>
            <message key="ws.notPreceded"
              value="GenericWhitespace ''{0}'' is not preceded with whitespace."/>
        </module>
        <module name="Indentation">
            <!-- Dockstore override, 2 to 4 -->
            <property name="basicOffset" value="4"/>
            <property name="braceAdjustment" value="0"/>
            <!-- Dockstore override, 2 to 0 -->
            <property name="caseIndent" value="0"/>
            <property name="throwsIndent" value="4"/>
            <property name="lineWrappingIndentation" value="4"/>
            <property name="arrayInitIndent" value="2"/>
        </module>
        <module name="AbbreviationAsWordInName">
            <property name="ignoreFinal" value="false"/>
            <!-- Dockstore override, 1 to 6 -->
            <property name="allowedAbbreviationLength" value="6"/>
            <property name="tokens"
              value="CLASS_DEF, INTERFACE_DEF, ENUM_DEF, ANNOTATION_DEF, ANNOTATION_FIELD_DEF,
                    PARAMETER_DEF, VARIABLE_DEF, METHOD_DEF"/>
        </module>
        <module name="OverloadMethodsDeclarationOrder"/>
        <!-- Dockstore override, removal -->
<!--        <module name="VariableDeclarationUsageDistance"/>-->
        <module name="CustomImportOrder">
            <property name="sortImportsInGroupAlphabetically" value="true"/>
            <property name="separateLineBetweenGroups" value="true"/>
            <property name="customImportOrderRules" value="STATIC###THIRD_PARTY_PACKAGE"/>
            <property name="tokens" value="IMPORT, STATIC_IMPORT, PACKAGE_DEF"/>
        </module>
        <module name="MethodParamPad">
            <property name="tokens"
              value="CTOR_DEF, LITERAL_NEW, METHOD_CALL, METHOD_DEF,
                    SUPER_CTOR_CALL, ENUM_CONSTANT_DEF"/>
        </module>
        <module name="NoWhitespaceBefore">
            <property name="tokens"
              value="COMMA, SEMI, POST_INC, POST_DEC, DOT,
                    LABELED_STAT, METHOD_REF"/>
            <property name="allowLineBreaks" value="true"/>
        </module>
        <module name="ParenPad">
            <property name="tokens"
              value="ANNOTATION, ANNOTATION_FIELD_DEF, CTOR_CALL, CTOR_DEF, DOT, ENUM_CONSTANT_DEF,
                    EXPR, LITERAL_CATCH, LITERAL_DO, LITERAL_FOR, LITERAL_IF, LITERAL_NEW,
                    LITERAL_SWITCH, LITERAL_SYNCHRONIZED, LITERAL_WHILE, METHOD_CALL,
                    METHOD_DEF, QUESTION, RESOURCE_SPECIFICATION, SUPER_CTOR_CALL, LAMBDA"/>
        </module>
        <module name="OperatorWrap">
            <property name="option" value="NL"/>
            <property name="tokens"
              value="BAND, BOR, BSR, BXOR, DIV, EQUAL, GE, GT, LAND, LE, LITERAL_INSTANCEOF, LOR,
                    LT, MINUS, MOD, NOT_EQUAL, PLUS, QUESTION, SL, SR, STAR, METHOD_REF "/>
        </module>
        <module name="AnnotationLocation">
            <property name="id" value="AnnotationLocationMostCases"/>
            <property name="tokens"
              value="CLASS_DEF, INTERFACE_DEF, ENUM_DEF, METHOD_DEF, CTOR_DEF"/>
        </module>
        <module name="AnnotationLocation">
            <property name="id" value="AnnotationLocationVariables"/>
            <property name="tokens" value="VARIABLE_DEF"/>
            <property name="allowSamelineMultipleAnnotations" value="true"/>
        </module>
        <!-- Dockstore override, removal -->
<!--        <module name="NonEmptyAtclauseDescription"/>-->
        <module name="InvalidJavadocPosition"/>
        <module name="JavadocTagContinuationIndentation"/>
        <module name="SummaryJavadoc">
            <!-- Dockstore -->
            <property name="severity" value="warning"/>
            <property name="forbiddenSummaryFragments"
              value="^@return the *|^This method returns |^A [{]@code [a-zA-Z0-9]+[}]( is a )"/>
        </module>
        <!-- Dockstore override, removal -->
<!--        <module name="JavadocParagraph"/>-->
        <module name="AtclauseOrder">
            <property name="tagOrder" value="@param, @return, @throws, @deprecated"/>
            <property name="target"
              value="CLASS_DEF, INTERFACE_DEF, ENUM_DEF, METHOD_DEF, CTOR_DEF, VARIABLE_DEF"/>
        </module>
        <module name="JavadocMethod">
            <!-- Dockstore override, addition -->
            <property name="severity" value="warning"/>
            <property name="allowMissingParamTags" value="true"/>
            <property name="accessModifiers" value="public, protected"/>
            <property name="allowMissingReturnTag" value="true"/>
            <property name="allowedAnnotations" value="Override, Test"/>
            <property name="tokens" value="METHOD_DEF, CTOR_DEF, ANNOTATION_FIELD_DEF"/>
        </module>
        <module name="MissingJavadocMethod">
            <!-- Dockstore override, addition -->
            <property name="severity" value="warning"/>
            <property name="scope" value="public"/>
            <property name="minLineCount" value="2"/>
            <property name="allowedAnnotations" value="Override, Test"/>
            <property name="tokens" value="METHOD_DEF, CTOR_DEF, ANNOTATION_FIELD_DEF"/>
        </module>
        <module name="MethodName">
            <property name="format" value="^[a-z][a-z0-9][a-zA-Z0-9_]*$"/>
            <message key="name.invalidPattern"
              value="Method name ''{0}'' must match pattern ''{1}''."/>
        </module>
        <module name="SingleLineJavadoc">
            <property name="ignoreInlineTags" value="false"/>
        </module>
        <module name="EmptyCatchBlock">
            <property name="exceptionVariableName" value="expected"/>
        </module>
        <module name="CommentsIndentation">
            <property name="tokens" value="SINGLE_LINE_COMMENT, BLOCK_COMMENT_BEGIN"/>
        </module>
        <!-- https://checkstyle.org/config_filters.html#SuppressionXpathFilter -->
        <module name="SuppressionXpathFilter">
            <property name="file" value="${org.checkstyle.google.suppressionxpathfilter.config}"
              default="checkstyle-xpath-suppressions.xml" />
            <property name="optional" value="true"/>
        </module>

        <!-- Dockstore override, everything below is additions -->
        <property name="tabWidth" value="4"/>

        <!-- Checks for Naming Conventions.                  -->
        <!-- See http://checkstyle.sf.net/config_naming.html -->
        <module name="ConstantName"/>
        <module name="LocalFinalVariableName"/>
        <module name="StaticVariableName"/>

        <!-- ban new references to old commons lang and configuration -->
        <module name="IllegalImport">
            <property name="illegalPkgs"
              value="sun, org.apache.commons.lang, org.apache.commons.configuration, org.apache.commons.httpclient"/>
        </module>

        <module name="RedundantImport"/>
        <module name="UnusedImports"/>
        <module name="MethodLength">
            <property name="max" value="150"/>
        </module>
        <module name="ParameterNumber"/>
        <module name="MissingDeprecated"/>
        <module name="MissingOverride"/>
        <module name="PackageAnnotation"/>
        <module name="EmptyStatement"/>
        <module name="TypecastParenPad"/>
        <module name="RedundantModifier"/>

        <!-- Checks for blocks. You know, those {}'s         -->
        <!-- See http://checkstyle.sf.net/config_blocks.html -->
        <module name="AvoidNestedBlocks"/>

        <!-- Checks for common coding problems               -->
        <!-- See http://checkstyle.sf.net/config_coding.html -->
        <module name="CovariantEquals"/>
        <module name="EmptyStatement"/>
        <module name="EqualsAvoidNull"/>
        <module name="EqualsHashCode"/>
        <module name="HiddenField">
            <property name="ignoreConstructorParameter" value="true"/>
            <property name="ignoreSetter" value="true"/>
        </module>
        <module name="IllegalInstantiation"/>
        <module name="IllegalType"/>
        <module name="InnerAssignment"/>
        <module name="MagicNumber">
            <property name="ignoreHashCodeMethod" value="true"/>
        </module>
        <module name="PackageDeclaration"/>
        <module name="StringLiteralEquality"/>

        <module name="SimplifyBooleanExpression"/>
        <module name="SimplifyBooleanReturn"/>

        <!-- Checks for class design                         -->
        <!-- See http://checkstyle.sf.net/config_design.html -->
        <module name="InterfaceIsType"/>
        <module name="FinalClass"/>
        <module name="HideUtilityClassConstructor"/>
        <module name="InnerTypeLast"/>
        <module name="MutableException"/>

        <!-- Miscellaneous other checks.                   -->
        <!-- See http://checkstyle.sf.net/config_misc.html -->
        <module name="ArrayTypeStyle"/>
        <module name="DefaultComesLast"/>
    </module>
    <!-- Dockstore override, everything below is additions -->
    <!-- Checks that a package-info.java file exists for each package.     -->
    <!-- See http://checkstyle.sf.net/config_javadoc.html#JavadocPackage -->
    <module name="JavadocPackage"/>

    <!-- Checks whether files end with a new line.                        -->
    <!-- See http://checkstyle.sf.net/config_misc.html#NewlineAtEndOfFile -->
    <module name="NewlineAtEndOfFile"/>

    <!-- Checks that property files contain the same keys.         -->
    <!-- See http://checkstyle.sf.net/config_misc.html#Translation -->
    <module name="Translation"/>

    <!-- Miscellaneous other checks.                   -->
    <!-- See http://checkstyle.sf.net/config_misc.html -->
    <module name="RegexpSingleline">
        <property name="severity" value="ignore"/>
        <property name="format" value="\s+$"/>
        <property name="minimum" value="0"/>
        <property name="maximum" value="0"/>
        <property name="message" value="Line has trailing spaces."/>
    </module>
</module>