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‎.bumpversion.cfg

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[bumpversion]
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current_version = 0.0.1
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commit = True
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message = Update version {current_version} -> {new_version}
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[bumpversion:file:README.md]
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search = {current_version}
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replace = {new_version}

‎CODE_OF_CONDUCT.md

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# Contributor Covenant Code of Conduct
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## Our Pledge
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In the interest of fostering an open and welcoming environment, we as
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contributors and maintainers pledge to making participation in our project and
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our community a harassment-free experience for everyone, regardless of age, body
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size, disability, ethnicity, sex characteristics, gender identity and expression,
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level of experience, education, socio-economic status, nationality, personal
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appearance, race, religion, or sexual identity and orientation.
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## Our Standards
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Examples of behavior that contributes to creating a positive environment
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include:
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* Using welcoming and inclusive language
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* Being respectful of differing viewpoints and experiences
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* Gracefully accepting constructive criticism
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* Focusing on what is best for the community
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* Showing empathy towards other community members
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Examples of unacceptable behavior by participants include:
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* The use of sexualized language or imagery and unwelcome sexual attention or
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advances
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* Trolling, insulting/derogatory comments, and personal or political attacks
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* Public or private harassment
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* Publishing others' private information, such as a physical or electronic
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address, without explicit permission
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* Other conduct which could reasonably be considered inappropriate in a
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professional setting
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## Our Responsibilities
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Project maintainers are responsible for clarifying the standards of acceptable
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behavior and are expected to take appropriate and fair corrective action in
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response to any instances of unacceptable behavior.
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Project maintainers have the right and responsibility to remove, edit, or
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reject comments, commits, code, wiki edits, issues, and other contributions
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that are not aligned to this Code of Conduct, or to ban temporarily or
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permanently any contributor for other behaviors that they deem inappropriate,
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threatening, offensive, or harmful.
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## Scope
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This Code of Conduct applies both within project spaces and in public spaces
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when an individual is representing the project or its community. Examples of
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representing a project or community include using an official project e-mail
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address, posting via an official social media account, or acting as an appointed
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representative at an online or offline event. Representation of a project may be
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further defined and clarified by project maintainers.
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## Enforcement
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Instances of abusive, harassing, or otherwise unacceptable behavior may be
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reported by contacting the project team at [email protected]. All
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complaints will be reviewed and investigated and will result in a response that
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is deemed necessary and appropriate to the circumstances. The project team is
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obligated to maintain confidentiality with regard to the reporter of an incident.
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Further details of specific enforcement policies may be posted separately.
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Project maintainers who do not follow or enforce the Code of Conduct in good
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faith may face temporary or permanent repercussions as determined by other
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members of the project's leadership.
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## Attribution
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This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
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available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
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[homepage]: https://www.contributor-covenant.org
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For answers to common questions about this code of conduct, see
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https://www.contributor-covenant.org/faq

‎checkstyle.xml

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<!DOCTYPE module PUBLIC
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"-//Puppy Crawl//DTD Check Configuration 1.3//EN"
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"http://www.puppycrawl.com/dtds/configuration_1_3.dtd">
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<!--
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Checkstyle configuration based on the Google coding conventions from:
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- Google Java Style
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https://google.github.io/styleguide/javaguide.html
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-->
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<module name="Checker">
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<module name="NewlineAtEndOfFile"/>
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<module name="FileLength">
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<property name="max" value="2500"/>
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</module>
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<module name="FileTabCharacter"/>
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<!-- Trailing spaces -->
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<module name="RegexpSingleline">
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<property name="format" value="\s+$"/>
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<property name="message" value="Line has trailing spaces."/>
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</module>
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<!-- Space after 'for' and 'if' -->
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<module name="RegexpSingleline">
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<property name="format" value="^\s*(for|if)\b[^ ]"/>
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<property name="message" value="Space needed before opening parenthesis."/>
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</module>
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<!-- For each spacing -->
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<module name="RegexpSingleline">
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<property name="format" value="^\s*for \(.*?([^ ]:|:[^ ])"/>
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<property name="message" value="Space needed around ':' character."/>
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</module>
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<module name="TreeWalker">
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<!-- Checks for Javadoc comments. -->
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<!-- See http://checkstyle.sf.net/config_javadoc.html -->
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<module name="JavadocStyle"/>
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<!-- Checks for Naming Conventions. -->
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<!-- See http://checkstyle.sf.net/config_naming.html -->
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<!--<module name="ConstantName"/>-->
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<module name="LocalFinalVariableName"/>
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<module name="LocalVariableName"/>
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<module name="MemberName"/>
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<module name="MethodName"/>
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<module name="ParameterName"/>
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<module name="StaticVariableName"/>
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<module name="TypeName"/>
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<module name="PackageName">
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<property name="format" value="^[a-z]+(\.[a-z][a-z0-9_]*)*$"/>
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<message key="name.invalidPattern"
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value="Package name ''{0}'' must match pattern ''{1}''."/>
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</module>
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<!-- Checks for imports -->
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<!-- See http://checkstyle.sf.net/config_import.html -->
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<module name="AvoidStarImport"/>
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<module name="IllegalImport"/>
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<!-- defaults to sun.* packages -->
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<module name="RedundantImport"/>
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<module name="UnusedImports">
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<property name="processJavadoc" value="true"/>
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</module>
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<!-- Checks for Size Violations. -->
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<!-- See http://checkstyle.sf.net/config_sizes.html -->
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<module name="MethodLength">
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<property name="max" value="200"/>
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</module>
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<!-- Checks for whitespace -->
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<!-- See http://checkstyle.sf.net/config_whitespace.html -->
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<module name="GenericWhitespace"/>
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<module name="MethodParamPad"/>
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<module name="OperatorWrap"/>
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<module name="ParenPad"/>
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<module name="TypecastParenPad"/>
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<module name="WhitespaceAfter"/>
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<module name="WhitespaceAround">
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<property name="tokens"
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value="ASSIGN, BAND, BAND_ASSIGN, BOR, BOR_ASSIGN, BSR, BSR_ASSIGN, BXOR, BXOR_ASSIGN,
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COLON, DIV, DIV_ASSIGN, DO_WHILE, EQUAL, GE, GT, LAND, LCURLY, LE, LITERAL_CATCH,
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LITERAL_DO, LITERAL_ELSE, LITERAL_FINALLY, LITERAL_FOR, LITERAL_IF, LITERAL_RETURN,
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LITERAL_SWITCH, LITERAL_SYNCHRONIZED, LITERAL_TRY, LITERAL_WHILE, LOR, LT, MINUS,
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MINUS_ASSIGN, MOD, MOD_ASSIGN, NOT_EQUAL, PLUS, PLUS_ASSIGN, QUESTION, SL, SLIST,
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SL_ASSIGN, SR, SR_ASSIGN, STAR, STAR_ASSIGN, LITERAL_ASSERT, TYPE_EXTENSION_AND"/>
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</module>
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<!-- Modifier Checks -->
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<!-- See http://checkstyle.sf.net/config_modifiers.html -->
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<module name="ModifierOrder"/>
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<module name="RedundantModifier"/>
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<!-- Checks for blocks. You know, those { }'s -->
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<!-- See http://checkstyle.sf.net/config_blocks.html -->
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<module name="AvoidNestedBlocks"/>
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<module name="LeftCurly"/>
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<module name="RightCurly"/>
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<!-- Checks for common coding problems -->
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<!-- See http://checkstyle.sf.net/config_coding.html -->
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<module name="CovariantEquals"/>
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<module name="EmptyStatement"/>
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<module name="EqualsHashCode"/>
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<module name="IllegalInstantiation"/>
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<module name="SimplifyBooleanExpression"/>
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<module name="SimplifyBooleanReturn"/>
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<!-- Checks for class design -->
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<!-- See http://checkstyle.sf.net/config_design.html -->
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<module name="HideUtilityClassConstructor"/>
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<!-- Miscellaneous other checks. -->
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<!-- See http://checkstyle.sf.net/config_misc.html -->
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<module name="ArrayTypeStyle"/>
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<module name="UpperEll"/>
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</module>
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</module>

‎modules/annotator-for-clinical-data/.classpath

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<?xml version="1.0" encoding="UTF-8"?>
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<classpath>
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<classpathentry kind="src" output="target/classes" path="src/main/java">
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<attributes>
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<attribute name="optional" value="true"/>
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<attribute name="maven.pomderived" value="true"/>
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</attributes>
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</classpathentry>
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<classpathentry kind="src" output="target/test-classes" path="src/test/java">
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<attributes>
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<attribute name="optional" value="true"/>
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<attribute name="maven.pomderived" value="true"/>
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</attributes>
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</classpathentry>
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<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
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<attributes>
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<attribute name="maven.pomderived" value="true"/>
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</attributes>
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</classpathentry>
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<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
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<attributes>
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<attribute name="maven.pomderived" value="true"/>
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<attribute name="org.eclipse.jst.component.nondependency" value=""/>
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</attributes>
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</classpathentry>
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<classpathentry excluding="**" kind="src" output="target/test-classes" path="src/test/resources">
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<attributes>
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<attribute name="maven.pomderived" value="true"/>
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</attributes>
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</classpathentry>
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<classpathentry kind="src" path=".apt_generated">
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<attributes>
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<attribute name="optional" value="true"/>
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</attributes>
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</classpathentry>
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<classpathentry kind="output" path="target/classes"/>
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</classpath>

‎modules/annotator-for-clinical-data/.project

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<?xml version="1.0" encoding="UTF-8"?>
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<projectDescription>
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<name>annotator-for-clinical-data</name>
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<comment></comment>
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<projects>
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</projects>
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<buildSpec>
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<buildCommand>
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<name>org.eclipse.wst.common.project.facet.core.builder</name>
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<arguments>
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</arguments>
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</buildCommand>
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<buildCommand>
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<name>org.eclipse.jdt.core.javabuilder</name>
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<arguments>
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</arguments>
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</buildCommand>
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<buildCommand>
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<name>org.eclipse.m2e.core.maven2Builder</name>
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<arguments>
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</arguments>
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</buildCommand>
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<buildCommand>
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<name>org.eclipse.wst.validation.validationbuilder</name>
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<arguments>
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</arguments>
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</buildCommand>
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<buildCommand>
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<name>net.sf.eclipsecs.core.CheckstyleBuilder</name>
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<arguments>
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</arguments>
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</buildCommand>
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</buildSpec>
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<natures>
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<nature>org.eclipse.jdt.core.javanature</nature>
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<nature>org.eclipse.m2e.core.maven2Nature</nature>
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<nature>org.eclipse.wst.common.project.facet.core.nature</nature>
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<nature>org.eclipse.wst.common.modulecore.ModuleCoreNature</nature>
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<nature>net.sf.eclipsecs.core.CheckstyleNature</nature>
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</natures>
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</projectDescription>

‎modules/annotator-for-clinical-data/.settings/org.eclipse.core.resources.prefs

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eclipse.preferences.version=1
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encoding//src/main/java=UTF-8
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encoding//src/test/java=UTF-8
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encoding/<project>=UTF-8

‎modules/annotator-for-clinical-data/.settings/org.eclipse.jdt.apt.core.prefs

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eclipse.preferences.version=1
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org.eclipse.jdt.apt.aptEnabled=true
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org.eclipse.jdt.apt.reconcileEnabled=true

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