Normalizing line endings to .gitattributes file

Author: Sigmonia

.gitattributes

@@ -1,178 +1,47 @@
-* text=auto !eol
-java/README.md -text
-java/build.gradle -text
-java/gradle.properties -text
-java/gradle/wrapper/gradle-wrapper.jar -text
-java/gradle/wrapper/gradle-wrapper.properties -text
-java/gradlew -text
-java/gradlew.bat -text
-java/settings.gradle -text
-java/src/META-INF/services/java.sql.Driver -text
-java/src/log4j.xml -text
-java/src/org/labkey/remoteapi/ApiKeyCredentialsProvider.java -text
-java/src/org/labkey/remoteapi/ApiVersionException.java -text
-java/src/org/labkey/remoteapi/BasicAuthCredentialsProvider.java -text
-java/src/org/labkey/remoteapi/Command.java -text
-java/src/org/labkey/remoteapi/CommandException.java -text
-java/src/org/labkey/remoteapi/CommandResponse.java -text
-java/src/org/labkey/remoteapi/Connection.java -text
-java/src/org/labkey/remoteapi/CredentialsProvider.java -text
-java/src/org/labkey/remoteapi/GuestCredentialsProvider.java -text
-java/src/org/labkey/remoteapi/NetrcCredentialsProvider.java -text
-java/src/org/labkey/remoteapi/NetrcFileParser.java -text
-java/src/org/labkey/remoteapi/PostCommand.java -text
-java/src/org/labkey/remoteapi/ResponseObject.java -text
-java/src/org/labkey/remoteapi/assay/AssayListCommand.java -text
-java/src/org/labkey/remoteapi/assay/AssayListResponse.java -text
-java/src/org/labkey/remoteapi/assay/Batch.java -text
-java/src/org/labkey/remoteapi/assay/Data.java -text
-java/src/org/labkey/remoteapi/assay/ExpObject.java -text
-java/src/org/labkey/remoteapi/assay/GetAssayRunCommand.java -text
-java/src/org/labkey/remoteapi/assay/GetAssayRunResponse.java -text
-java/src/org/labkey/remoteapi/assay/GetProtocolCommand.java -text
-java/src/org/labkey/remoteapi/assay/ImportRunCommand.java -text
-java/src/org/labkey/remoteapi/assay/ImportRunResponse.java -text
-java/src/org/labkey/remoteapi/assay/LoadAssayBatchCommand.java -text
-java/src/org/labkey/remoteapi/assay/LoadAssayBatchResponse.java -text
-java/src/org/labkey/remoteapi/assay/Material.java -text
-java/src/org/labkey/remoteapi/assay/Protocol.java -text
-java/src/org/labkey/remoteapi/assay/ProtocolResponse.java -text
-java/src/org/labkey/remoteapi/assay/Run.java -text
-java/src/org/labkey/remoteapi/assay/SaveAssayBatchCommand.java -text
-java/src/org/labkey/remoteapi/assay/SaveAssayBatchResponse.java -text
-java/src/org/labkey/remoteapi/assay/SaveAssayRunsCommand.java -text
-java/src/org/labkey/remoteapi/assay/SaveAssayRunsResponse.java -text
-java/src/org/labkey/remoteapi/assay/SaveProtocolCommand.java -text
-java/src/org/labkey/remoteapi/assay/nab/NAbRunsCommand.java -text
-java/src/org/labkey/remoteapi/assay/nab/NAbRunsResponse.java -text
-java/src/org/labkey/remoteapi/assay/nab/model/NAbCurveParameters.java -text
-java/src/org/labkey/remoteapi/assay/nab/model/NAbNeutralizationResult.java -text
-java/src/org/labkey/remoteapi/assay/nab/model/NAbReplicate.java -text
-java/src/org/labkey/remoteapi/assay/nab/model/NAbRun.java -text
-java/src/org/labkey/remoteapi/assay/nab/model/NAbSample.java -text
-java/src/org/labkey/remoteapi/assay/nab/model/NAbWell.java -text
-java/src/org/labkey/remoteapi/assay/nab/model/NAbWellGroup.java -text
-java/src/org/labkey/remoteapi/collections/CaseInsensitiveHashMap.java -text
-java/src/org/labkey/remoteapi/di/BaseTransformCommand.java -text
-java/src/org/labkey/remoteapi/di/BaseTransformResponse.java -text
-java/src/org/labkey/remoteapi/di/ResetTransformStateCommand.java -text
-java/src/org/labkey/remoteapi/di/ResetTransformStateResponse.java -text
-java/src/org/labkey/remoteapi/di/RunTransformCommand.java -text
-java/src/org/labkey/remoteapi/di/RunTransformResponse.java -text
-java/src/org/labkey/remoteapi/di/UpdateTransformConfigurationCommand.java -text
-java/src/org/labkey/remoteapi/di/UpdateTransformConfigurationResponse.java -text
-java/src/org/labkey/remoteapi/domain/AbstractDomainUpdateCommand.java -text
-java/src/org/labkey/remoteapi/domain/CreateDomainCommand.java -text
-java/src/org/labkey/remoteapi/domain/Domain.java -text
-java/src/org/labkey/remoteapi/domain/DomainResponse.java -text
-java/src/org/labkey/remoteapi/domain/DropDomainCommand.java -text
-java/src/org/labkey/remoteapi/domain/GetDomainCommand.java -text
-java/src/org/labkey/remoteapi/domain/ListDomainsCommand.java -text
-java/src/org/labkey/remoteapi/domain/ListDomainsResponse.java -text
-java/src/org/labkey/remoteapi/domain/PropertyDescriptor.java -text
-java/src/org/labkey/remoteapi/domain/SaveDomainCommand.java -text
-java/src/org/labkey/remoteapi/experiment/LineageCommand.java -text
-java/src/org/labkey/remoteapi/experiment/LineageNode.java -text
-java/src/org/labkey/remoteapi/experiment/LineageResponse.java -text
-java/src/org/labkey/remoteapi/ms2/StartSearchCommand.java -text
-java/src/org/labkey/remoteapi/ms2/StartSearchResponse.java -text
-java/src/org/labkey/remoteapi/pipeline/FileNotificationCommand.java -text
-java/src/org/labkey/remoteapi/pipeline/FileNotificationResponse.java -text
-java/src/org/labkey/remoteapi/query/BaseQueryCommand.java -text
-java/src/org/labkey/remoteapi/query/BaseSelect.java -text
-java/src/org/labkey/remoteapi/query/ContainerFilter.java -text
-java/src/org/labkey/remoteapi/query/DateParser.java -text
-java/src/org/labkey/remoteapi/query/DeleteRowsCommand.java -text
-java/src/org/labkey/remoteapi/query/ExecuteSqlCommand.java -text
-java/src/org/labkey/remoteapi/query/Filter.java -text
-java/src/org/labkey/remoteapi/query/GetQueriesCommand.java -text
-java/src/org/labkey/remoteapi/query/GetQueriesResponse.java -text
-java/src/org/labkey/remoteapi/query/GetQueryDetailsCommand.java -text
-java/src/org/labkey/remoteapi/query/GetQueryDetailsResponse.java -text
-java/src/org/labkey/remoteapi/query/GetSchemasCommand.java -text
-java/src/org/labkey/remoteapi/query/GetSchemasResponse.java -text
-java/src/org/labkey/remoteapi/query/ImportDataCommand.java -text
-java/src/org/labkey/remoteapi/query/ImportDataResponse.java -text
-java/src/org/labkey/remoteapi/query/InsertRowsCommand.java -text
-java/src/org/labkey/remoteapi/query/Row.java -text
-java/src/org/labkey/remoteapi/query/RowMap.java -text
-java/src/org/labkey/remoteapi/query/RowsResponse.java -text
-java/src/org/labkey/remoteapi/query/RowsResponseRowset.java -text
-java/src/org/labkey/remoteapi/query/Rowset.java -text
-java/src/org/labkey/remoteapi/query/SaveRowsCommand.java -text
-java/src/org/labkey/remoteapi/query/SaveRowsResponse.java -text
-java/src/org/labkey/remoteapi/query/SelectRowsCommand.java -text
-java/src/org/labkey/remoteapi/query/SelectRowsResponse.java -text
-java/src/org/labkey/remoteapi/query/Sort.java -text
-java/src/org/labkey/remoteapi/query/SqlExecuteCommand.java -text
-java/src/org/labkey/remoteapi/query/TruncateTableCommand.java -text
-java/src/org/labkey/remoteapi/query/TruncateTableResponse.java -text
-java/src/org/labkey/remoteapi/query/UpdateRowsCommand.java -text
-java/src/org/labkey/remoteapi/sas/Main.java -text
-java/src/org/labkey/remoteapi/sas/SASBaseSelectCommand.java -text
-java/src/org/labkey/remoteapi/sas/SASConnection.java -text
-java/src/org/labkey/remoteapi/sas/SASDeleteRowsCommand.java -text
-java/src/org/labkey/remoteapi/sas/SASExecuteSqlCommand.java -text
-java/src/org/labkey/remoteapi/sas/SASInsertRowsCommand.java -text
-java/src/org/labkey/remoteapi/sas/SASRow.java -text
-java/src/org/labkey/remoteapi/sas/SASSaveRowsCommand.java -text
-java/src/org/labkey/remoteapi/sas/SASSaveRowsResponse.java -text
-java/src/org/labkey/remoteapi/sas/SASSelectRowsCommand.java -text
-java/src/org/labkey/remoteapi/sas/SASSelectRowsResponse.java -text
-java/src/org/labkey/remoteapi/sas/SASUpdateRowsCommand.java -text
-java/src/org/labkey/remoteapi/security/ACL.java -text
-java/src/org/labkey/remoteapi/security/AddGroupMembersCommand.java -text
-java/src/org/labkey/remoteapi/security/CreateContainerCommand.java -text
-java/src/org/labkey/remoteapi/security/CreateContainerResponse.java -text
-java/src/org/labkey/remoteapi/security/CreateGroupCommand.java -text
-java/src/org/labkey/remoteapi/security/CreateGroupResponse.java -text
-java/src/org/labkey/remoteapi/security/CreateUserCommand.java -text
-java/src/org/labkey/remoteapi/security/CreateUserResponse.java -text
-java/src/org/labkey/remoteapi/security/DeleteContainerCommand.java -text
-java/src/org/labkey/remoteapi/security/DeleteContainerResponse.java -text
-java/src/org/labkey/remoteapi/security/DeleteGroupCommand.java -text
-java/src/org/labkey/remoteapi/security/DeleteUserCommand.java -text
-java/src/org/labkey/remoteapi/security/EnsureLoginCommand.java -text
-java/src/org/labkey/remoteapi/security/GetContainersCommand.java -text
-java/src/org/labkey/remoteapi/security/GetContainersResponse.java -text
-java/src/org/labkey/remoteapi/security/GetGroupPermsCommand.java -text
-java/src/org/labkey/remoteapi/security/GetGroupPermsResponse.java -text
-java/src/org/labkey/remoteapi/security/GetUsersCommand.java -text
-java/src/org/labkey/remoteapi/security/GetUsersResponse.java -text
-java/src/org/labkey/remoteapi/security/GroupMembersCommand.java -text
-java/src/org/labkey/remoteapi/security/ImpersonateUserCommand.java -text
-java/src/org/labkey/remoteapi/security/LogoutCommand.java -text
-java/src/org/labkey/remoteapi/security/RemoveGroupMembersCommand.java -text
-java/src/org/labkey/remoteapi/security/RenameGroupCommand.java -text
-java/src/org/labkey/remoteapi/security/RenameGroupResponse.java -text
-java/src/org/labkey/remoteapi/security/StopImpersonatingCommand.java -text
-java/src/org/labkey/remoteapi/security/WhoAmICommand.java -text
-java/src/org/labkey/remoteapi/security/WhoAmIResponse.java -text
-java/src/org/labkey/remoteapi/study/CheckForStudyReloadCommand.java -text
-java/src/org/labkey/remoteapi/study/ParticipantGroup.java -text
-java/src/org/labkey/remoteapi/study/UpdateParticipantGroupCommand.java -text
-java/src/org/labkey/remoteapi/study/UpdateParticipantGroupResponse.java -text
-java/src/org/labkey/remoteapi/test/ClientConfig.java -text
-java/src/org/labkey/remoteapi/test/Demo.java -text
-java/src/org/labkey/remoteapi/test/ImportRunDemo.java -text
-java/src/org/labkey/remoteapi/test/MS2SearchClient.java -text
-java/src/org/labkey/remoteapi/test/PipelineFileAvailableClient.java -text
-java/src/org/labkey/remoteapi/test/SaveAssayBatchDemo.java -text
-java/src/org/labkey/remoteapi/test/Test.java -text
-sas/MorePeople.xls -text
-sas/People.xls -text
-sas/build.gradle -text
-sas/deleteMacros.sas -text
-sas/demo.sas -text
-sas/macros/_labkeycreateconnection.sas -text
-sas/macros/_labkeyexceptiondescribe.sas -text
-sas/macros/_labkeysaverows.sas -text
-sas/macros/_labkeysendcommand.sas -text
-sas/macros/_labkeysharedselectrowshandling.sas -text
-sas/macros/labkeydeleterows.sas -text
-sas/macros/labkeyexecutesql.sas -text
-sas/macros/labkeyinsertrows.sas -text
-sas/macros/labkeymakefilter.sas -text
-sas/macros/labkeyselectrows.sas -text
-sas/macros/labkeysetdefaults.sas -text
-sas/macros/labkeyupdaterows.sas -text
+# Convert text files to OS line-endings on checkout, and LF on check-in
+*               text=auto !eol
+
+# Text files to convert
+*.css           text diff=css
+*.htm           text diff=html
+*.html          text diff=html
+*.java          text diff=java
+*.js            text
+*.json          text
+*.jsp           text
+*.jspf          text
+*.jspx          text
+*.properties    text
+*.py            text diff=python
+*.sql           text
+*.tld           text
+*.ts            text
+*.txt           text
+*.xml           text
+*.yml           text
+
+# Keep unix endings
+*.bash          text eol=lf
+*.sh            text eol=lf
+
+# Keep Windows endings
+*.bat           text eol=crlf
+*.cmd           text eol=crlf
+
+# Known binary files -- Don't change (binary is a macro for -text -diff)
+*.bin           binary
+*.class         binary
+*.dll           binary
+*.ear           binary
+*.exe           binary
+*.gif           binary
+*.gz            binary
+*.ico           binary
+*.jar           binary
+*.jpg           binary
+*.jpeg          binary
+*.png           binary
+*.so            binary
+*.tar           binary
+*.war           binary
+*.zip           binary

java/README.md

@@ -1,21 +1,21 @@
-##The LabKey Remote API Library for Java
-
-Welcome to the LabKey Remote API library for Java. This library allows Java developers to access the data and services exposed from a LabKey Server installation.
-
-For detailed information on the library, its classes, and programming interfaces, see the [JavaDoc](https://www.labkey.org/download/clientapi_docs/java-api/).
-
-If you have any questions about this library or the LabKey Server, see our [Community Support Forums](https://www.labkey.org/wiki/home/page.view?name=support).
-
-This library is licensed under the [Apache 2.0 open-source license](http://www.apache.org/licenses/LICENSE-2.0).
-
----
-
-###Changes in version 1.0.0
-- Migration to [SemVer](https://semver.org/) for library versioning. With 1.0.0 we will move away from using the LabKey server version 
-and adopt the standard used in our other API libraries. Version 1.0.0 will succeed the previous published version of : 19.1.0.
-- Support for truncating tables, there is a new TruncateTableCommand to expose this functionality.
-- CRUD operations for Domains. 
-- Improved support for Assay data import. LoadAssayBatchCommand and SaveAssayRunCommand have been added to allow support for ad-hoc properties.
-- New ListDomainsCommand.
-- New SaveAssayRunsCommand.
-- Update PropertyDescriptor to expose missing value toggling. 
+##The LabKey Remote API Library for Java
+
+Welcome to the LabKey Remote API library for Java. This library allows Java developers to access the data and services exposed from a LabKey Server installation.
+
+For detailed information on the library, its classes, and programming interfaces, see the [JavaDoc](https://www.labkey.org/download/clientapi_docs/java-api/).
+
+If you have any questions about this library or the LabKey Server, see our [Community Support Forums](https://www.labkey.org/wiki/home/page.view?name=support).
+
+This library is licensed under the [Apache 2.0 open-source license](http://www.apache.org/licenses/LICENSE-2.0).
+
+---
+
+###Changes in version 1.0.0
+- Migration to [SemVer](https://semver.org/) for library versioning. With 1.0.0 we will move away from using the LabKey server version 
+and adopt the standard used in our other API libraries. Version 1.0.0 will succeed the previous published version of : 19.1.0.
+- Support for truncating tables, there is a new TruncateTableCommand to expose this functionality.
+- CRUD operations for Domains. 
+- Improved support for Assay data import. LoadAssayBatchCommand and SaveAssayRunCommand have been added to allow support for ad-hoc properties.
+- New ListDomainsCommand.
+- New SaveAssayRunsCommand.
+- Update PropertyDescriptor to expose missing value toggling. 

java/src/log4j.xml

@@ -1,17 +1,17 @@
-<?xml version="1.0" encoding="UTF-8" ?>
-<!DOCTYPE log4j:configuration SYSTEM "log4j.dtd">
-
-<log4j:configuration xmlns:log4j="http://jakarta.apache.org/log4j/">
-  <appender name="console" class="org.apache.log4j.ConsoleAppender">
-    <param name="Target" value="System.out"/>
-    <layout class="org.apache.log4j.PatternLayout">
-      <param name="ConversionPattern" value="%-5p %c{1} - %m%n"/>
-    </layout>
-  </appender>
-
-  <root>
-    <priority value ="error" /> 
-    <appender-ref ref="console" />
-  </root>
-
-</log4j:configuration>
+<?xml version="1.0" encoding="UTF-8" ?>
+<!DOCTYPE log4j:configuration SYSTEM "log4j.dtd">
+
+<log4j:configuration xmlns:log4j="http://jakarta.apache.org/log4j/">
+  <appender name="console" class="org.apache.log4j.ConsoleAppender">
+    <param name="Target" value="System.out"/>
+    <layout class="org.apache.log4j.PatternLayout">
+      <param name="ConversionPattern" value="%-5p %c{1} - %m%n"/>
+    </layout>
+  </appender>
+
+  <root>
+    <priority value ="error" /> 
+    <appender-ref ref="console" />
+  </root>
+
+</log4j:configuration>

java/src/org/labkey/remoteapi/ApiKeyCredentialsProvider.java

@@ -1,41 +1,41 @@
-/*
- * Copyright (c) 2016 LabKey Corporation
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package org.labkey.remoteapi;
-
-import org.apache.http.auth.AuthenticationException;
-import org.apache.http.client.methods.HttpUriRequest;
-import org.apache.http.client.protocol.HttpClientContext;
-
-import java.net.URISyntaxException;
-
-/**
- * Created by adam on 4/15/2016.
- */
-public class ApiKeyCredentialsProvider implements CredentialsProvider
-{
-    private final String _apiKey;
-
-    public ApiKeyCredentialsProvider(String apiKey)
-    {
-        _apiKey = apiKey;
-    }
-
-    @Override
-    public void configureRequest(String baseUrl, HttpUriRequest request, HttpClientContext httpClientContext) throws AuthenticationException, URISyntaxException
-    {
-        request.setHeader("apikey", _apiKey);
-    }
-}
+/*
+ * Copyright (c) 2016 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.labkey.remoteapi;
+
+import org.apache.http.auth.AuthenticationException;
+import org.apache.http.client.methods.HttpUriRequest;
+import org.apache.http.client.protocol.HttpClientContext;
+
+import java.net.URISyntaxException;
+
+/**
+ * Created by adam on 4/15/2016.
+ */
+public class ApiKeyCredentialsProvider implements CredentialsProvider
+{
+    private final String _apiKey;
+
+    public ApiKeyCredentialsProvider(String apiKey)
+    {
+        _apiKey = apiKey;
+    }
+
+    @Override
+    public void configureRequest(String baseUrl, HttpUriRequest request, HttpClientContext httpClientContext) throws AuthenticationException, URISyntaxException
+    {
+        request.setHeader("apikey", _apiKey);
+    }
+}