Reorgnize the files.

Author: fcyu

.travis.yml

@@ -1,19 +1,19 @@
-# Default ignored files
-/.idea/shelf/
-/.idea/workspace.xml
-
-# Project exclude paths
-/.gradle/
-/build/
-/out/
-/out/production/classes/
-
-# Datasource local storage ignored files
-/.idea/dataSources/
-dataSources.local.xml
-
-# Editor-based HTTP Client requests
-/.idea/httpRequests/
-rest-client.private.env.json
-http-client.private.env.json
-.DS_Store
+# Default ignored files
+/.idea/shelf/
+/.idea/workspace.xml
+
+# Project exclude paths
+/.gradle/
+/build/
+/out/
+/out/production/classes/
+
+# Datasource local storage ignored files
+/.idea/dataSources/
+dataSources.local.xml
+
+# Editor-based HTTP Client requests
+/.idea/httpRequests/
+rest-client.private.env.json
+http-client.private.env.json
+.DS_Store

MSFragger-GUI/.gitignore FragPipe-GUI/.gitignore

@@ -25,7 +25,7 @@ plugins {
     id 'nebula.lint' version '19.0.1'
 }
 
-group = 'com.github.chhh'
+group = 'org.nesvilab'
 version = '23.0-build13'
 
 description = """FragPipe - run complete proteomics analyses from the GUI"""
@@ -42,7 +42,7 @@ tasks.withType(JavaCompile) {
 }
 
 // Define the main class for the application
-def startClass = 'com.dmtavt.fragpipe.FragPipeMain'
+def startClass = 'org.nesvilab.fragpipe.FragPipeMain'
 application {
     mainClass = "${startClass}"
 }
@@ -57,17 +57,17 @@ repositories {
 sourceSets {
     main {
         java {
-            srcDirs = ['src']
+            srcDirs = ['src/main/java']
         }
         resources {
-            srcDirs = ['resources', 'src']
+            srcDirs = ['src/main/resources', 'src/main/java']
             excludes = ['*.java']
         }
     }
     // add tests sources here (this project didn't have them!)
     test {
-        java.srcDirs = ['test']
-        resources.srcDirs = ["test/resources"]
+        java.srcDirs = ['src/test/java']
+        resources.srcDirs = ["src/test/resources"]
     }
 }
 
@@ -98,7 +98,7 @@ distributions {
 
 dependencies {
     implementation 'com.github.albfernandez:juniversalchardet:2.4.0'
-    implementation files("tools/batmass-io-1.34.4.jar")
+    implementation files("../tools/batmass-io-1.34.4.jar")
     implementation 'com.google.code.gson:gson:2.10.1'
     implementation 'one.util:streamex:0.8.2'
     implementation 'org.jooq:jool-java-8:0.9.15'
@@ -144,53 +144,53 @@ test {
     }
 }
 
-task listJars(group: 'chhh-help') {
+task listJars(group: 'fragpipe-help') {
     doLast {
         configurations.runtimeClasspath.each { File file -> println file.name }
     }
 }
 
-task showImplDeps(type: DependencyReportTask, group: 'chhh-help',
+task showImplDeps(type: DependencyReportTask, group: 'fragpipe-help',
         description: "Show only implementation dependencies") {
     configurations = [project.configurations.implementation] as Set
 }
 
-task createStartScripts(type: CreateStartScripts, group: "chhh-release") {
+task createStartScripts(type: CreateStartScripts, group: "fragpipe-release") {
     outputDir = file('build/pre-zip-release')
     mainClass = "${startClass}"
     applicationName = 'FragPipe'
     classpath = files("fragpipe-${project.version}.jar")
 }
 
-task makeExeAndCopyToScripts(type: Copy, group: 'chhh-release', description: 'The .exe file ' +
+task makeExeAndCopyToScripts(type: Copy, group: 'fragpipe-release', description: 'The .exe file ' +
         'created requires to be placed in ./bin/ sub-direcotry of the final distribution and ' +
         'having fragpipe-x.x.x.jar in ./lib/ sub-directory') {
     dependsOn 'createExe'
     from getLayout().buildDirectory.dir('launch4j/bin').get()
     into getLayout().buildDirectory.dir('scripts').get().asFile
 }
 
-task copyJre(type: Copy, group: 'chhh-release', description: "Copies JRE to build/install/${project.name}-${project.version}") {
+task copyJre(type: Copy, group: 'fragpipe-release', description: "Copies JRE to build/install/${project.name}-${project.version}") {
     from getLayout().buildDirectory.dir('../../jre/OpenJDK17U-jre_x64_windows_hotspot_17.0.10_7').get()
     into getLayout().buildDirectory.dir("install/${project.name}-${project.version}").get().asFile
 }
 
 void createTaskCopyToInstallRelToBuild(String taskNameSuffix, String fromRelToBuild, String toRelToInstallProjname) {
     String taskName = "copy" + taskNameSuffix
-    task (taskName, type: Copy, group: 'chhh-release', description: "Copies JRE") {
+    task (taskName, type: Copy, group: 'fragpipe-release', description: "Copies JRE") {
         from getLayout().buildDirectory.dir("$fromRelToBuild").get()
         into getLayout().buildDirectory.dir("install/${project.name}-${project.version}/$toRelToInstallProjname").get().asFile
         exclude { details -> (details.file.name.endsWith('.tar.gz') and details.file.name.startsWith('cpython')) || (details.file.name == 'python.zip') || (details.file.name == 'python')
         }
     }
 }
 
-createTaskCopyToInstallRelToBuild('Tools', "../tools", "tools")
-createTaskCopyToInstallRelToBuild('Workflows', "../workflows/", "workflows")
+createTaskCopyToInstallRelToBuild('Tools', "../../tools", "tools")
+createTaskCopyToInstallRelToBuild('Workflows', "../../workflows/", "workflows")
 
 void createTaskUnpackToInstallRelToBuild(String taskNameSuffix, String fromRelToBuild, String toRelToInstallProjname) {
     String taskName = "unpack" + taskNameSuffix
-    task (taskName, type: Copy, group: 'chhh-release', description: "Unzips $fromRelToBuild to $toRelToInstallProjname") {
+    task (taskName, type: Copy, group: 'fragpipe-release', description: "Unzips $fromRelToBuild to $toRelToInstallProjname") {
         dependsOn 'copyTools'
         from zipTree(getLayout().buildDirectory.dir("$fromRelToBuild").get())
         // tarTree has issues with symlinks, so use zipTree
@@ -199,13 +199,13 @@ void createTaskUnpackToInstallRelToBuild(String taskNameSuffix, String fromRelTo
     }
 }
 
-createTaskUnpackToInstallRelToBuild('PythonLinux', "../tools/python_Linux/python.zip", "tools/python_Linux")
-createTaskUnpackToInstallRelToBuild('PythonWindows', "../tools/python_Windows/python.zip", "tools/python_Windows")
+createTaskUnpackToInstallRelToBuild('PythonLinux', "../../tools/python_Linux/python.zip", "tools/python_Linux")
+createTaskUnpackToInstallRelToBuild('PythonWindows', "../../tools/python_Windows/python.zip", "tools/python_Windows")
 
 void createTaskMakeReleaseZip(boolean withJre, String releaseDir, String startClass) {
     String taskName = "makeReleaseZip" + (withJre ? "WithJre" : "NoJre")
 
-    task (taskName, type: Zip, group: 'chhh-release') {
+    task (taskName, type: Zip, group: 'fragpipe-release') {
         // for build on Windows, zip with execute bit
         // for a gradle Windows build, files requiring execute bit set (ELF and Unix shell scripts)
         // are zipped without execute bit. The default file mode is 0644
@@ -261,7 +261,7 @@ void createTaskMakeReleaseZip(boolean withJre, String releaseDir, String startCl
 createTaskMakeReleaseZip(true, releaseDir, startClass)
 createTaskMakeReleaseZip(false, releaseDir, startClass)
 
-task makeReleaseZips(group: 'chhh-release') {
+task makeReleaseZips(group: 'fragpipe-release') {
     dependsOn('clean')
     dependsOn('makeReleaseZipNoJre')
     dependsOn('makeReleaseZipWithJre')

MSFragger-GUI/build.gradle FragPipe-GUI/build.gradle

@@ -1,92 +1,92 @@
-@rem
-@rem Copyright 2015 the original author or authors.
-@rem
-@rem Licensed under the Apache License, Version 2.0 (the "License");
-@rem you may not use this file except in compliance with the License.
-@rem You may obtain a copy of the License at
-@rem
-@rem      https://www.apache.org/licenses/LICENSE-2.0
-@rem
-@rem Unless required by applicable law or agreed to in writing, software
-@rem distributed under the License is distributed on an "AS IS" BASIS,
-@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-@rem See the License for the specific language governing permissions and
-@rem limitations under the License.
-@rem
-
-@if "%DEBUG%"=="" @echo off
-@rem ##########################################################################
-@rem
-@rem  Gradle startup script for Windows
-@rem
-@rem ##########################################################################
-
-@rem Set local scope for the variables with windows NT shell
-if "%OS%"=="Windows_NT" setlocal
-
-set DIRNAME=%~dp0
-if "%DIRNAME%"=="" set DIRNAME=.
-@rem This is normally unused
-set APP_BASE_NAME=%~n0
-set APP_HOME=%DIRNAME%
-
-@rem Resolve any "." and ".." in APP_HOME to make it shorter.
-for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi
-
-@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m"
-
-@rem Find java.exe
-if defined JAVA_HOME goto findJavaFromJavaHome
-
-set JAVA_EXE=java.exe
-%JAVA_EXE% -version >NUL 2>&1
-if %ERRORLEVEL% equ 0 goto execute
-
-echo. 1>&2
-echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. 1>&2
-echo. 1>&2
-echo Please set the JAVA_HOME variable in your environment to match the 1>&2
-echo location of your Java installation. 1>&2
-
-goto fail
-
-:findJavaFromJavaHome
-set JAVA_HOME=%JAVA_HOME:"=%
-set JAVA_EXE=%JAVA_HOME%/bin/java.exe
-
-if exist "%JAVA_EXE%" goto execute
-
-echo. 1>&2
-echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME% 1>&2
-echo. 1>&2
-echo Please set the JAVA_HOME variable in your environment to match the 1>&2
-echo location of your Java installation. 1>&2
-
-goto fail
-
-:execute
-@rem Setup the command line
-
-set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
-
-
-@rem Execute Gradle
-"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %*
-
-:end
-@rem End local scope for the variables with windows NT shell
-if %ERRORLEVEL% equ 0 goto mainEnd
-
-:fail
-rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
-rem the _cmd.exe /c_ return code!
-set EXIT_CODE=%ERRORLEVEL%
-if %EXIT_CODE% equ 0 set EXIT_CODE=1
-if not ""=="%GRADLE_EXIT_CONSOLE%" exit %EXIT_CODE%
-exit /b %EXIT_CODE%
-
-:mainEnd
-if "%OS%"=="Windows_NT" endlocal
-
-:omega
+@rem
+@rem Copyright 2015 the original author or authors.
+@rem
+@rem Licensed under the Apache License, Version 2.0 (the "License");
+@rem you may not use this file except in compliance with the License.
+@rem You may obtain a copy of the License at
+@rem
+@rem      https://www.apache.org/licenses/LICENSE-2.0
+@rem
+@rem Unless required by applicable law or agreed to in writing, software
+@rem distributed under the License is distributed on an "AS IS" BASIS,
+@rem WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+@rem See the License for the specific language governing permissions and
+@rem limitations under the License.
+@rem
+
+@if "%DEBUG%"=="" @echo off
+@rem ##########################################################################
+@rem
+@rem  Gradle startup script for Windows
+@rem
+@rem ##########################################################################
+
+@rem Set local scope for the variables with windows NT shell
+if "%OS%"=="Windows_NT" setlocal
+
+set DIRNAME=%~dp0
+if "%DIRNAME%"=="" set DIRNAME=.
+@rem This is normally unused
+set APP_BASE_NAME=%~n0
+set APP_HOME=%DIRNAME%
+
+@rem Resolve any "." and ".." in APP_HOME to make it shorter.
+for %%i in ("%APP_HOME%") do set APP_HOME=%%~fi
+
+@rem Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+set DEFAULT_JVM_OPTS="-Xmx64m" "-Xms64m"
+
+@rem Find java.exe
+if defined JAVA_HOME goto findJavaFromJavaHome
+
+set JAVA_EXE=java.exe
+%JAVA_EXE% -version >NUL 2>&1
+if %ERRORLEVEL% equ 0 goto execute
+
+echo. 1>&2
+echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. 1>&2
+echo. 1>&2
+echo Please set the JAVA_HOME variable in your environment to match the 1>&2
+echo location of your Java installation. 1>&2
+
+goto fail
+
+:findJavaFromJavaHome
+set JAVA_HOME=%JAVA_HOME:"=%
+set JAVA_EXE=%JAVA_HOME%/bin/java.exe
+
+if exist "%JAVA_EXE%" goto execute
+
+echo. 1>&2
+echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME% 1>&2
+echo. 1>&2
+echo Please set the JAVA_HOME variable in your environment to match the 1>&2
+echo location of your Java installation. 1>&2
+
+goto fail
+
+:execute
+@rem Setup the command line
+
+set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
+
+
+@rem Execute Gradle
+"%JAVA_EXE%" %DEFAULT_JVM_OPTS% %JAVA_OPTS% %GRADLE_OPTS% "-Dorg.gradle.appname=%APP_BASE_NAME%" -classpath "%CLASSPATH%" org.gradle.wrapper.GradleWrapperMain %*
+
+:end
+@rem End local scope for the variables with windows NT shell
+if %ERRORLEVEL% equ 0 goto mainEnd
+
+:fail
+rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
+rem the _cmd.exe /c_ return code!
+set EXIT_CODE=%ERRORLEVEL%
+if %EXIT_CODE% equ 0 set EXIT_CODE=1
+if not ""=="%GRADLE_EXIT_CONSOLE%" exit %EXIT_CODE%
+exit /b %EXIT_CODE%
+
+:mainEnd
+if "%OS%"=="Windows_NT" endlocal
+
+:omega