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Adding new/updated io.github.betaseg_cellsketch-create-project_0.2.2
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@frauzufall
frauzufall committed Mar 6, 2024
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3 changes: 3 additions & 0 deletions solutions/io.github.betaseg/cellsketch-create-project/CHANGELOG.md
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Expand Up @@ -4,6 +4,9 @@ All notable changes to this project will be documented in this file.
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## [0.2.2] - 2024-03-06
Fix executable issue with gradlew

## [0.2.1] - 2023-12-28
Add x, y scale

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178 changes: 89 additions & 89 deletions solutions/io.github.betaseg/cellsketch-create-project/gradlew.bat
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@@ -1,89 +1,89 @@
@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=.
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%" == "0" goto execute

echo.
echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
echo.
echo Please set the JAVA_HOME variable in your environment to match the
echo location of your Java installation.

goto fail

:findJavaFromJavaHome
set JAVA_HOME=%JAVA_HOME:"=%
set JAVA_EXE=%JAVA_HOME%/bin/java.exe

if exist "%JAVA_EXE%" goto execute

echo.
echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
echo.
echo Please set the JAVA_HOME variable in your environment to match the
echo location of your Java installation.

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%"=="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!
if not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
exit /b 1

: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=.
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%" == "0" goto execute

echo.
echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
echo.
echo Please set the JAVA_HOME variable in your environment to match the
echo location of your Java installation.

goto fail

:findJavaFromJavaHome
set JAVA_HOME=%JAVA_HOME:"=%
set JAVA_EXE=%JAVA_HOME%/bin/java.exe

if exist "%JAVA_EXE%" goto execute

echo.
echo ERROR: JAVA_HOME is set to an invalid directory: %JAVA_HOME%
echo.
echo Please set the JAVA_HOME variable in your environment to match the
echo location of your Java installation.

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%"=="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!
if not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
exit /b 1

:mainEnd
if "%OS%"=="Windows_NT" endlocal

:omega
8 changes: 5 additions & 3 deletions solutions/io.github.betaseg/cellsketch-create-project/solution.py
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Expand Up @@ -14,17 +14,19 @@ def install():
shutil.copy(get_package_path().joinpath('gradlew.bat'), get_app_path())
shutil.copytree(get_package_path().joinpath('src'), get_app_path().joinpath('src'))
shutil.copytree(get_package_path().joinpath('gradle'), get_app_path().joinpath('gradle'))

subprocess.run([(get_gradle_executable()), 'build', '-Dorg.gradle.internal.http.socketTimeout=300000'],
cwd=get_app_path(), check=True)


def get_gradle_executable():
from sys import platform
import os
from album.runner.api import get_app_path
if platform == "win32":
return str(get_app_path().joinpath('gradlew.bat').absolute())
return str(get_app_path().joinpath('gradlew').absolute())
gradle_executable = str(get_app_path().joinpath('gradlew').absolute())
os.chmod(gradle_executable, 0o755)
return gradle_executable


def run():
Expand Down Expand Up @@ -60,7 +62,7 @@ def is_file_arg(arg_name):
setup(
group="io.github.betaseg",
name="cellsketch-create-project",
version="0.2.1",
version="0.2.2",
solution_creators=["Deborah Schmidt"],
title="CellSketch: Create new project",
description="This solution creates a new CellSketch project by importing the raw dataset as well as masks and labelings of cell components.",
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16 changes: 7 additions & 9 deletions solutions/io.github.betaseg/cellsketch-create-project/solution.yml
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Expand Up @@ -32,15 +32,13 @@ args:
description: Do not open the CellSketch Viewer after creating the project
name: headless
type: boolean
changelog: 'Add x, y scale
'
changelog: Fix executable issue with gradlew
cite:
- doi: https://doi.org/10.1083/jcb.202010039
text: "A. M\xC3\xBCller, D. Schmidt, C. S. Xu, S. Pang, J. V. D'Costa, S. Kretschmar,\
\ C. M\xC3\xBCnster, T. Kurth, F. Jug, M. Weigert, H. F. Hess, M. Solimena; 3D\
\ FIB-SEM reconstruction of microtubule-organelle interaction in whole primary\
\ mouse \xCE\xB2 cells. J Cell Biol 1 February 2021; 220 (2): e202010039."
text: "A. M\xFCller, D. Schmidt, C. S. Xu, S. Pang, J. V. D'Costa, S. Kretschmar,\
\ C. M\xFCnster, T. Kurth, F. Jug, M. Weigert, H. F. Hess, M. Solimena; 3D FIB-SEM\
\ reconstruction of microtubule-organelle interaction in whole primary mouse \u03B2\
\ cells. J Cell Biol 1 February 2021; 220 (2): e202010039."
- doi: 10.1038/nmeth.3392
text: 'Pietzsch, T., Saalfeld, S., Preibisch, S., & Tomancak, P. (2015). BigDataViewer:
visualization and processing for large image data sets. Nature Methods, 12(6),
Expand All @@ -60,6 +58,6 @@ tags:
- cellsketch
- segmentation
- annotation
timestamp: '2023-12-28T20:33:06.687915'
timestamp: '2024-03-06T16:37:13.017132'
title: 'CellSketch: Create new project'
version: 0.2.1
version: 0.2.2
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