From c5258a7a620c63a38cabea9985a75420348673bf Mon Sep 17 00:00:00 2001 From: Jan Kozusznik <jan@kozusznik.cz> Date: Wed, 17 Jan 2018 15:03:53 +0100 Subject: [PATCH] split to more modules --- .../cz/it4i/fiji/haas/{ => ui}/FXFrame.java | 2 +- .../it4i/fiji/haas/{ => ui}/ModalDialogs.java | 2 +- .../cz/it4i/fiji/haas/ui/ProgressDialog.java | 2 +- haas-snakemake-spim/pom.xml | 94 +++++++++++++++++++ .../commands}/CheckStatusOfHaaS.java | 6 +- .../commands}/RunWithHaaS.java | 5 +- .../ui/CheckStatusOfHaaS.fxml | 2 +- .../ui/CheckStatusOfHaaSController.java | 6 +- .../ui}/CheckStatusOfHaaSWindow.java | 4 +- .../haas_snakemake_spim/ui/package-info.java | 8 ++ haas-spim-benchmark/pom.xml | 94 +++++++++++++++++++ .../core}/BenchmarkJobManager.java | 5 +- .../java/cz/it4i/fiji/haas/RunBenchmark.java | 1 + 13 files changed, 220 insertions(+), 11 deletions(-) rename haas-imagej-client/src/main/java/cz/it4i/fiji/haas/{ => ui}/FXFrame.java (98%) rename haas-imagej-client/src/main/java/cz/it4i/fiji/haas/{ => ui}/ModalDialogs.java (91%) create mode 100644 haas-snakemake-spim/pom.xml rename {haas-imagej-client/src/main/java/cz/it4i/fiji/haas => haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/commands}/CheckStatusOfHaaS.java (91%) rename {haas-imagej-client/src/main/java/cz/it4i/fiji/haas => haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/commands}/RunWithHaaS.java (93%) rename {haas-imagej-client/src/main/java/cz/it4i/fiji/haas => haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim}/ui/CheckStatusOfHaaS.fxml (89%) rename {haas-imagej-client/src/main/java/cz/it4i/fiji/haas => haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim}/ui/CheckStatusOfHaaSController.java (92%) rename {haas-imagej-client/src/main/java/cz/it4i/fiji/haas => haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/ui}/CheckStatusOfHaaSWindow.java (92%) create mode 100644 haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/ui/package-info.java create mode 100644 haas-spim-benchmark/pom.xml rename {haas-imagej-client/src/main/java/cz/it4i/fiji/haas => haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core}/BenchmarkJobManager.java (95%) rename {haas-imagej-client => haas-spim-benchmark}/src/test/java/cz/it4i/fiji/haas/RunBenchmark.java (97%) diff --git a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/FXFrame.java b/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/FXFrame.java similarity index 98% rename from haas-imagej-client/src/main/java/cz/it4i/fiji/haas/FXFrame.java rename to haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/FXFrame.java index 3c71c41c..c0a72385 100644 --- a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/FXFrame.java +++ b/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/FXFrame.java @@ -1,4 +1,4 @@ -package cz.it4i.fiji.haas; +package cz.it4i.fiji.haas.ui; import java.awt.Dimension; import java.awt.Frame; diff --git a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ModalDialogs.java b/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/ModalDialogs.java similarity index 91% rename from haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ModalDialogs.java rename to haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/ModalDialogs.java index fe19f07d..45d845b0 100644 --- a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ModalDialogs.java +++ b/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/ModalDialogs.java @@ -1,4 +1,4 @@ -package cz.it4i.fiji.haas; +package cz.it4i.fiji.haas.ui; import javax.swing.JDialog; import javax.swing.WindowConstants; diff --git a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/ProgressDialog.java b/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/ProgressDialog.java index bad0f6b0..acd80508 100644 --- a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/ProgressDialog.java +++ b/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/ProgressDialog.java @@ -1,4 +1,4 @@ -package cz.it4i.fiji.haas.ui; + package cz.it4i.fiji.haas.ui; import java.awt.Adjustable; diff --git a/haas-snakemake-spim/pom.xml b/haas-snakemake-spim/pom.xml new file mode 100644 index 00000000..c3eebd11 --- /dev/null +++ b/haas-snakemake-spim/pom.xml @@ -0,0 +1,94 @@ +<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" + xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd"> + <modelVersion>4.0.0</modelVersion> + <parent> + <groupId>org.scijava</groupId> + <artifactId>pom-scijava</artifactId> + <version>17.1.1</version> + <relativePath /> + </parent> + <groupId>cz.it4i.fiji</groupId> + <artifactId>haas-snakemake-spim</artifactId> + <version>0.0.1-SNAPSHOT</version> + <packaging>jar</packaging> + <name>Plugins for running SPIM automated workflow by IT4I HaaS.</name> + <description>This example provides an introduction to writing ImageJ commands.</description> + <url>https://github.com/[MY-ORG]/[MY-REPO]</url> + <inceptionYear>2013</inceptionYear> + <organization> + <name>[MY-ORGANIZATION-NAME]</name> + <url>[MY-ORGANIZATION-WEB-SITE]</url> + </organization> + <licenses> + <license> + <name>CC0 1.0 Universal License</name> + <url>http://creativecommons.org/publicdomain/zero/1.0/</url> + <distribution>repo</distribution> + </license> + </licenses> + + <developers> + <developer> + <id>[MY-GITHUB-ID]</id> + <name>[MY-FULL-NAME]</name> + <url>https://imagej.net/User:[MY-IMAGEJ-WIKI-ACCOUNT]</url> + </developer> + </developers> + <contributors> + <contributor> + <name>None</name> + </contributor> + </contributors> + + <mailingLists> + <mailingList> + <name>ImageJ Forum</name> + <archive>http://forum.imagej.net/</archive> + </mailingList> + </mailingLists> + + <scm> + <connection>scm:git:git://github.com/[MY-ORG]/[MY-REPO]</connection> + <developerConnection>scm:git:git@github.com:[MY-ORG]/[MY-REPO]</developerConnection> + <tag>HEAD</tag> + <url>https://github.com/[MY-ORG]/[MY-REPO]</url> + </scm> + <issueManagement> + <system>GitHub Issues</system> + <url>http://github.com/[MY-ORG]/[MY-REPO]/issues</url> + </issueManagement> + <ciManagement> + <system>None</system> + </ciManagement> + + + <repositories> + <repository> + <id>imagej.public</id> + <url>http://maven.imagej.net/content/groups/public</url> + </repository> + </repositories> + + <dependencies> + <dependency> + <groupId>net.imagej</groupId> + <artifactId>imagej</artifactId> + </dependency> + + <dependency> + <groupId>cz.it4i.fiji</groupId> + <artifactId>haas-imagej-client</artifactId> + <version>0.0.1-SNAPSHOT</version> + </dependency> + <!-- https://mvnrepository.com/artifact/org.slf4j/slf4j-api --> + <dependency> + <groupId>org.slf4j</groupId> + <artifactId>slf4j-api</artifactId> + </dependency> + <!-- https://mvnrepository.com/artifact/org.slf4j/slf4j-jdk14 --> + <dependency> + <groupId>org.slf4j</groupId> + <artifactId>slf4j-simple</artifactId> + </dependency> + </dependencies> +</project> \ No newline at end of file diff --git a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/CheckStatusOfHaaS.java b/haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/commands/CheckStatusOfHaaS.java similarity index 91% rename from haas-imagej-client/src/main/java/cz/it4i/fiji/haas/CheckStatusOfHaaS.java rename to haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/commands/CheckStatusOfHaaS.java index b03c09ff..bc9e974e 100644 --- a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/CheckStatusOfHaaS.java +++ b/haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/commands/CheckStatusOfHaaS.java @@ -1,4 +1,4 @@ -package cz.it4i.fiji.haas; +package cz.it4i.fiji.haas_snakemake_spim.commands; import java.awt.Frame; import java.io.File; @@ -16,8 +16,12 @@ import org.scijava.ui.ApplicationFrame; import org.scijava.ui.UIService; import org.scijava.widget.UIComponent; +import cz.it4i.fiji.haas.JobManager; +import cz.it4i.fiji.haas.TestingConstants; import cz.it4i.fiji.haas.JobManager.JobInfo; +import cz.it4i.fiji.haas.ui.ModalDialogs; import cz.it4i.fiji.haas.ui.ProgressDialog; +import cz.it4i.fiji.haas_snakemake_spim.ui.CheckStatusOfHaaSWindow; import net.imagej.ImageJ; /** diff --git a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/RunWithHaaS.java b/haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/commands/RunWithHaaS.java similarity index 93% rename from haas-imagej-client/src/main/java/cz/it4i/fiji/haas/RunWithHaaS.java rename to haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/commands/RunWithHaaS.java index 5265f178..96cda95d 100644 --- a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/RunWithHaaS.java +++ b/haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/commands/RunWithHaaS.java @@ -1,4 +1,4 @@ -package cz.it4i.fiji.haas; +package cz.it4i.fiji.haas_snakemake_spim.commands; import java.awt.Frame; import java.io.File; @@ -18,6 +18,9 @@ import org.scijava.ui.ApplicationFrame; import org.scijava.ui.UIService; import org.scijava.widget.UIComponent; +import cz.it4i.fiji.haas.JobManager; +import cz.it4i.fiji.haas.TestingConstants; +import cz.it4i.fiji.haas.ui.ModalDialogs; import cz.it4i.fiji.haas.ui.ProgressDialog; import cz.it4i.fiji.haas_java_client.HaaSClient; import net.imagej.ImageJ; diff --git a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/CheckStatusOfHaaS.fxml b/haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/ui/CheckStatusOfHaaS.fxml similarity index 89% rename from haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/CheckStatusOfHaaS.fxml rename to haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/ui/CheckStatusOfHaaS.fxml index c0b50d22..07201409 100644 --- a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/CheckStatusOfHaaS.fxml +++ b/haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/ui/CheckStatusOfHaaS.fxml @@ -4,7 +4,7 @@ <?import javafx.scene.control.TableView?> <?import javafx.scene.layout.BorderPane?> -<BorderPane maxHeight="-Infinity" maxWidth="-Infinity" minHeight="-Infinity" minWidth="-Infinity" prefHeight="400.0" prefWidth="912.0" xmlns="http://javafx.com/javafx/8.0.65" xmlns:fx="http://javafx.com/fxml/1" fx:controller="cz.it4i.fiji.haas.ui.CheckStatusOfHaaSController"> +<BorderPane maxHeight="-Infinity" maxWidth="-Infinity" minHeight="-Infinity" minWidth="-Infinity" prefHeight="400.0" prefWidth="912.0" xmlns="http://javafx.com/javafx/8.0.65" xmlns:fx="http://javafx.com/fxml/1" fx:controller="cz.it4i.fiji.haas_snakemake_spim.ui.CheckStatusOfHaaSController"> <center> <TableView fx:id="jobs" prefHeight="400.0" prefWidth="675.0" BorderPane.alignment="CENTER"> <columns> diff --git a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/CheckStatusOfHaaSController.java b/haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/ui/CheckStatusOfHaaSController.java similarity index 92% rename from haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/CheckStatusOfHaaSController.java rename to haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/ui/CheckStatusOfHaaSController.java index d814f587..92fa18ed 100644 --- a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/ui/CheckStatusOfHaaSController.java +++ b/haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/ui/CheckStatusOfHaaSController.java @@ -1,4 +1,4 @@ -package cz.it4i.fiji.haas.ui; +package cz.it4i.fiji.haas_snakemake_spim.ui; import java.awt.Window; import java.util.function.Function; @@ -7,7 +7,9 @@ import org.scijava.log.LogService; import org.scijava.plugin.Parameter; import cz.it4i.fiji.haas.JobManager.JobInfo; -import cz.it4i.fiji.haas.ModalDialogs; +import cz.it4i.fiji.haas.ui.ModalDialogs; +import cz.it4i.fiji.haas.ui.ObservableValueAdapter; +import cz.it4i.fiji.haas.ui.ProgressDialog; import javafx.application.Platform; import javafx.event.ActionEvent; import javafx.event.EventHandler; diff --git a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/CheckStatusOfHaaSWindow.java b/haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/ui/CheckStatusOfHaaSWindow.java similarity index 92% rename from haas-imagej-client/src/main/java/cz/it4i/fiji/haas/CheckStatusOfHaaSWindow.java rename to haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/ui/CheckStatusOfHaaSWindow.java index 6cccae8f..b2b13c67 100644 --- a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/CheckStatusOfHaaSWindow.java +++ b/haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/ui/CheckStatusOfHaaSWindow.java @@ -1,4 +1,4 @@ -package cz.it4i.fiji.haas; +package cz.it4i.fiji.haas_snakemake_spim.ui; import java.awt.Frame; @@ -6,7 +6,7 @@ import org.scijava.Context; import org.scijava.plugin.Parameter; import cz.it4i.fiji.haas.JobManager.JobInfo; -import cz.it4i.fiji.haas.ui.CheckStatusOfHaaSController; +import cz.it4i.fiji.haas.ui.FXFrame; import javafx.application.Platform; public class CheckStatusOfHaaSWindow extends FXFrame<CheckStatusOfHaaSController> { diff --git a/haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/ui/package-info.java b/haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/ui/package-info.java new file mode 100644 index 00000000..1465d1c6 --- /dev/null +++ b/haas-snakemake-spim/src/main/java/cz/it4i/fiji/haas_snakemake_spim/ui/package-info.java @@ -0,0 +1,8 @@ +/** + * + */ +/** + * @author koz01 + * + */ +package cz.it4i.fiji.haas_snakemake_spim.ui; \ No newline at end of file diff --git a/haas-spim-benchmark/pom.xml b/haas-spim-benchmark/pom.xml new file mode 100644 index 00000000..9a7a84fb --- /dev/null +++ b/haas-spim-benchmark/pom.xml @@ -0,0 +1,94 @@ +<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" + xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd"> + <modelVersion>4.0.0</modelVersion> + <parent> + <groupId>org.scijava</groupId> + <artifactId>pom-scijava</artifactId> + <version>17.1.1</version> + <relativePath /> + </parent> + <groupId>cz.it4i.fiji</groupId> + <artifactId>haas-spim-benchmark</artifactId> + <version>0.0.1-SNAPSHOT</version> + <packaging>jar</packaging> + <name>Plugins for running SPIM automated workflow by IT4I HaaS.</name> + <description>This example provides an introduction to writing ImageJ commands.</description> + <url>https://github.com/[MY-ORG]/[MY-REPO]</url> + <inceptionYear>2013</inceptionYear> + <organization> + <name>[MY-ORGANIZATION-NAME]</name> + <url>[MY-ORGANIZATION-WEB-SITE]</url> + </organization> + <licenses> + <license> + <name>CC0 1.0 Universal License</name> + <url>http://creativecommons.org/publicdomain/zero/1.0/</url> + <distribution>repo</distribution> + </license> + </licenses> + + <developers> + <developer> + <id>[MY-GITHUB-ID]</id> + <name>[MY-FULL-NAME]</name> + <url>https://imagej.net/User:[MY-IMAGEJ-WIKI-ACCOUNT]</url> + </developer> + </developers> + <contributors> + <contributor> + <name>None</name> + </contributor> + </contributors> + + <mailingLists> + <mailingList> + <name>ImageJ Forum</name> + <archive>http://forum.imagej.net/</archive> + </mailingList> + </mailingLists> + + <scm> + <connection>scm:git:git://github.com/[MY-ORG]/[MY-REPO]</connection> + <developerConnection>scm:git:git@github.com:[MY-ORG]/[MY-REPO]</developerConnection> + <tag>HEAD</tag> + <url>https://github.com/[MY-ORG]/[MY-REPO]</url> + </scm> + <issueManagement> + <system>GitHub Issues</system> + <url>http://github.com/[MY-ORG]/[MY-REPO]/issues</url> + </issueManagement> + <ciManagement> + <system>None</system> + </ciManagement> + + + <repositories> + <repository> + <id>imagej.public</id> + <url>http://maven.imagej.net/content/groups/public</url> + </repository> + </repositories> + + <dependencies> + <dependency> + <groupId>net.imagej</groupId> + <artifactId>imagej</artifactId> + </dependency> + + <dependency> + <groupId>cz.it4i.fiji</groupId> + <artifactId>haas-imagej-client</artifactId> + <version>0.0.1-SNAPSHOT</version> + </dependency> + <!-- https://mvnrepository.com/artifact/org.slf4j/slf4j-api --> + <dependency> + <groupId>org.slf4j</groupId> + <artifactId>slf4j-api</artifactId> + </dependency> + <!-- https://mvnrepository.com/artifact/org.slf4j/slf4j-jdk14 --> + <dependency> + <groupId>org.slf4j</groupId> + <artifactId>slf4j-simple</artifactId> + </dependency> + </dependencies> +</project> \ No newline at end of file diff --git a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/BenchmarkJobManager.java b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/BenchmarkJobManager.java similarity index 95% rename from haas-imagej-client/src/main/java/cz/it4i/fiji/haas/BenchmarkJobManager.java rename to haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/BenchmarkJobManager.java index 37b1daa0..26e65fd2 100644 --- a/haas-imagej-client/src/main/java/cz/it4i/fiji/haas/BenchmarkJobManager.java +++ b/haas-spim-benchmark/src/main/java/cz/it4i/fiji/haas_spim_benchmark/core/BenchmarkJobManager.java @@ -1,4 +1,4 @@ -package cz.it4i.fiji.haas; +package cz.it4i.fiji.haas_spim_benchmark.core; import java.io.IOException; import java.io.InputStream; @@ -14,6 +14,9 @@ import java.util.stream.Collectors; import org.yaml.snakeyaml.Yaml; +import cz.it4i.fiji.haas.JobManager; +import cz.it4i.fiji.haas.TestingConstants; +import cz.it4i.fiji.haas.UploadingFileFromResource; import cz.it4i.fiji.haas.JobManager.JobInfo; import cz.it4i.fiji.haas.JobManager.JobSynchronizableFile; import cz.it4i.fiji.haas_java_client.HaaSClient; diff --git a/haas-imagej-client/src/test/java/cz/it4i/fiji/haas/RunBenchmark.java b/haas-spim-benchmark/src/test/java/cz/it4i/fiji/haas/RunBenchmark.java similarity index 97% rename from haas-imagej-client/src/test/java/cz/it4i/fiji/haas/RunBenchmark.java rename to haas-spim-benchmark/src/test/java/cz/it4i/fiji/haas/RunBenchmark.java index 01b62934..3a36e0e8 100644 --- a/haas-imagej-client/src/test/java/cz/it4i/fiji/haas/RunBenchmark.java +++ b/haas-spim-benchmark/src/test/java/cz/it4i/fiji/haas/RunBenchmark.java @@ -11,6 +11,7 @@ import org.slf4j.LoggerFactory; import cz.it4i.fiji.haas_java_client.JobState; import cz.it4i.fiji.haas_java_client.SynchronizableFileType; +import cz.it4i.fiji.haas_spim_benchmark.core.BenchmarkJobManager; import net.imagej.updater.util.Progress; public class RunBenchmark { -- GitLab