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[bot] Fast-forward for 24.11.3 #475

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merged 2 commits into from
Dec 17, 2024
Merged

[bot] Fast-forward for 24.11.3 #475

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8b13c2a
Let users launch NextFlow from file browser (#470)
labkey-jeckels Dec 11, 2024
8d4f1a4
Minor NextFlow fixes (#472)
labkey-jeckels Dec 16, 2024
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7 changes: 6 additions & 1 deletion nextflow/build.gradle
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Original file line number Diff line number Diff line change
Expand Up @@ -6,5 +6,10 @@ plugins {

dependencies {
BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: BuildUtils.getPlatformModuleProjectPath(project.gradle, "pipeline"), depProjectConfig: "published", depExtension: "module")
}

compileOnly "org.projectlombok:lombok:${lombokVersion}"
annotationProcessor "org.projectlombok:lombok:${lombokVersion}"

BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: BuildUtils.getPlatformModuleProjectPath(project.gradle, "experiment"), depProjectConfig: "published", depExtension: "module")
BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: BuildUtils.getPlatformModuleProjectPath(project.gradle, "pipeline"), depProjectConfig: "published", depExtension: "module")
}
162 changes: 103 additions & 59 deletions nextflow/src/org/labkey/nextflow/NextFlowController.java
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Original file line number Diff line number Diff line change
@@ -1,12 +1,13 @@
package org.labkey.nextflow;

import lombok.Getter;
import lombok.Setter;
import org.apache.commons.lang3.StringUtils;
import org.apache.logging.log4j.Logger;
import org.labkey.api.action.ApiResponse;
import org.labkey.api.action.ApiSimpleResponse;
import org.labkey.api.action.FormViewAction;
import org.labkey.api.action.MutatingApiAction;
import org.labkey.api.action.SimpleViewAction;
import org.labkey.api.action.SpringActionController;
import org.labkey.api.admin.AdminUrls;
import org.labkey.api.data.PropertyManager;
Expand All @@ -15,17 +16,21 @@
import org.labkey.api.pipeline.PipelineJob;
import org.labkey.api.pipeline.PipelineService;
import org.labkey.api.pipeline.PipelineStatusUrls;
import org.labkey.api.pipeline.browse.PipelinePathForm;
import org.labkey.api.security.AdminConsoleAction;
import org.labkey.api.security.RequiresPermission;
import org.labkey.api.security.permissions.AdminOperationsPermission;
import org.labkey.api.security.permissions.InsertPermission;
import org.labkey.api.security.permissions.ReadPermission;
import org.labkey.api.security.permissions.SiteAdminPermission;
import org.labkey.api.util.Button;
import org.labkey.api.util.DOM;
import org.labkey.api.util.FileUtil;
import org.labkey.api.util.HtmlString;
import org.labkey.api.util.PageFlowUtil;
import org.labkey.api.util.Path;
import org.labkey.api.util.URLHelper;
import org.labkey.api.util.element.Select;
import org.labkey.api.util.logging.LogHelper;
import org.labkey.api.view.ActionURL;
import org.labkey.api.view.HtmlView;
import org.labkey.api.view.JspView;
import org.labkey.api.view.NavTree;
Expand All @@ -36,14 +41,20 @@
import org.springframework.validation.Errors;
import org.springframework.web.servlet.ModelAndView;

import java.io.File;
import java.util.Arrays;
import java.util.List;

import static org.labkey.api.util.DOM.Attribute.checked;
import static org.labkey.api.util.DOM.Attribute.hidden;
import static org.labkey.api.util.DOM.Attribute.method;
import static org.labkey.api.util.DOM.Attribute.name;
import static org.labkey.api.util.DOM.Attribute.type;
import static org.labkey.api.util.DOM.Attribute.value;
import static org.labkey.api.util.DOM.DIV;
import static org.labkey.api.util.DOM.INPUT;
import static org.labkey.api.util.DOM.LK.FORM;
import static org.labkey.api.util.DOM.UL;
import static org.labkey.api.util.DOM.at;
import static org.labkey.nextflow.NextFlowManager.NEXTFLOW_CONFIG;

Expand All @@ -59,32 +70,6 @@ public NextFlowController()
setActionResolver(_actionResolver);
}

@RequiresPermission(ReadPermission.class)
public static class BeginAction extends SimpleViewAction<Object>
{
@Override
public ModelAndView getView(Object o, BindException errors)
{
boolean enabled = NextFlowManager.get().isEnabled(getContainer());
return new HtmlView("NextFlow",
DIV(
DIV("NextFlow integration is " + (enabled ? "enabled" : "disabled") + " in this " + (getContainer().isProject() ? "project" : "folder") + "."),
DIV(
getContainer().hasPermission(getUser(), SiteAdminPermission.class) ?
new Button.ButtonBuilder("Enable/Disable").href(new ActionURL(NextFlowEnableAction.class, getContainer())).build() : null,
" ",
enabled && getContainer().hasPermission(getUser(), InsertPermission.class) ?
new Button.ButtonBuilder("Run NextFlow Analysis").href(new ActionURL(NextFlowRunAction.class, getContainer())).build() : null)));
}

@Override
public void addNavTrail(NavTree root)
{
root.addChild("NextFlow");
}
}


@RequiresPermission(SiteAdminPermission.class)
public static class DeleteNextFlowConfigurationAction extends MutatingApiAction<Object>
{
Expand Down Expand Up @@ -196,8 +181,8 @@ public void setEnabled(Boolean enabled)
}
}

@RequiresPermission(SiteAdminPermission.class)
public static class NextFlowEnableAction extends FormViewAction<EnabledForm>
@RequiresPermission(ReadPermission.class)
public static class BeginAction extends FormViewAction<EnabledForm>
{
@Override
public void validateCommand(EnabledForm target, Errors errors)
Expand All @@ -208,21 +193,30 @@ public void validateCommand(EnabledForm target, Errors errors)
@Override
public ModelAndView getView(EnabledForm form, boolean reshow, BindException errors)
{
Boolean status = NextFlowManager.get().getEnabledState(getContainer());
boolean inheritedStatus = NextFlowManager.get().isEnabled(getContainer().getParent());

return new HtmlView("Enable/Disable NextFlow",
FORM(at(method, "POST"),
DIV(INPUT(at(type, "radio", name, "enabled", value, Boolean.TRUE.toString(), (status == Boolean.TRUE ? checked : null), null)),
"Enabled"),
DIV(INPUT(at(type, "radio", name, "enabled", value, Boolean.FALSE.toString(), (status == Boolean.FALSE ? checked : null), null)),
"Disabled"),
DIV(INPUT(at(type, "radio", name, "enabled", value, "", (status == null ? checked : null), null)),
getContainer().isRoot() ?
"Unset" :
"Inherited from " + getContainer().getParent().getPath() + " (currently " + (inheritedStatus ? "enabled" : "disabled") + ")"),
new Button.ButtonBuilder("Save").submit(true).build(), " ",
new Button.ButtonBuilder("Cancel").href(getContainer().getStartURL(getUser())).build()));
if (getUser().hasSiteAdminPermission())
{
Boolean status = NextFlowManager.get().getEnabledState(getContainer());
boolean inheritedStatus = NextFlowManager.get().isEnabled(getContainer().getParent());

return new HtmlView("Enable or Disable NextFlow",
FORM(at(method, "POST"),
DIV(INPUT(at(type, "radio", name, "enabled", value, Boolean.TRUE.toString(), (status == Boolean.TRUE ? checked : null), null)),
"Enabled"),
DIV(INPUT(at(type, "radio", name, "enabled", value, Boolean.FALSE.toString(), (status == Boolean.FALSE ? checked : null), null)),
"Disabled"),
DIV(INPUT(at(type, "radio", name, "enabled", value, "", (status == null ? checked : null), null)),
getContainer().isRoot() ?
"Unset" :
"Inherited from " + getContainer().getParent().getPath() + " (currently " + (inheritedStatus ? "enabled" : "disabled") + ")"),
new Button.ButtonBuilder("Save").submit(true).build(), " ",
new Button.ButtonBuilder("Cancel").href(getContainer().getStartURL(getUser())).build()));
}
else
{
return new HtmlView("NextFlow Integration Status",
DIV("NextFlow integration is " + (NextFlowManager.get().isEnabled(getContainer()) ? "enabled" : "disabled") + " in this " + (getContainer().isProject() ? "project" : "folder") + ".")
);
}
}

@Override
Expand All @@ -235,7 +229,7 @@ public boolean handlePost(EnabledForm form, BindException errors)
@Override
public void addNavTrail(NavTree root)
{
root.addChild("Enable/Disable NextFlow");
root.addChild("NextFlow Integration Status");
}

@Override
Expand All @@ -245,11 +239,18 @@ public URLHelper getSuccessURL(EnabledForm o)
}
}

@Getter @Setter
public static class AnalyzeForm extends PipelinePathForm
{
private boolean launch = false;
private String configFile;
}

@RequiresPermission(AdminOperationsPermission.class)
public class NextFlowRunAction extends FormViewAction<Object>
public class NextFlowRunAction extends FormViewAction<AnalyzeForm>
{
@Override
public void validateCommand(Object o, Errors errors)
public void validateCommand(AnalyzeForm o, Errors errors)
{
if (!NextFlowManager.get().isEnabled(getContainer()))
{
Expand All @@ -258,26 +259,69 @@ public void validateCommand(Object o, Errors errors)
}

@Override
public ModelAndView getView(Object o, boolean b, BindException errors)
public ModelAndView getView(AnalyzeForm o, boolean b, BindException errors)
{
return new HtmlView("NextFlow Runner", DIV("Run NextFlow Pipeline",
FORM(at(method, "POST"),
new Button.ButtonBuilder("Start NextFlow").submit(true).build())));
NextFlowConfiguration config = NextFlowManager.get().getConfiguration();
if (config.getNextFlowConfigFilePath() != null)
{
File configDir = new File(config.getNextFlowConfigFilePath());
if (configDir.isDirectory())
{
File[] files = configDir.listFiles();
if (files != null && files.length > 0)
{
List<File> configFiles = Arrays.asList(files);
return new HtmlView("NextFlow Runner", DIV(
FORM(at(method, "POST"),
INPUT(at(hidden, true, name, "launch", value, true)),
Arrays.stream(o.getFile()).map(f -> INPUT(at(hidden, true, name, "file", value, f))).toList(),
"Files: ",
UL(Arrays.stream(o.getFile()).map(DOM::LI)),
"Config: ",
new Select.SelectBuilder().name("configFile").addOptions(configFiles.stream().filter(f -> f.isFile() && f.getName().toLowerCase().endsWith(".config")).map(File::getName).sorted(String.CASE_INSENSITIVE_ORDER).toList()).build(),
new Button.ButtonBuilder("Start NextFlow").submit(true).build())));
}
}
}
return new HtmlView(HtmlString.of("Couldn't find NextFlow config file(s)"));
}

@Override
public boolean handlePost(Object o, BindException errors) throws Exception
public boolean handlePost(AnalyzeForm form, BindException errors) throws Exception
{
ViewBackgroundInfo info = getViewBackgroundInfo();
PipeRoot root = PipelineService.get().findPipelineRoot(info.getContainer());
PipelineJob job = new NextFlowPipelineJob(info, root);
PipelineService.get().queueJob(job);
if (!form.isLaunch())
{
return false;
}

NextFlowConfiguration config = NextFlowManager.get().getConfiguration();
File configDir = new File(config.getNextFlowConfigFilePath());
File configFile = FileUtil.appendPath(configDir, Path.parse(form.getConfigFile()));
if (!configFile.exists())
{
errors.reject(ERROR_MSG, "Config file does not exist");
}
else
{
List<File> inputFiles = form.getValidatedFiles(getContainer());
if (inputFiles.isEmpty())
{
errors.reject(ERROR_MSG, "No input files");
}
else
{
ViewBackgroundInfo info = getViewBackgroundInfo();
PipeRoot root = PipelineService.get().findPipelineRoot(info.getContainer());
PipelineJob job = NextFlowPipelineJob.create(info, root, configFile.toPath(), inputFiles.stream().map(File::toPath).toList());
PipelineService.get().queueJob(job);
}
}

return !errors.hasErrors();
}

@Override
public URLHelper getSuccessURL(Object o)
public URLHelper getSuccessURL(AnalyzeForm o)
{
return PageFlowUtil.urlProvider(PipelineStatusUrls.class).urlBegin(getContainer());
}
Expand Down
9 changes: 9 additions & 0 deletions nextflow/src/org/labkey/nextflow/NextFlowManager.java
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,9 @@
import org.labkey.api.data.PropertyManager;
import org.springframework.validation.BindException;

import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.util.HashMap;
import java.util.Map;

Expand Down Expand Up @@ -44,6 +47,12 @@ private void checkArgs(NextFlowConfiguration config, BindException errors)
if (StringUtils.isEmpty(config.getNextFlowConfigFilePath()))
errors.rejectValue("nextFlowConfigFilePath", ERROR_MSG, "NextFlow config file path is required");

Path configPath = Paths.get(config.getNextFlowConfigFilePath());
if (!Files.isDirectory(configPath))
{
errors.rejectValue("nextFlowConfigFilePath", ERROR_MSG, "NextFlow config file path must be a directory");
}

// Not yet used
// if (StringUtils.isEmpty(config.getAccountName()))
// errors.rejectValue("accountName", ERROR_MSG, "AWS account name is required");
Expand Down
4 changes: 2 additions & 2 deletions nextflow/src/org/labkey/nextflow/NextFlowModule.java
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Original file line number Diff line number Diff line change
Expand Up @@ -21,14 +21,14 @@ protected void startupAfterSpringConfig(ModuleContext moduleContext)
{
ActionURL adminUrl = new ActionURL(NextFlowController.NextFlowConfigurationAction.class, ContainerManager.getRoot());
AdminConsole.addLink(AdminConsole.SettingsLinkType.Configuration, "NextFlow Configuration", adminUrl, AdminPermission.class);

PipelineService.get().registerPipelineProvider(new NextFlowPipelineProvider(this));
}

@Override
protected void init()
{
addController(NextFlowController.NAME, NextFlowController.class);

PipelineService.get().registerPipelineProvider(new NextFlowPipelineProvider(this));
}

@Override
Expand Down
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