Minor NextFlow fixes (#472)

LabKey · Dec 16, 2024 · 8d4f1a4 · 8d4f1a4
1 parent 8b13c2a
commit 8d4f1a4
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Showing 6 changed files with 36 additions and 57 deletions.
diff --git a/nextflow/src/org/labkey/nextflow/NextFlowController.java b/nextflow/src/org/labkey/nextflow/NextFlowController.java
@@ -1,6 +1,5 @@
 package org.labkey.nextflow;
 
-import lombok.Data;
 import lombok.Getter;
 import lombok.Setter;
 import org.apache.commons.lang3.StringUtils;
@@ -9,7 +8,6 @@
 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;
@@ -22,7 +20,6 @@
 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;
@@ -34,7 +31,6 @@
 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;
@@ -45,10 +41,7 @@
 import org.springframework.validation.Errors;
 import org.springframework.web.servlet.ModelAndView;
 
-import javax.swing.text.html.FormView;
-
 import java.io.File;
-import java.nio.file.Paths;
 import java.util.Arrays;
 import java.util.List;
 
@@ -60,7 +53,6 @@
 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.LI;
 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;
@@ -78,32 +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>
     {
@@ -215,8 +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)
@@ -227,21 +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
@@ -254,7 +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

diff --git a/nextflow/src/org/labkey/nextflow/NextFlowManager.java b/nextflow/src/org/labkey/nextflow/NextFlowManager.java
@@ -48,7 +48,7 @@ private void checkArgs(NextFlowConfiguration config, BindException errors)
             errors.rejectValue("nextFlowConfigFilePath", ERROR_MSG, "NextFlow config file path is required");
 
         Path configPath = Paths.get(config.getNextFlowConfigFilePath());
-        if (Files.isDirectory(configPath))
+        if (!Files.isDirectory(configPath))
         {
             errors.rejectValue("nextFlowConfigFilePath", ERROR_MSG, "NextFlow config file path must be a directory");
         }

diff --git a/nextflow/src/org/labkey/nextflow/NextFlowModule.java b/nextflow/src/org/labkey/nextflow/NextFlowModule.java
@@ -29,8 +29,6 @@ protected void startupAfterSpringConfig(ModuleContext moduleContext)
     protected void init()
     {
         addController(NextFlowController.NAME, NextFlowController.class);
-
-        PipelineService.get().registerPipelineProvider(new NextFlowPipelineProvider(this));
     }
 
     @Override

diff --git a/nextflow/src/org/labkey/nextflow/pipeline/NextFlowPipelineJob.java b/nextflow/src/org/labkey/nextflow/pipeline/NextFlowPipelineJob.java
@@ -41,7 +41,7 @@ public static NextFlowPipelineJob create(ViewBackgroundInfo info, @NotNull PipeR
         Path log = jobDir.resolve(jobName + ".log");
         FileUtil.createDirectory(jobDir);
 
-        Path config = createConfig(templateConfig, log.getParent(), jobDir, info.getContainer());
+        Path config = createConfig(templateConfig, parentDir, jobDir, info.getContainer());
 
         return new NextFlowPipelineJob(info, root, config, inputFiles, log);
     }

diff --git a/nextflow/src/org/labkey/nextflow/pipeline/NextFlowPipelineProvider.java b/nextflow/src/org/labkey/nextflow/pipeline/NextFlowPipelineProvider.java
@@ -19,6 +19,13 @@ public NextFlowPipelineProvider(NextFlowModule owningModule)
         super(NAME, owningModule);
     }
 
+    @Override
+    public boolean isShowActionsIfModuleInactive()
+    {
+        // We rely on a setting that folder admins can't control to determine if NextFlow is available
+        return true;
+    }
+
     @Override
     public void updateFileProperties(ViewContext context, PipeRoot pr, PipelineDirectory directory, boolean includeAll)
     {

diff --git a/nextflow/src/org/labkey/nextflow/pipeline/NextFlowRunTask.java b/nextflow/src/org/labkey/nextflow/pipeline/NextFlowRunTask.java
@@ -8,7 +8,6 @@
 import org.labkey.api.pipeline.PipelineJobException;
 import org.labkey.api.pipeline.RecordedAction;
 import org.labkey.api.pipeline.RecordedActionSet;
-import org.labkey.api.pipeline.ToolExecutionException;
 import org.labkey.api.pipeline.WorkDirectoryTask;
 import org.labkey.api.security.SecurityManager;
 import org.labkey.api.util.FileType;