Merge 24.11 to develop

LabKey · Nov 6, 2024 · 43868b7 · 43868b7
2 parents 6cdbf76 + 4a3e040
commit 43868b7
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diff --git a/nextflow/build.gradle b/nextflow/build.gradle
@@ -0,0 +1,10 @@
+import org.labkey.gradle.util.BuildUtils
+
+plugins {
+    id 'org.labkey.build.module'
+}
+
+dependencies {
+    BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: BuildUtils.getPlatformModuleProjectPath(project.gradle, "pipeline"), depProjectConfig: "published", depExtension: "module")
+}
+
diff --git a/nextflow/module.properties b/nextflow/module.properties
@@ -0,0 +1,8 @@
+ModuleClass: org.labkey.nextflow.NextFlowModule
+Label: NextFlow module
+Description: This module provides the functionality \
+    for running the NextFlow pipeline jobs on PanoramaWeb.
+License: Apache 2.0
+LicenseURL: http://www.apache.org/licenses/LICENSE-2.0
+SupportedDatabases: pgsql
+ManageVersion: false
diff --git a/nextflow/resources/views/begin.html b/nextflow/resources/views/begin.html
@@ -0,0 +1,17 @@
+<html>
+<button id="enable-button">Enable/Disable Nextflow</button>
+<button id="run-button">Nextflow Pipeline</button>
+</html>
+
+<script type = "text/javascript" nonce="<%=scriptNonce%>">
+
+    $(document).ready(function() {
+        $('#enable-button').click(function() {
+            window.location = LABKEY.ActionURL.buildURL('nextflow', 'nextFlowEnable.view');
+        });
+
+        $('#run-button').click(function() {
+            window.location = LABKEY.ActionURL.buildURL('nextflow', 'nextFlowRun.api');
+        });
+    })
+</script>
diff --git a/nextflow/resources/views/nextFlowConfiguration.html b/nextflow/resources/views/nextFlowConfiguration.html
@@ -0,0 +1,88 @@
+<table>
+    <tr>
+        <td class="labkey-form-label">NextFlow Config File Path</td>
+        <td><input type="text" name="nextFlowConfigFilePath" size=64></td>
+    </tr>
+    <tr>
+        <td class="labkey-form-label">AWS Account Name</td>
+        <td><input type="text" name="name" size=64></td>
+    </tr>
+    <tr>
+        <td class="labkey-form-label">AWS Identity</td>
+        <td><input type="text" name="identity" size=64></td>
+    </tr>
+    <tr>
+        <td class="labkey-form-label">AWS S3 Bucket Path</td>
+        <td><input type="text" name="s3BucketPath" size=64></td>
+    </tr>
+    <tr>
+        <td class="labkey-form-label">AWS Credential</td>
+        <td><input type="password" name="credential" size=64></td>
+    </tr>
+</table>
+<button id="submit-button">Submit</button>
+<button id="delete-button">Delete</button>
+<button id="cancel-button">Cancel</button>
+
+<script type="text/javascript" nonce="<%=scriptNonce%>">
+    $(document).ready(function() {
+        // load the current configuration on page load
+        LABKEY.Ajax.request({
+            url: LABKEY.ActionURL.buildURL('nextflow', 'GetNextFlowConfiguration.api'),
+            method: 'GET',
+            success: function(response) {
+                const parsed = JSON.parse(response.responseText);
+                if (parsed.config) {
+                    const response = parsed.config;
+                    $('input[name=nextFlowConfigFilePath]').val(response.nextFlowConfigFilePath);
+                    $('input[name=name]').val(response.accountName);
+                    $('input[name=identity]').val(response.identity);
+                    $('input[name=s3BucketPath]').val(response.s3BucketPath);
+                    $('input[name=credential]').val(response.credential);
+                }
+
+            },
+            failure: function(response) {
+                alert('Failed to load configuration');
+            }
+        });
+
+        $('#submit-button').click(function() {
+            let data = {
+                nextFlowConfigFilePath: $('input[name=nextFlowConfigFilePath]').val(),
+                accountName: $('input[name=name]').val(),
+                identity: $('input[name=identity]').val(),
+                s3BucketPath: $('input[name=s3BucketPath]').val(),
+                credential: $('input[name=credential]').val()
+            };
+            LABKEY.Ajax.request({
+                url: LABKEY.ActionURL.buildURL('nextflow', 'nextFlowConfiguration.api'),
+                method: 'POST',
+                params: data,
+                success: function(response) {
+                    window.location = LABKEY.ActionURL.buildURL('project', 'start');
+                },
+                failure: function(response) {
+                    alert('Failed to save configuration');
+                }
+            });
+        });
+
+        $('#delete-button').click(function() {
+            LABKEY.Ajax.request({
+                url: LABKEY.ActionURL.buildURL('nextflow', 'DeleteNextFlowConfiguration.api'),
+                method: 'POST',
+                success: function(response) {
+                    window.location = LABKEY.ActionURL.buildURL('project', 'start');
+                },
+                failure: function(response) {
+                    alert('Failed to delete configuration');
+                }
+            });
+        });
+
+        $('#cancel-button').click(function() {
+            window.location = LABKEY.ActionURL.buildURL('project', 'start');
+        });
+    });
+</script>
diff --git a/nextflow/resources/views/nextFlowConfiguration.view.xml b/nextflow/resources/views/nextFlowConfiguration.view.xml
@@ -0,0 +1,5 @@
+<view xmlns="http://labkey.org/data/xml/view" title="NextFlow Configuration">
+    <dependencies>
+        <dependency path="internal/jQuery"/>
+    </dependencies>
+</view>