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ankurjunejaankurjuneja
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Nextflow integration with pipeline (#453)
1 parent ea0dbc9 commit 3507a86

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‎nextflow/build.gradle‎

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import org.labkey.gradle.util.BuildUtils
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plugins {
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id 'org.labkey.build.module'
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}
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dependencies {
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BuildUtils.addLabKeyDependency(project: project, config: "modules", depProjectPath: BuildUtils.getPlatformModuleProjectPath(project.gradle, "pipeline"), depProjectConfig: "published", depExtension: "module")
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}
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‎nextflow/module.properties‎

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ModuleClass: org.labkey.nextflow.NextFlowModule
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Label: NextFlow module
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Description: This module provides the functionality \
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for running the NextFlow pipeline jobs on PanoramaWeb.
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License: Apache 2.0
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LicenseURL: http://www.apache.org/licenses/LICENSE-2.0
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SupportedDatabases: pgsql
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ManageVersion: false

‎nextflow/resources/views/begin.html‎

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<html>
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<button id="enable-button">Enable/Disable Nextflow</button>
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<button id="run-button">Nextflow Pipeline</button>
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</html>
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<script type = "text/javascript" nonce="<%=scriptNonce%>">
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$(document).ready(function() {
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$('#enable-button').click(function() {
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window.location = LABKEY.ActionURL.buildURL('nextflow', 'nextFlowEnable.view');
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});
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$('#run-button').click(function() {
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window.location = LABKEY.ActionURL.buildURL('nextflow', 'nextFlowRun.api');
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});
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})
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</script>

‎nextflow/resources/views/nextFlowConfiguration.html‎

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<table>
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<tr>
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<td class="labkey-form-label">NextFlow Config File Path</td>
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<td><input type="text" name="nextFlowConfigFilePath" size=64></td>
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</tr>
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<tr>
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<td class="labkey-form-label">AWS Account Name</td>
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<td><input type="text" name="name" size=64></td>
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</tr>
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<tr>
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<td class="labkey-form-label">AWS Identity</td>
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<td><input type="text" name="identity" size=64></td>
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</tr>
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<tr>
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<td class="labkey-form-label">AWS S3 Bucket Path</td>
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<td><input type="text" name="s3BucketPath" size=64></td>
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</tr>
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<tr>
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<td class="labkey-form-label">AWS Credential</td>
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<td><input type="password" name="credential" size=64></td>
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</tr>
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</table>
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<button id="submit-button">Submit</button>
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<button id="delete-button">Delete</button>
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<button id="cancel-button">Cancel</button>
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<script type="text/javascript" nonce="<%=scriptNonce%>">
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$(document).ready(function() {
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// load the current configuration on page load
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LABKEY.Ajax.request({
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url: LABKEY.ActionURL.buildURL('nextflow', 'GetNextFlowConfiguration.api'),
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method: 'GET',
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success: function(response) {
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const parsed = JSON.parse(response.responseText);
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if (parsed.config) {
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const response = parsed.config;
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$('input[name=nextFlowConfigFilePath]').val(response.nextFlowConfigFilePath);
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$('input[name=name]').val(response.accountName);
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$('input[name=identity]').val(response.identity);
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$('input[name=s3BucketPath]').val(response.s3BucketPath);
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$('input[name=credential]').val(response.credential);
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}
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},
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failure: function(response) {
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alert('Failed to load configuration');
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}
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});
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$('#submit-button').click(function() {
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let data = {
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nextFlowConfigFilePath: $('input[name=nextFlowConfigFilePath]').val(),
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accountName: $('input[name=name]').val(),
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identity: $('input[name=identity]').val(),
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s3BucketPath: $('input[name=s3BucketPath]').val(),
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credential: $('input[name=credential]').val()
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};
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LABKEY.Ajax.request({
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url: LABKEY.ActionURL.buildURL('nextflow', 'nextFlowConfiguration.api'),
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method: 'POST',
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params: data,
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success: function(response) {
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window.location = LABKEY.ActionURL.buildURL('project', 'start');
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},
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failure: function(response) {
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alert('Failed to save configuration');
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}
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});
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});
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$('#delete-button').click(function() {
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LABKEY.Ajax.request({
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url: LABKEY.ActionURL.buildURL('nextflow', 'DeleteNextFlowConfiguration.api'),
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method: 'POST',
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success: function(response) {
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window.location = LABKEY.ActionURL.buildURL('project', 'start');
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},
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failure: function(response) {
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alert('Failed to delete configuration');
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}
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});
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});
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$('#cancel-button').click(function() {
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window.location = LABKEY.ActionURL.buildURL('project', 'start');
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});
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});
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</script>

‎nextflow/resources/views/nextFlowConfiguration.view.xml‎

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<view xmlns="http://labkey.org/data/xml/view" title="NextFlow Configuration">
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<dependencies>
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<dependency path="internal/jQuery"/>
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</dependencies>
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</view>

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