Support shared pipelines (#279)

* Allow to choose pipeline visibility when listing pipelines * Allow to launch shared pipelines * Add visibility column at list * Add missing license header * Fix tests * Search for multiple pipelines at launch command
seqeralabs · Dec 5, 2022 · 503eaad · 503eaad
1 parent 4ee5c5a
commit 503eaad
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Showing 14 changed files with 95 additions and 42 deletions.
diff --git a/build.gradle b/build.gradle
@@ -23,7 +23,7 @@ dependencies {
     implementation 'org.slf4j:slf4j-api:1.7.36'
     implementation 'ch.qos.logback:logback-core:1.2.11'
     implementation 'ch.qos.logback:logback-classic:1.2.11'
-    implementation 'io.seqera.tower:tower-java-sdk:1.4.2'
+    implementation 'io.seqera.tower:tower-java-sdk:1.4.3'
     implementation 'info.picocli:picocli:4.6.3'
     annotationProcessor 'info.picocli:picocli-codegen:4.6.3'
 

diff --git a/conf/resource-config.json b/conf/resource-config.json
@@ -17,11 +17,17 @@
   "bundles":[
     {
       "name":"org.glassfish.jersey.client.internal.localization",
-      "locales":["und"]
+      "locales":[
+        "", 
+        "und"
+      ]
     }, 
     {
       "name":"org.glassfish.jersey.internal.localization",
-      "locales":["und"]
+      "locales":[
+        "", 
+        "und"
+      ]
     }, 
     {
       "name":"org.glassfish.jersey.media.multipart.internal.localization"

diff --git a/src/main/java/io/seqera/tower/cli/commands/AbstractApiCmd.java b/src/main/java/io/seqera/tower/cli/commands/AbstractApiCmd.java
@@ -30,6 +30,7 @@
 import io.seqera.tower.model.ListComputeEnvsResponseEntry;
 import io.seqera.tower.model.ListWorkspacesAndOrgResponse;
 import io.seqera.tower.model.OrgAndWorkspaceDbDto;
+import io.seqera.tower.model.PipelineDbDto;
 import io.seqera.tower.model.User;
 import io.seqera.tower.model.WorkflowQueryAttribute;
 import org.glassfish.jersey.client.ClientConfig;
@@ -381,6 +382,19 @@ protected String workspaceRef(Long workspaceId) throws ApiException {
         return buildWorkspaceRef(orgName(workspaceId), workspaceName(workspaceId));
     }
 
+    protected Long sourceWorkspaceId(Long currentWorkspace, PipelineDbDto pipeline) {
+        if (pipeline == null)
+            return null;
+
+        if (pipeline.getWorkspaceId() == null)
+            return null;
+
+        if (pipeline.getWorkspaceId().equals(currentWorkspace))
+            return null;
+
+        return pipeline.getWorkspaceId();
+    }
+
     @Override
     public Integer call() {
         try {

diff --git a/src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java b/src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java
@@ -20,6 +20,7 @@
 import io.seqera.tower.model.ComputeEnvResponseDto;
 import io.seqera.tower.model.Launch;
 import io.seqera.tower.model.ListPipelinesResponse;
+import io.seqera.tower.model.PipelineDbDto;
 import io.seqera.tower.model.SubmitWorkflowLaunchRequest;
 import io.seqera.tower.model.SubmitWorkflowLaunchResponse;
 import io.seqera.tower.model.WorkflowLaunchRequest;
@@ -104,7 +105,7 @@ protected Response runNextflowPipeline(Long wspId) throws ApiException, IOExcept
                 .workDir(ce.getConfig().getWorkDir())
                 .preRunScript(ce.getConfig().getPreRunScript())
                 .postRunScript(ce.getConfig().getPostRunScript())
-        ), wspId);
+        ), wspId, null);
     }
 
     private WorkflowLaunchRequest updateLaunchRequest(WorkflowLaunchRequest base) throws IOException {
@@ -130,28 +131,46 @@ private WorkflowLaunchRequest updateLaunchRequest(WorkflowLaunchRequest base) th
     }
 
     protected Response runTowerPipeline(Long wspId) throws ApiException, IOException {
-        ListPipelinesResponse pipelines = api().listPipelines(Collections.emptyList(), wspId, 2, 0, pipeline, null);
+        ListPipelinesResponse pipelines = api().listPipelines(Collections.emptyList(), wspId, 50, 0, pipeline, "all");
         if (pipelines.getTotalSize() == 0) {
             throw new InvalidResponseException(String.format("Pipeline '%s' not found on this workspace.", pipeline));
         }
 
-        if (pipelines.getTotalSize() > 1) {
-            throw new InvalidResponseException(String.format("Multiple pipelines match '%s'", pipeline));
+        PipelineDbDto pipe = null;
+        for (PipelineDbDto p : pipelines.getPipelines()) {
+            if (pipeline.equals(p.getName())) {
+                pipe = p;
+                break;
+            }
         }
 
-        Long pipelineId = pipelines.getPipelines().get(0).getPipelineId();
-        Launch launch = api().describePipelineLaunch(pipelineId, wspId).getLaunch();
+        if (pipe == null) {
+            throw new InvalidResponseException(String.format("Pipeline '%s' not found", pipe));
+        }
+
+        Long sourceWorkspaceId = sourceWorkspaceId(wspId, pipe);
+
+        Launch launch = api().describePipelineLaunch(pipe.getPipelineId(), wspId, sourceWorkspaceId).getLaunch();
 
         WorkflowLaunchRequest launchRequest = createLaunchRequest(launch);
         if (computeEnv != null) {
             launchRequest.computeEnvId(computeEnvByRef(wspId, computeEnv).getId());
         }
 
-        return submitWorkflow(updateLaunchRequest(launchRequest), wspId);
+        if (launchRequest.getComputeEnvId() == null) {
+            launchRequest.computeEnvId(primaryComputeEnv(wspId).getId());
+        }
+
+        if (launchRequest.getWorkDir() == null) {
+            ComputeEnvResponseDto ce = api().describeComputeEnv(launchRequest.getComputeEnvId(), wspId, NO_CE_ATTRIBUTES).getComputeEnv();
+            launchRequest.workDir(ce.getConfig().getWorkDir());
+        }
+
+        return submitWorkflow(updateLaunchRequest(launchRequest), wspId, sourceWorkspaceId);
     }
 
-    protected Response submitWorkflow(WorkflowLaunchRequest launch, Long wspId) throws ApiException {
-        SubmitWorkflowLaunchResponse response = api().createWorkflowLaunch(new SubmitWorkflowLaunchRequest().launch(launch), wspId, null, null);
+    protected Response submitWorkflow(WorkflowLaunchRequest launch, Long wspId, Long sourceWorkspaceId) throws ApiException {
+        SubmitWorkflowLaunchResponse response = api().createWorkflowLaunch(new SubmitWorkflowLaunchRequest().launch(launch), wspId, null, sourceWorkspaceId);
         String workflowId = response.getWorkflowId();
         return new RunSubmited(workflowId, wspId, baseWorkspaceUrl(wspId), workspaceRef(wspId));
     }

diff --git a/src/main/java/io/seqera/tower/cli/commands/pipelines/AbstractPipelinesCmd.java b/src/main/java/io/seqera/tower/cli/commands/pipelines/AbstractPipelinesCmd.java
@@ -29,7 +29,7 @@ public AbstractPipelinesCmd() {
 
     protected PipelineDbDto pipelineByName(Long workspaceId, String name) throws ApiException {
 
-        ListPipelinesResponse list = api().listPipelines(Collections.emptyList(), workspaceId, null, null, name, null);
+        ListPipelinesResponse list = api().listPipelines(Collections.emptyList(), workspaceId, null, null, name, "all");
 
         if (list.getPipelines().isEmpty()) {
             throw new PipelineNotFoundException(name, workspaceRef(workspaceId));

diff --git a/src/main/java/io/seqera/tower/cli/commands/pipelines/ExportCmd.java b/src/main/java/io/seqera/tower/cli/commands/pipelines/ExportCmd.java
@@ -44,8 +44,8 @@ public class ExportCmd extends AbstractPipelinesCmd {
     protected Response exec() throws ApiException {
         Long wspId = workspaceId(workspace.workspace);
         PipelineDbDto pipeline = fetchPipeline(pipelineRefOptions, wspId);
-
-        Launch launch = api().describePipelineLaunch(pipeline.getPipelineId(), wspId).getLaunch();
+        Long sourceWorkspaceId = sourceWorkspaceId(wspId, pipeline);
+        Launch launch = api().describePipelineLaunch(pipeline.getPipelineId(), wspId, sourceWorkspaceId).getLaunch();
 
         WorkflowLaunchRequest workflowLaunchRequest = ModelHelper.createLaunchRequest(launch);
 

diff --git a/src/main/java/io/seqera/tower/cli/commands/pipelines/ListCmd.java b/src/main/java/io/seqera/tower/cli/commands/pipelines/ListCmd.java
@@ -36,6 +36,9 @@ public class ListCmd extends AbstractPipelinesCmd {
     @CommandLine.Option(names = {"-f", "--filter"}, description = "Show only pipelines that contain the given word.")
     public String filter;
 
+    @CommandLine.Option(names = {"--visibility"}, description = "Show pipelines: ${COMPLETION-CANDIDATES} [default: private].", defaultValue = "private")
+    public PipelineVisibility visibility;
+
     @CommandLine.Mixin
     PaginationOptions paginationOptions;
 
@@ -48,7 +51,7 @@ protected Response exec() throws ApiException, IOException {
         ListPipelinesResponse response = new ListPipelinesResponse();
 
         try {
-           response = api().listPipelines(Collections.emptyList(), wspId, max, offset, filter, null);
+           response = api().listPipelines(Collections.emptyList(), wspId, max, offset, filter, visibility.toString());
 
         } catch (ApiException apiException) {
             if (apiException.getCode() == 404){

diff --git a/src/main/java/io/seqera/tower/cli/commands/pipelines/PipelineVisibility.java b/src/main/java/io/seqera/tower/cli/commands/pipelines/PipelineVisibility.java
@@ -0,0 +1,29 @@
+/*
+ * Copyright (c) 2021, Seqera Labs.
+ *
+ * This Source Code Form is subject to the terms of the Mozilla Public
+ * License, v. 2.0. If a copy of the MPL was not distributed with this
+ * file, You can obtain one at http://mozilla.org/MPL/2.0/.
+ *
+ * This Source Code Form is "Incompatible With Secondary Licenses", as
+ * defined by the Mozilla Public License, v. 2.0.
+ */
+
+package io.seqera.tower.cli.commands.pipelines;
+
+public enum PipelineVisibility {
+    ALL("all"),
+    PRIVATE("private"),
+    SHARED("shared");
+
+    private final String value;
+
+    PipelineVisibility(String value) {
+        this.value = value;
+    }
+
+    @Override
+    public String toString() {
+        return value;
+    }
+}
diff --git a/src/main/java/io/seqera/tower/cli/commands/pipelines/UpdateCmd.java b/src/main/java/io/seqera/tower/cli/commands/pipelines/UpdateCmd.java
@@ -67,7 +67,8 @@ protected Response exec() throws ApiException, IOException {
             id = pipe.getPipelineId();
         }
 
-        Launch launch = api().describePipelineLaunch(id, wspId).getLaunch();
+        Long sourceWorkspaceId = sourceWorkspaceId(wspId, pipe);
+        Launch launch = api().describePipelineLaunch(id, wspId, sourceWorkspaceId).getLaunch();
 
         // Retrieve the provided computeEnv or use the primary if not provided
         String ceId = opts.computeEnv != null ? computeEnvByRef(wspId, opts.computeEnv).getId() : launch.getComputeEnv().getId();

diff --git a/src/main/java/io/seqera/tower/cli/commands/pipelines/ViewCmd.java b/src/main/java/io/seqera/tower/cli/commands/pipelines/ViewCmd.java
@@ -36,8 +36,9 @@ public class ViewCmd extends AbstractPipelinesCmd {
     protected Response exec() throws ApiException {
         Long wspId = workspaceId(workspace.workspace);
         PipelineDbDto pipeline = fetchPipeline(pipelineRefOptions, wspId);
+        Long sourceWorkspaceId = sourceWorkspaceId(wspId, pipeline);
 
-        Launch launch = api().describePipelineLaunch(pipeline.getPipelineId(), wspId).getLaunch();
+        Launch launch = api().describePipelineLaunch(pipeline.getPipelineId(), wspId, sourceWorkspaceId).getLaunch();
 
         return new PipelinesView(workspaceRef(wspId), pipeline, launch, baseWorkspaceUrl(wspId));
     }

diff --git a/src/main/java/io/seqera/tower/cli/responses/pipelines/PipelinesList.java b/src/main/java/io/seqera/tower/cli/responses/pipelines/PipelinesList.java
@@ -45,13 +45,13 @@ public void toString(PrintWriter out) {
             return;
         }
 
-        TableList table = new TableList(out, 3, "ID", "Name", "Repository", "Description").sortBy(0);
+        TableList table = new TableList(out, 4, "ID", "Name", "Repository", "Visibility").sortBy(0);
         table.setPrefix("    ");
         pipelines.forEach(pipe -> table.addRow(
                 formatPipelineId(pipe.getPipelineId(), baseWorkspaceUrl),
                 pipe.getName(),
                 pipe.getRepository(),
-                pipe.getDescription()
+                pipe.getVisibility()
         ));
         table.print();
         out.println("");

diff --git a/src/main/java/io/seqera/tower/cli/responses/pipelines/PipelinesView.java b/src/main/java/io/seqera/tower/cli/responses/pipelines/PipelinesView.java
@@ -58,7 +58,7 @@ public void toString(PrintWriter out) {
         table.addRow("Name", info.getName());
         table.addRow("Description", info.getDescription());
         table.addRow("Repository", info.getRepository());
-        table.addRow("Compute env.", launch.getComputeEnv().getName());
+        table.addRow("Compute env.", launch.getComputeEnv() == null ? "(not defined)" : launch.getComputeEnv().getName());
         table.print();
 
         out.println(String.format("%n  Configuration:%n%n%s%n", configJson.replaceAll("(?m)^", "     ")));

diff --git a/src/main/java/io/seqera/tower/cli/utils/ModelHelper.java b/src/main/java/io/seqera/tower/cli/utils/ModelHelper.java
@@ -25,7 +25,7 @@ private ModelHelper() {
     public static WorkflowLaunchRequest createLaunchRequest(Launch launch) {
         return new WorkflowLaunchRequest()
                 .id(launch.getId())
-                .computeEnvId(launch.getComputeEnv().getId())
+                .computeEnvId(launch.getComputeEnv() != null ? launch.getComputeEnv().getId() : null)
                 .pipeline(launch.getPipeline())
                 .workDir(launch.getWorkDir())
                 .revision(launch.getRevision())

diff --git a/src/test/java/io/seqera/tower/cli/LaunchCmdTest.java b/src/test/java/io/seqera/tower/cli/LaunchCmdTest.java
@@ -72,26 +72,6 @@ void testPipelineNotfound(MockServerClient mock) {
         assertEquals(1, out.exitCode);
     }
 
-    @Test
-    void testMultiplePipelinesFound(MockServerClient mock) {
-
-        mock.reset();
-
-        // Create server expectation
-        mock.when(
-                request().withMethod("GET").withPath("/pipelines"), exactly(1)
-        ).respond(
-                response().withStatusCode(200).withBody(loadResource("pipelines_multiple")).withContentType(MediaType.APPLICATION_JSON)
-        );
-
-        // Run the command
-        ExecOut out = exec(mock, "launch", "hello");
-
-        // Assert results
-        assertEquals(errorMessage(out.app, new InvalidResponseException("Multiple pipelines match 'hello'")), out.stdErr);
-        assertEquals(1, out.exitCode);
-    }
-
     @ParameterizedTest
     @EnumSource(OutputType.class)
     void testSubmitLaunchpadPipeline(OutputType format, MockServerClient mock) {