feat: add the lineage commands and studio logs

USAGE.md

@@ -754,6 +754,16 @@ tw managed-identities add -o my-org -n hpc1 -p slurm -H login.hpc.example.com
 tw managed-identities credentials -o my-org -n hpc1 add -l my_linux_user -k ~/.ssh/id_rsa
 ```
 
+## Lineage
+
+Run `tw lineage -h` to view the supported operations: `resolve`, `view`, `search`, `upstream`, and `downstream`. Lineage must be enabled for the workspace.
+
+```bash
+tw lineage resolve -w my-org/my-workspace --file-path s3://bucket/results/out.bam
+tw lineage resolve -w my-org/my-workspace --session-id <session-id> --run-name <run-name>
+tw lineage upstream -w my-org/my-workspace -i <lid>
+```
+
 ## Other additions
 
 - `tw compute-envs enable|disable`: enable or disable a compute environment.
@@ -765,7 +775,7 @@ tw managed-identities credentials -o my-org -n hpc1 add -l my_linux_user -k ~/.s
 - `tw launch`, `tw pipelines add|update`, `tw runs relaunch`, and `tw actions add|update`: `--tower-config`. List the Nextflow and Fusion versions you can launch with `tw info versions` (`-c fusion` for Fusion).
 - `tw runs star|unstar`, `tw runs view log [--next <cursor>]`, and `tw runs delete -i <id>,<id>`.
 - `tw pipelines schema`: show a pipeline's parameter schema.
-- `tw studios star|unstar|extend|rename-checkpoint`. `--mount-data-uris` also accepts a folder inside a data link.
+- `tw studios star|unstar|extend|logs|rename-checkpoint`. `--mount-data-uris` also accepts a folder inside a data link.
 - `tw data-links delete-content|download-script`.
 - `tw datasets add --url`, `tw datasets update --url`, and `tw datasets disable-version`.
 

conf/reflect-config.json

@@ -214,6 +214,12 @@
   "allDeclaredMethods":true,
   "methods":[{"name":"<init>","parameterTypes":[] }]
 },
+{
+  "name":"io.seqera.tower.cli.commands.LineageCmd",
+  "queryAllDeclaredMethods":true,
+  "queryAllDeclaredConstructors":true,
+  "methods":[{"name":"<init>","parameterTypes":[] }]
+},
 {
   "name":"io.seqera.tower.cli.commands.ManagedIdentitiesCmd",
   "queryAllDeclaredMethods":true,
@@ -1503,6 +1509,71 @@
   "queryAllDeclaredMethods":true,
   "methods":[{"name":"<init>","parameterTypes":[] }]
 },
+{
+  "name":"io.seqera.tower.cli.commands.lineage.AbstractLineageCmd",
+  "queryAllDeclaredMethods":true,
+  "queryAllDeclaredConstructors":true
+},
+{
+  "name":"io.seqera.tower.cli.commands.lineage.AbstractNavigateCmd",
+  "queryAllDeclaredMethods":true,
+  "queryAllDeclaredConstructors":true,
+  "fields":[{"name":"lidOptions"}, {"name":"type"}, {"name":"workspace"}]
+},
+{
+  "name":"io.seqera.tower.cli.commands.lineage.DownstreamCmd",
+  "queryAllDeclaredMethods":true,
+  "queryAllDeclaredConstructors":true,
+  "methods":[{"name":"<init>","parameterTypes":[] }]
+},
+{
+  "name":"io.seqera.tower.cli.commands.lineage.LidOptions",
+  "queryAllDeclaredMethods":true,
+  "queryAllDeclaredConstructors":true,
+  "fields":[{"name":"lid"}],
+  "methods":[{"name":"<init>","parameterTypes":[] }]
+},
+{
+  "name":"io.seqera.tower.cli.commands.lineage.ResolveCmd",
+  "queryAllDeclaredMethods":true,
+  "queryAllDeclaredConstructors":true,
+  "fields":[{"name":"source"}, {"name":"workspace"}],
+  "methods":[{"name":"<init>","parameterTypes":[] }]
+},
+{
+  "name":"io.seqera.tower.cli.commands.lineage.ResolveCmd$Run",
+  "queryAllDeclaredMethods":true,
+  "queryAllDeclaredConstructors":true,
+  "fields":[{"name":"runName"}, {"name":"sessionId"}],
+  "methods":[{"name":"<init>","parameterTypes":[] }]
+},
+{
+  "name":"io.seqera.tower.cli.commands.lineage.ResolveCmd$Source",
+  "queryAllDeclaredMethods":true,
+  "queryAllDeclaredConstructors":true,
+  "fields":[{"name":"filePath"}, {"name":"run"}],
+  "methods":[{"name":"<init>","parameterTypes":[] }]
+},
+{
+  "name":"io.seqera.tower.cli.commands.lineage.SearchCmd",
+  "queryAllDeclaredMethods":true,
+  "queryAllDeclaredConstructors":true,
+  "fields":[{"name":"max"}, {"name":"pageToken"}, {"name":"query"}],
+  "methods":[{"name":"<init>","parameterTypes":[] }]
+},
+{
+  "name":"io.seqera.tower.cli.commands.lineage.UpstreamCmd",
+  "queryAllDeclaredMethods":true,
+  "queryAllDeclaredConstructors":true,
+  "methods":[{"name":"<init>","parameterTypes":[] }]
+},
+{
+  "name":"io.seqera.tower.cli.commands.lineage.ViewCmd",
+  "queryAllDeclaredMethods":true,
+  "queryAllDeclaredConstructors":true,
+  "fields":[{"name":"lidOptions"}, {"name":"summary"}, {"name":"workspace"}],
+  "methods":[{"name":"<init>","parameterTypes":[] }]
+},
 {
   "name":"io.seqera.tower.cli.commands.managedidentities.AbstractManagedIdentitiesCmd",
   "queryAllDeclaredMethods":true,
@@ -2171,6 +2242,13 @@
   "queryAllDeclaredMethods":true,
   "methods":[{"name":"<init>","parameterTypes":[] }]
 },
+{
+  "name":"io.seqera.tower.cli.commands.studios.LogsCmd",
+  "queryAllDeclaredMethods":true,
+  "queryAllDeclaredConstructors":true,
+  "fields":[{"name":"maxLength"}, {"name":"next"}, {"name":"studioRefOptions"}, {"name":"workspace"}],
+  "methods":[{"name":"<init>","parameterTypes":[] }]
+},
 {
   "name":"io.seqera.tower.cli.commands.studios.ParentStudioRefOptions",
   "allDeclaredFields":true,
@@ -2776,6 +2854,24 @@
   "queryAllDeclaredMethods":true,
   "queryAllDeclaredConstructors":true
 },
+{
+  "name":"io.seqera.tower.cli.responses.lineage.LineageRecordView",
+  "allDeclaredFields":true,
+  "queryAllDeclaredMethods":true,
+  "queryAllDeclaredConstructors":true
+},
+{
+  "name":"io.seqera.tower.cli.responses.lineage.LineageRecordsList",
+  "allDeclaredFields":true,
+  "queryAllDeclaredMethods":true,
+  "queryAllDeclaredConstructors":true
+},
+{
+  "name":"io.seqera.tower.cli.responses.lineage.LineageResolved",
+  "allDeclaredFields":true,
+  "queryAllDeclaredMethods":true,
+  "queryAllDeclaredConstructors":true
+},
 {
   "name":"io.seqera.tower.cli.responses.managedidentities.ManagedCredentialsAdded",
   "allDeclaredFields":true,
@@ -3210,6 +3306,12 @@
   "queryAllDeclaredMethods":true,
   "queryAllDeclaredConstructors":true
 },
+{
+  "name":"io.seqera.tower.cli.responses.studios.StudioLog",
+  "allDeclaredFields":true,
+  "queryAllDeclaredMethods":true,
+  "queryAllDeclaredConstructors":true
+},
 {
   "name":"io.seqera.tower.cli.responses.studios.StudioStarred",
   "allDeclaredFields":true,

src/main/java/io/seqera/tower/cli/Tower.java

@@ -31,6 +31,7 @@
 import io.seqera.tower.cli.commands.DatasetsCmd;
 import io.seqera.tower.cli.commands.InfoCmd;
 import io.seqera.tower.cli.commands.LaunchCmd;
+import io.seqera.tower.cli.commands.LineageCmd;
 import io.seqera.tower.cli.commands.ManagedIdentitiesCmd;
 import io.seqera.tower.cli.commands.MembersCmd;
 import io.seqera.tower.cli.commands.OrganizationsCmd;
@@ -72,6 +73,7 @@
                 InfoCmd.class,
                 LabelsCmd.class,
                 LaunchCmd.class,
+                LineageCmd.class,
                 ManagedIdentitiesCmd.class,
                 MembersCmd.class,
                 OrganizationsCmd.class,

src/main/java/io/seqera/tower/cli/commands/AbstractApiCmd.java

@@ -31,6 +31,7 @@
 import io.seqera.tower.api.IdentitiesApi;
 import io.seqera.tower.api.LabelsApi;
 import io.seqera.tower.api.LaunchApi;
+import io.seqera.tower.api.LineageApi;
 import io.seqera.tower.api.NextflowApi;
 import io.seqera.tower.api.OrgsApi;
 import io.seqera.tower.api.PipelineSchemasApi;
@@ -253,6 +254,10 @@ protected LaunchApi launchApi() throws ApiException {
         return launchApi == null ? new LaunchApi(apiClient()) : launchApi;
     }
 
+    protected LineageApi lineageApi() throws ApiException {
+        return new LineageApi(apiClient());
+    }
+
     protected NextflowApi nextflowApi() throws ApiException {
         return nextflowApi == null ? new NextflowApi(apiClient()) : nextflowApi;
     }

src/main/java/io/seqera/tower/cli/commands/LineageCmd.java

@@ -0,0 +1,39 @@
+/*
+ * Copyright 2021-2026, Seqera.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+package io.seqera.tower.cli.commands;
+
+import io.seqera.tower.cli.commands.lineage.DownstreamCmd;
+import io.seqera.tower.cli.commands.lineage.ResolveCmd;
+import io.seqera.tower.cli.commands.lineage.SearchCmd;
+import io.seqera.tower.cli.commands.lineage.UpstreamCmd;
+import io.seqera.tower.cli.commands.lineage.ViewCmd;
+import picocli.CommandLine.Command;
+
+@Command(
+        name = "lineage",
+        description = "Explore data lineage records. Lineage must be enabled for the workspace.",
+        subcommands = {
+                ResolveCmd.class,
+                ViewCmd.class,
+                SearchCmd.class,
+                UpstreamCmd.class,
+                DownstreamCmd.class,
+        }
+)
+public class LineageCmd extends AbstractRootCmd {
+}

src/main/java/io/seqera/tower/cli/commands/StudiosCmd.java

@@ -20,6 +20,7 @@
 import io.seqera.tower.cli.commands.studios.CheckpointsCmd;
 import io.seqera.tower.cli.commands.studios.DeleteCmd;
 import io.seqera.tower.cli.commands.studios.ExtendCmd;
+import io.seqera.tower.cli.commands.studios.LogsCmd;
 import io.seqera.tower.cli.commands.studios.RenameCheckpointCmd;
 import io.seqera.tower.cli.commands.studios.StarCmd;
 import io.seqera.tower.cli.commands.studios.UnstarCmd;
@@ -50,6 +51,7 @@
                 StarCmd.class,
                 UnstarCmd.class,
                 ExtendCmd.class,
+                LogsCmd.class,
         }
 )
 public class StudiosCmd extends AbstractRootCmd {

src/main/java/io/seqera/tower/cli/commands/lineage/AbstractLineageCmd.java

@@ -0,0 +1,36 @@
+/*
+ * Copyright 2021-2026, Seqera.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+package io.seqera.tower.cli.commands.lineage;
+
+import io.seqera.tower.cli.commands.AbstractApiCmd;
+import picocli.CommandLine.Command;
+
+import java.net.URLEncoder;
+import java.nio.charset.StandardCharsets;
+
+@Command
+public abstract class AbstractLineageCmd extends AbstractApiCmd {
+
+    /**
+     * The SDK encodes the LID path segment once, and the API decodes it twice: proxies normalize an
+     * encoded '/' or ':' in paths, so the web UI double-encodes LIDs. Encode once more here to match.
+     */
+    protected static String lidPathSegment(String lid) {
+        return URLEncoder.encode(lid, StandardCharsets.UTF_8);
+    }
+}

src/main/java/io/seqera/tower/cli/commands/lineage/AbstractNavigateCmd.java

@@ -0,0 +1,53 @@
+/*
+ * Copyright 2021-2026, Seqera.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+package io.seqera.tower.cli.commands.lineage;
+
+import io.seqera.tower.ApiException;
+import io.seqera.tower.cli.commands.global.WorkspaceRequiredOptions;
+import io.seqera.tower.cli.responses.Response;
+import io.seqera.tower.cli.responses.lineage.LineageRecordsList;
+import io.seqera.tower.model.SearchResult;
+import picocli.CommandLine.Command;
+import picocli.CommandLine.Mixin;
+import picocli.CommandLine.Option;
+
+@Command
+public abstract class AbstractNavigateCmd extends AbstractLineageCmd {
+
+    public enum RecordType {FileOutput, TaskRun}
+
+    @Mixin
+    public WorkspaceRequiredOptions workspace;
+
+    @Mixin
+    public LidOptions lidOptions;
+
+    @Option(names = {"-t", "--type"}, description = "Show only records of this type (${COMPLETION-CANDIDATES})")
+    public RecordType type;
+
+    protected abstract String direction();
+
+    protected abstract SearchResult navigate(String lid, Long wspId, String type) throws ApiException;
+
+    @Override
+    protected Response exec() throws ApiException {
+        Long wspId = workspaceId(workspace.workspace);
+        SearchResult result = navigate(lidPathSegment(lidOptions.lid), wspId, type == null ? null : type.name());
+        return new LineageRecordsList(String.format("Lineage records %s of '%s'", direction(), lidOptions.lid), result.getRecords(), result.getNextPageToken());
+    }
+}

src/main/java/io/seqera/tower/cli/commands/lineage/DownstreamCmd.java

@@ -0,0 +1,39 @@
+/*
+ * Copyright 2021-2026, Seqera.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+
+package io.seqera.tower.cli.commands.lineage;
+
+import io.seqera.tower.ApiException;
+import io.seqera.tower.model.SearchResult;
+import picocli.CommandLine.Command;
+
+@Command(
+        name = "downstream",
+        description = "List the records one hop downstream of a task or file record. By default, the tasks that consumed a file, or the output files of a task."
+)
+public class DownstreamCmd extends AbstractNavigateCmd {
+
+    @Override
+    protected String direction() {
+        return "downstream";
+    }
+
+    @Override
+    protected SearchResult navigate(String lid, Long wspId, String type) throws ApiException {
+        return lineageApi().navigateLineageDownstream(lid, wspId, type);
+    }
+}