Merge branch 'master' into 285-overwrite-when-importing-pipelines-and…

…-ces

.github/workflows/build.yml

@@ -118,6 +118,33 @@ jobs:
           GITHUB_USERNAME: ${{ github.actor }}
           GITHUB_TOKEN: ${{ secrets.GH_SEQERA_TOKEN }}
           PLATFORM: osx-x86_64
+      - name: Codesign binary
+        if: "contains(github.event.head_commit.message, '[release]') && github.event.ref=='refs/heads/master'"
+        env:
+          MACOS_CERTIFICATE: ${{ secrets.MACOS_CERTIFICATE }}
+          MACOS_CERTIFICATE_PWD: ${{ secrets.MACOS_CERTIFICATE_PWD }}
+          MACOS_CERTIFICATE_NAME: ${{ secrets.MACOS_CERTIFICATE_NAME }}
+          MACOS_CI_KEYCHAIN_PWD: ${{ secrets.MACOS_CI_KEYCHAIN_PWD }}
+        run: |
+          echo $MACOS_CERTIFICATE | base64 --decode > certificate.p12
+          security create-keychain -p "$MACOS_CI_KEYCHAIN_PWD" build.keychain
+          security default-keychain -s build.keychain
+          security unlock-keychain -p "$MACOS_CI_KEYCHAIN_PWD" build.keychain
+          security import certificate.p12 -k build.keychain -P "$MACOS_CERTIFICATE_PWD" -T /usr/bin/codesign
+          security set-key-partition-list -S apple-tool:,apple:,codesign: -s -k "$MACOS_CI_KEYCHAIN_PWD" build.keychain
+          /usr/bin/codesign --force -s "$MACOS_CERTIFICATE_NAME" --options runtime build/native/nativeCompile/tw -v
+
+      - name: Notarize binary
+        if: "contains(github.event.head_commit.message, '[release]') && github.event.ref=='refs/heads/master'"
+        env:
+          MACOS_AC_API_CERT: ${{ secrets.MACOS_AC_API_CERT }}
+          MACOS_AC_API_ISSUER_ID: ${{ secrets.MACOS_AC_API_ISSUER_ID }}
+          MACOS_AC_API_KEY_ID: ${{ secrets.MACOS_AC_API_KEY_ID }}
+        run: |
+          echo $MACOS_AC_API_CERT | base64 --decode > AuthKey.p8
+          xcrun notarytool store-credentials "notarytool-profile" -k AuthKey.p8 -d "$MACOS_AC_API_KEY_ID" -i "$MACOS_AC_API_ISSUER_ID"
+          ditto -c -k --keepParent "build/native/nativeCompile/tw" "notarization.zip"
+          xcrun notarytool submit "notarization.zip" --keychain-profile "notarytool-profile" --wait
 
       - name: Upload Mac native image artifact
         uses: actions/upload-artifact@v2

conf/reflect-config.json

@@ -1666,6 +1666,12 @@
   "queryAllDeclaredMethods":true,
   "queryAllDeclaredConstructors":true
 },
+{
+  "name":"io.seqera.tower.cli.responses.computeenvs.ComputeEnvUpdated",
+  "allDeclaredFields":true,
+  "queryAllDeclaredMethods":true,
+  "queryAllDeclaredConstructors":true
+},
 {
   "name":"io.seqera.tower.cli.responses.computeenvs.ComputeEnvExport",
   "allDeclaredFields":true,
@@ -2131,7 +2137,8 @@
   "name":"io.seqera.tower.model.AwsBatchConfig",
   "allDeclaredFields":true,
   "allDeclaredMethods":true,
-  "allDeclaredConstructors":true
+  "allDeclaredConstructors":true,
+  "methods":[{"name":"<init>","parameterTypes":[] }, {"name":"getCliPath","parameterTypes":[] }, {"name":"getComputeJobRole","parameterTypes":[] }, {"name":"getComputeQueue","parameterTypes":[] }, {"name":"getDiscriminator","parameterTypes":[] }, {"name":"getDragenQueue","parameterTypes":[] }, {"name":"getEnvironment","parameterTypes":[] }, {"name":"getExecutionRole","parameterTypes":[] }, {"name":"getForge","parameterTypes":[] }, {"name":"getForgedResources","parameterTypes":[] }, {"name":"getFusion2Enabled","parameterTypes":[] }, {"name":"getHeadJobCpus","parameterTypes":[] }, {"name":"getHeadJobMemoryMb","parameterTypes":[] }, {"name":"getHeadJobRole","parameterTypes":[] }, {"name":"getHeadQueue","parameterTypes":[] }, {"name":"getLogGroup","parameterTypes":[] }, {"name":"getNvnmeStorageEnabled","parameterTypes":[] }, {"name":"getPostRunScript","parameterTypes":[] }, {"name":"getPreRunScript","parameterTypes":[] }, {"name":"getRegion","parameterTypes":[] }, {"name":"getVolumes","parameterTypes":[] }, {"name":"getWaveEnabled","parameterTypes":[] }, {"name":"getWorkDir","parameterTypes":[] }, {"name":"setCliPath","parameterTypes":["java.lang.String"] }, {"name":"setComputeJobRole","parameterTypes":["java.lang.String"] }, {"name":"setComputeQueue","parameterTypes":["java.lang.String"] }, {"name":"setDragenQueue","parameterTypes":["java.lang.String"] }, {"name":"setEnvironment","parameterTypes":["java.util.List"] }, {"name":"setExecutionRole","parameterTypes":["java.lang.String"] }, {"name":"setForge","parameterTypes":["io.seqera.tower.model.ForgeConfig"] }, {"name":"setForgedResources","parameterTypes":["java.util.List"] }, {"name":"setFusion2Enabled","parameterTypes":["java.lang.Boolean"] }, {"name":"setHeadJobCpus","parameterTypes":["java.lang.Integer"] }, {"name":"setHeadJobMemoryMb","parameterTypes":["java.lang.Integer"] }, {"name":"setHeadJobRole","parameterTypes":["java.lang.String"] }, {"name":"setHeadQueue","parameterTypes":["java.lang.String"] }, {"name":"setLogGroup","parameterTypes":["java.lang.String"] }, {"name":"setNvnmeStorageEnabled","parameterTypes":["java.lang.Boolean"] }, {"name":"setPostRunScript","parameterTypes":["java.lang.String"] }, {"name":"setPreRunScript","parameterTypes":["java.lang.String"] }, {"name":"setRegion","parameterTypes":["java.lang.String"] }, {"name":"setVolumes","parameterTypes":["java.util.List"] }, {"name":"setWaveEnabled","parameterTypes":["java.lang.Boolean"] }, {"name":"setWorkDir","parameterTypes":["java.lang.String"] }]
 },
 {
   "name":"io.seqera.tower.model.AwsSecurityKeys",
@@ -2212,7 +2219,8 @@
 {
   "name":"io.seqera.tower.model.ComputeEnvStatus",
   "allDeclaredFields":true,
-  "allDeclaredMethods":true
+  "allDeclaredMethods":true,
+  "methods":[{"name":"fromValue","parameterTypes":["java.lang.String"] }]
 },
 {
   "name":"io.seqera.tower.model.ComputePlatformDto",
@@ -2400,7 +2408,8 @@
   "name":"io.seqera.tower.model.DescribeComputeEnvResponse",
   "allDeclaredFields":true,
   "allDeclaredMethods":true,
-  "allDeclaredConstructors":true
+  "allDeclaredConstructors":true,
+  "methods":[{"name":"<init>","parameterTypes":[] }, {"name":"setComputeEnv","parameterTypes":["io.seqera.tower.model.ComputeEnvResponseDto"] }]
 },
 {
   "name":"io.seqera.tower.model.DescribeCredentialsResponse",
@@ -2800,11 +2809,6 @@
   "allDeclaredMethods":true,
   "allDeclaredConstructors":true
 },
-{
-  "name":"io.seqera.tower.model.PipelineOptimizationStatus",
-  "allDeclaredFields":true,
-  "queryAllDeclaredMethods":true
-},
 {
   "name":"io.seqera.tower.model.PipelineSecret",
   "allDeclaredFields":true,
@@ -2913,6 +2917,13 @@
   "allDeclaredMethods":true,
   "allDeclaredConstructors":true
 },
+{
+  "name":"io.seqera.tower.model.UpdateComputeEnvRequest",
+  "allDeclaredFields":true,
+  "queryAllDeclaredMethods":true,
+  "queryAllDeclaredConstructors":true,
+  "methods":[{"name":"getName","parameterTypes":[] }]
+},
 {
   "name":"io.seqera.tower.model.UpdateCredentialsRequest",
   "allDeclaredFields":true,

conf/resource-config.json

@@ -8,15 +8,21 @@
     "pattern":"\\QMETA-INF/services/org.glassfish.jersey.internal.inject.InjectionManagerFactory\\E"
   }, {
     "pattern":"\\QMETA-INF/services/org.glassfish.jersey.internal.spi.AutoDiscoverable\\E"
+  }, {
+    "pattern":"java.base:\\Qjdk/internal/icu/impl/data/icudt67b/nfkc.nrm\\E"
+  }, {
+    "pattern":"java.base:\\Qjdk/internal/icu/impl/data/icudt67b/uprops.icu\\E"
+  }, {
+    "pattern":"java.base:\\Qsun/net/idn/uidna.spp\\E"
   }, {
     "pattern":"java.base:\\Qsun/text/resources/LineBreakIteratorData\\E"
   }]},
   "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"
   }]

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

@@ -17,6 +17,7 @@
 import io.seqera.tower.cli.commands.computeenvs.ImportCmd;
 import io.seqera.tower.cli.commands.computeenvs.ListCmd;
 import io.seqera.tower.cli.commands.computeenvs.PrimaryCmd;
+import io.seqera.tower.cli.commands.computeenvs.UpdateCmd;
 import io.seqera.tower.cli.commands.computeenvs.ViewCmd;
 import picocli.CommandLine.Command;
 
@@ -26,6 +27,7 @@
         description = "Manage workspace compute environments.",
         subcommands = {
                 AddCmd.class,
+                UpdateCmd.class,
                 DeleteCmd.class,
                 ViewCmd.class,
                 ListCmd.class,

src/main/java/io/seqera/tower/cli/commands/actions/UpdateCmd.java

@@ -14,6 +14,7 @@
 import io.seqera.tower.ApiException;
 import io.seqera.tower.cli.commands.global.WorkspaceOptionalOptions;
 import io.seqera.tower.cli.commands.pipelines.LaunchOptions;
+import io.seqera.tower.cli.exceptions.InvalidResponseException;
 import io.seqera.tower.cli.exceptions.TowerException;
 import io.seqera.tower.cli.responses.Response;
 import io.seqera.tower.cli.responses.actions.ActionUpdate;
@@ -38,6 +39,9 @@ public class UpdateCmd extends AbstractActionsCmd {
     @CommandLine.Option(names = {"-s", "--status"}, description = "Action status (pause or active).")
     public String status;
 
+    @CommandLine.Option(names = {"--new-name"}, description = "Action new name.")
+    public String newName;
+
     @CommandLine.Mixin
     public WorkspaceOptionalOptions workspace;
 
@@ -50,6 +54,15 @@ protected Response exec() throws ApiException, IOException {
         ActionResponseDto action = fetchDescribeActionResponse(actionRefOptions, wspId).getAction();
         String actionName = action.getName();
 
+        // Validate new action name if any
+        if (newName != null) {
+            try {
+                api().validateActionName(wspId, newName);
+            } catch (ApiException ex) {
+                throw new InvalidResponseException(String.format("Action name '%s' is not valid", newName));
+            }
+        }
+
         // Retrieve the provided computeEnv or use the primary if not provided
         String ceId = opts.computeEnv != null ? computeEnvByRef(wspId, opts.computeEnv).getId() : action.getLaunch().getComputeEnv().getId();
 
@@ -78,6 +91,7 @@ protected Response exec() throws ApiException, IOException {
                 .entryName(opts.entryName);
 
         UpdateActionRequest request = new UpdateActionRequest();
+        request.setName(newName != null ? newName : actionName);
         request.setLaunch(workflowLaunchRequest);
 
         try {

src/main/java/io/seqera/tower/cli/commands/collaborators/ListCmd.java

@@ -15,6 +15,7 @@
 import io.seqera.tower.cli.commands.global.PaginationOptions;
 import io.seqera.tower.cli.responses.Response;
 import io.seqera.tower.cli.responses.collaborators.CollaboratorsList;
+import io.seqera.tower.cli.utils.PaginationInfo;
 import io.seqera.tower.model.ListMembersResponse;
 import io.seqera.tower.model.OrgAndWorkspaceDbDto;
 import picocli.CommandLine;
@@ -45,6 +46,6 @@ protected Response exec() throws ApiException, IOException {
 
         ListMembersResponse response = api().listOrganizationCollaborators(orgAndWorkspaceDbDto.getOrgId(), max, offset, startsWith);
 
-        return new CollaboratorsList(orgAndWorkspaceDbDto.getOrgId(), response.getMembers());
+        return new CollaboratorsList(orgAndWorkspaceDbDto.getOrgId(), response.getMembers(), PaginationInfo.from(paginationOptions, response.getTotalSize()));
     }
 }

src/main/java/io/seqera/tower/cli/commands/computeenvs/UpdateCmd.java

@@ -0,0 +1,83 @@
+/*
+ * 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.computeenvs;
+
+import io.seqera.tower.ApiException;
+import io.seqera.tower.cli.commands.global.WorkspaceOptionalOptions;
+import io.seqera.tower.cli.exceptions.ComputeEnvNotFoundException;
+import io.seqera.tower.cli.exceptions.InvalidResponseException;
+import io.seqera.tower.cli.responses.Response;
+import io.seqera.tower.cli.responses.computeenvs.ComputeEnvUpdated;
+import io.seqera.tower.model.ComputeEnvResponseDto;
+import io.seqera.tower.model.UpdateComputeEnvRequest;
+import picocli.CommandLine.Command;
+import picocli.CommandLine.Mixin;
+import picocli.CommandLine.Option;
+
+import java.io.IOException;
+
+@Command(
+        name = "update",
+        description = "Update compute environments."
+)
+public class UpdateCmd extends AbstractComputeEnvCmd {
+
+    @Mixin
+    public ComputeEnvRefOptions computeEnvRefOptions;
+
+    @Mixin
+    public WorkspaceOptionalOptions workspace;
+
+    @Option(names = {"--new-name"}, description = "Compute environment new name.")
+    public String newName;
+
+    @Override
+    protected Response exec() throws ApiException, IOException {
+        Long wspId = workspaceId(workspace.workspace);
+
+        if (newName != null) {
+            try {
+                api().validateComputeEnvName(wspId, newName);
+            } catch (ApiException ex) {
+                throw new InvalidResponseException(String.format("Compute environment name '%s' is not valid", newName));
+            }
+        }
+        ComputeEnvResponseDto ce = describeCE(computeEnvRefOptions, wspId);
+
+
+        UpdateComputeEnvRequest req = new UpdateComputeEnvRequest()
+                .name(newName != null ? newName : ce.getName());
+
+        api().updateComputeEnv(ce.getId(), req, wspId);
+
+
+        return new ComputeEnvUpdated(workspaceRef(wspId), ce.getName());
+
+    }
+
+    private ComputeEnvResponseDto describeCE(ComputeEnvRefOptions computeEnvRefOptions, Long wspId) throws ComputeEnvNotFoundException, ApiException {
+        try {
+            return fetchComputeEnv(computeEnvRefOptions, wspId);
+
+        } catch (ApiException e) {
+            if (e.getCode() == 403) {
+                String ref = computeEnvRefOptions.computeEnv.computeEnvId != null
+                        ? computeEnvRefOptions.computeEnv.computeEnvId
+                        : computeEnvRefOptions.computeEnv.computeEnvName;
+                // Customize the forbidden message
+                throw new ComputeEnvNotFoundException(ref, workspaceRef(wspId));
+            }
+
+            throw e;
+        }
+    }
+}

src/main/java/io/seqera/tower/cli/commands/labels/ListLabelsCmd.java

@@ -16,6 +16,7 @@
 import io.seqera.tower.cli.commands.global.WorkspaceOptionalOptions;
 import io.seqera.tower.cli.responses.Response;
 import io.seqera.tower.cli.responses.labels.ListLabelsCmdResponse;
+import io.seqera.tower.cli.utils.PaginationInfo;
 import io.seqera.tower.model.LabelType;
 import io.seqera.tower.model.ListLabelsResponse;
 import picocli.CommandLine;
@@ -53,6 +54,6 @@ protected Response exec() throws ApiException, IOException {
 
         ListLabelsResponse res = api().listLabels(wspId, max, offset, filter == null ? "" : filter, labelType, null);
 
-        return new ListLabelsCmdResponse(wspId, labelType, res.getLabels());
+        return new ListLabelsCmdResponse(wspId, labelType, res.getLabels(), PaginationInfo.from(paginationOptions, res.getTotalSize()));
     }
 }

src/main/java/io/seqera/tower/cli/commands/organizations/UpdateCmd.java

@@ -30,6 +30,9 @@ public class UpdateCmd extends AbstractOrganizationsCmd {
     @CommandLine.Mixin
     OrganizationRefOptions organizationRefOptions;
 
+    @CommandLine.Option(names = {"--new-name"}, description = "Organization new name.")
+    public String newName;
+
     @CommandLine.Option(names = {"-f", "--full-name"}, description = "Organization full name.")
     public String fullName;
 
@@ -43,6 +46,7 @@ protected Response exec() throws ApiException, IOException {
         OrganizationDbDto organization = response.getOrganization();
 
         UpdateOrganizationRequest request = new UpdateOrganizationRequest();
+        request.setName(newName != null ? newName : organization.getName());
         request.setFullName(fullName != null ? fullName : organization.getFullName());
         request.setDescription(opts.description != null ? opts.description : organization.getDescription());
         request.setLocation(opts.location != null ? opts.location : organization.getLocation());

src/main/java/io/seqera/tower/cli/commands/participants/ListCmd.java

@@ -16,6 +16,7 @@
 import io.seqera.tower.cli.commands.global.WorkspaceRequiredOptions;
 import io.seqera.tower.cli.responses.Response;
 import io.seqera.tower.cli.responses.participants.ParticipantsList;
+import io.seqera.tower.cli.utils.PaginationInfo;
 import io.seqera.tower.model.ParticipantDbDto;
 import io.seqera.tower.model.ParticipantType;
 import picocli.CommandLine;
@@ -55,6 +56,6 @@ protected Response exec() throws ApiException, IOException {
             response = response.stream().filter(it -> it.getType() == type).collect(Collectors.toList());
         }
 
-        return new ParticipantsList(orgName(wspId), workspaceName(wspId), response);
+        return new ParticipantsList(orgName(wspId), workspaceName(wspId), response, PaginationInfo.from(paginationOptions));
     }
 }

src/main/java/io/seqera/tower/cli/commands/pipelines/ListCmd.java

@@ -18,13 +18,13 @@
 import io.seqera.tower.cli.exceptions.WorkspaceNotFoundException;
 import io.seqera.tower.cli.responses.Response;
 import io.seqera.tower.cli.responses.pipelines.PipelinesList;
+import io.seqera.tower.cli.utils.PaginationInfo;
 import io.seqera.tower.model.ListPipelinesResponse;
 import io.seqera.tower.model.PipelineQueryAttribute;
 import picocli.CommandLine;
 import picocli.CommandLine.Command;
 
 import java.io.IOException;
-import java.util.Collections;
 import java.util.List;
 
 @Command(
@@ -68,6 +68,6 @@ protected Response exec() throws ApiException, IOException {
             }
         }
 
-        return new PipelinesList(workspaceRef(wspId), response.getPipelines(), baseWorkspaceUrl(wspId), showLabelsOption.showLabels);
+        return new PipelinesList(workspaceRef(wspId), response.getPipelines(), baseWorkspaceUrl(wspId), showLabelsOption.showLabels, PaginationInfo.from(paginationOptions, response.getTotalSize()));
     }
 }