Merge pull request #1295 from mvdbeek/dockstore_fixes

Control publish setting in .dockstore.yml, fix first release not appearing on dockstore

planemo/commands/cmd_dockstore_init.py

@@ -13,6 +13,7 @@
 
 @click.command("dockstore_init")
 @options.optional_project_arg()
+@options.publish_dockstore_option()
 @command_function
 def cli(ctx, path=".", **kwds):
     """Initialize a .dockstore.yml configuration file for workflows in directory.
@@ -27,6 +28,6 @@ def cli(ctx, path=".", **kwds):
     """
     # TODO: implement -f semantics
     dockstore_path = os.path.join(path, DOCKSTORE_REGISTRY_CONF)
-    contents = generate_dockstore_yaml(path)
+    contents = generate_dockstore_yaml(path, kwds["publish"])
     with open(dockstore_path, "w") as f:
         f.write(contents)

planemo/commands/cmd_workflow_test_init.py

@@ -28,7 +28,7 @@
 def cli(ctx, workflow_identifier, output=None, split_test=False, **kwds):
     """Initialize a Galaxy workflow test description for supplied workflow.
 
-    Be sure to your lint your workflow with ``workflow_lint`` before calling this
+    Be sure to lint your workflow with ``workflow_lint`` before calling this
     to ensure inputs and outputs comply with best practices that make workflow
     testing easier.
     """

planemo/github_util.py

@@ -5,6 +5,7 @@
 import stat
 import tarfile
 import tempfile
+import time
 from distutils.dir_util import copy_tree
 from pathlib import Path
 
@@ -29,6 +30,7 @@
 NO_GITHUB_DEP_ERROR = "Cannot use github functionality - " "PyGithub library not available."
 FAILED_TO_DOWNLOAD_GH = "No gh executable available and it could not be installed."
 DEFAULT_REMOTE_NAME = "planemo-remote"
+SLEEP_BEFORE_RELEASE = int(os.environ.get("PLANEMO_SLEEP_BEFORE_RELEASE", 60))
 
 
 def get_github_config(ctx, allow_anonymous=False):
@@ -183,6 +185,8 @@ def create_release(ctx, from_dir, target_dir, owner, repo, version, dry_run, bra
     ]
     cmd.extend(["--notes", notes or changelog_in_repo(target_repository_path)])
     if not dry_run:
+        # For new repositories dockstore needs a bit of time to register the new workflow.
+        time.sleep(SLEEP_BEFORE_RELEASE)
         communicate(cmd, env=gh_env)
     else:
         ctx.log("Would run command '{}'".format(" ".join(cmd)))

planemo/options.py

@@ -300,6 +300,15 @@ def run_download_outputs_option():
     )
 
 
+def publish_dockstore_option():
+    return planemo_option(
+        "--publish/--no_publish",
+        is_flag=True,
+        default=True,
+        help="Set publish attribute to true in .dockstore.yml file",
+    )
+
+
 def no_dependency_resolution():
     return planemo_option(
         "--no_dependency_resolution",

planemo/workflow_lint.py

@@ -53,13 +53,14 @@ class WorkflowLintContext(LintContext):
     training_topic = None
 
 
-def generate_dockstore_yaml(directory: str) -> str:
+def generate_dockstore_yaml(directory: str, publish: bool = True) -> str:
     workflows = []
     for workflow_path in find_workflow_descriptions(directory):
         test_parameter_path = f"{workflow_path.rsplit('.', 1)[0]}-tests.yml"
         workflow_entry: Dict[str, Any] = {
             # TODO: support CWL
             "subclass": "Galaxy",
+            "publish": publish,
             "name": "main",
             "primaryDescriptorPath": f"/{os.path.relpath(workflow_path, directory)}",
         }

tests/test_cmd_dockstore_init.py

@@ -1,5 +1,6 @@
 """Tests for the ``dockstore_init`` command."""
 import os
+from typing import Optional
 
 import yaml
 
@@ -8,14 +9,30 @@
 
 class CmdDockstoreInitTestCase(CliTestCase):
     def test_plain_init(self):
+        self.run_dockstore_init()
+
+    def test_init_publish_true(self):
+        self.run_dockstore_init(True)
+
+    def test_init_publish_false(self):
+        self.run_dockstore_init(False)
+
+    def run_dockstore_init(self, publish: Optional[bool] = None):
         with self._isolate_with_test_data("wf_repos/from_format2/0_basic_native") as f:
             init_cmd = ["dockstore_init"]
+            expect_published = True
+            if publish:
+                init_cmd.append("--publish")
+            elif publish is False:
+                expect_published = False
+                init_cmd.append("--no_publish")
             self._check_exit_code(init_cmd)
             assert os.path.exists(".dockstore.yml")
             with open(".dockstore.yml") as fh:
                 dockstore_config = yaml.safe_load(fh)
             assert str(dockstore_config["version"]) == "1.2"
             assert "workflows" in dockstore_config
             assert len(dockstore_config["workflows"]) == 1
+            assert dockstore_config["workflows"][0]["publish"] == expect_published
             workflow_lint_cmd = ["workflow_lint", "--fail_level", "error", f]
             self._check_exit_code(workflow_lint_cmd)