Merge pull request #894 from jmchilton/workflow_edit

Command to open workflow in a synchronized graphical editor.

Author: jmchilton

planemo/commands/cmd_shed_serve.py

@@ -1,13 +1,12 @@
 """Module describing the planemo ``shed_serve`` command."""
-import time
-
 import click
 
 from planemo import io
 from planemo import options
 from planemo import shed
 from planemo.cli import command_function
 from planemo.galaxy import shed_serve
+from planemo.galaxy.serve import sleep_for_serve
 
 
 @click.command("shed_serve")
@@ -33,6 +32,5 @@ def cli(ctx, paths, **kwds):
     """
     install_args_list = shed.install_arg_lists(ctx, paths, **kwds)
     with shed_serve(ctx, install_args_list, **kwds) as config:
-        gx_url = "http://localhost:%d/" % config.port
-        io.info("Galaxy running with tools installed at %s" % gx_url)
-        time.sleep(1000000)
+        io.info("Galaxy running with tools installed at %s" % config.galaxy_url)
+        sleep_for_serve()

planemo/commands/cmd_workflow_convert.py

@@ -45,7 +45,7 @@ def cli(ctx, workflow_path, output=None, force=False, **kwds):
 
     runnable = for_path(workflow_path)
     with engine_context(ctx, **kwds) as galaxy_engine:
-        with galaxy_engine.serve_runnables([runnable]) as config:
+        with galaxy_engine.ensure_runnables_served([runnable]) as config:
             workflow_id = config.workflow_id(workflow_path)
             output_dict = config.gi.workflows.export_workflow_dict(workflow_id)
 

planemo/commands/cmd_workflow_edit.py

@@ -0,0 +1,33 @@
+"""Module describing the planemo ``workflow_edit`` command."""
+import click
+
+from planemo import options
+from planemo.cli import command_function
+from planemo.engine import (
+    engine_context,
+    is_galaxy_engine,
+)
+from planemo.galaxy.serve import sleep_for_serve
+from planemo.runnable import (
+    for_path,
+)
+
+
+@click.command('workflow_edit')
+@options.required_workflow_arg()
+@options.galaxy_serve_options()
+@command_function
+def cli(ctx, workflow_path, output=None, force=False, **kwds):
+    """Open a synchronized Galaxy workflow editor.
+    """
+    assert is_galaxy_engine(**kwds)
+
+    kwds["workflows_from_path"] = True
+
+    runnable = for_path(workflow_path)
+    with engine_context(ctx, **kwds) as galaxy_engine:
+        with galaxy_engine.ensure_runnables_served([runnable]) as config:
+            workflow_id = config.workflow_id(workflow_path)
+            url = "%s/workflow/editor?id=%s" % (config.galaxy_url, workflow_id)
+            click.launch(url)
+            sleep_for_serve()

planemo/galaxy/config.py

@@ -752,9 +752,10 @@ def _install_workflow(self, runnable):
         if self._kwds["shed_install"]:
             install_shed_repos(runnable, self.gi, self._kwds.get("ignore_dependency_problems", False))
 
+        default_from_path = self._kwds.get("workflows_from_path", False)
         # TODO: Allow serialization so this doesn't need to assume a
         # shared filesystem with Galaxy server.
-        from_path = runnable.type.name == "cwl_workflow"
+        from_path = default_from_path or (runnable.type.name == "cwl_workflow")
         workflow = import_workflow(
             runnable.path, admin_gi=self.gi, user_gi=self.user_gi, from_path=from_path
         )

planemo/galaxy/serve.py

@@ -3,6 +3,7 @@
 
 import contextlib
 import os
+import time
 
 from planemo import io
 from planemo import network_util
@@ -101,6 +102,11 @@ def serve_daemon(ctx, runnables=[], **kwds):
                 config.cleanup()
 
 
+def sleep_for_serve():
+    # This is bad, do something better...
+    time.sleep(1000000)
+
+
 __all__ = (
     "serve",
     "serve_daemon",

planemo/galaxy/workflows.py

@@ -61,6 +61,7 @@ def import_workflow(path, admin_gi, user_gi, from_path=False):
         return importer.import_workflow(workflow)
     else:
         # TODO: Update bioblend to allow from_path.
+        path = os.path.abspath(path)
         payload = dict(
             from_path=path
         )