Merge pull request #213 from jmchilton/shed_install

Implement shed serve and test commands, other enhancements.

planemo/commands/cmd_lint.py

@@ -10,7 +10,7 @@
 
 
 @click.command('lint')
-@options.optional_tools_arg(-1)
+@options.optional_tools_arg(multiple=True)
 @options.report_level_option()
 @options.fail_level_option()
 @options.skip_option()

planemo/commands/cmd_serve.py

@@ -6,19 +6,10 @@
 
 
 @click.command('serve')
-@options.optional_tools_arg()
-@options.galaxy_root_option()
-@options.galaxy_port_option()
-@options.install_galaxy_option()
-@options.no_cache_galaxy_option()
-@options.no_cleanup_option()
-@options.test_data_option()
-@options.dependency_resolvers_option()
-@options.job_config_option()
-@options.tool_dependency_dir_option()
-@options.brew_dependency_resolution()
+@options.optional_tools_arg(multiple=True)
+@options.galaxy_serve_options()
 @pass_context
-def cli(ctx, path, **kwds):
+def cli(ctx, paths, **kwds):
     """Launch a Galaxy instance with the specified tool in the tool panel.
 
     The Galaxy tool panel will include just the referenced tool or tools (by
@@ -36,4 +27,4 @@ def cli(ctx, path, **kwds):
     proof yet so please careful and do not try this against production Galaxy
     instances.
     """
-    galaxy_serve.serve(ctx, path, **kwds)
+    galaxy_serve.serve(ctx, paths, **kwds)

planemo/commands/cmd_shed_create.py

@@ -11,17 +11,9 @@
 
 
 @click.command("shed_create")
-@options.shed_project_arg()
-@options.shed_owner_option()
-@options.shed_name_option()
-@options.shed_target_option()
-@options.shed_key_option()
-@options.shed_email_option()
-@options.shed_password_option()
-@options.recursive_shed_option()
-@options.shed_fail_fast_option()
+@options.shed_publish_options()
 @pass_context
-def cli(ctx, path, **kwds):
+def cli(ctx, paths, **kwds):
     """Create a repository in a Galaxy Tool Shed from a ``.shed.yml`` file.
     """
     tsi = shed.tool_shed_client(ctx, **kwds)
@@ -37,5 +29,5 @@ def create(realized_reposiotry):
         else:
             return 1
 
-    exit_code = shed.for_each_repository(ctx, create, path, **kwds)
+    exit_code = shed.for_each_repository(ctx, create, paths, **kwds)
     sys.exit(exit_code)

planemo/commands/cmd_shed_diff.py

@@ -10,11 +10,7 @@
 
 
 @click.command("shed_diff")
-@options.shed_project_arg()
-@options.shed_owner_option()
-@options.shed_name_option()
-@options.shed_target_option()
-@options.shed_fail_fast_option()
+@options.shed_read_options()
 @click.option(
     "-o", "--output",
     type=click.Path(file_okay=True, resolve_path=True),
@@ -34,9 +30,8 @@
     help="Do not attempt smart diff of XML to filter out attributes "
          "populated by the Tool Shed.",
 )
-@options.recursive_shed_option()
 @pass_context
-def cli(ctx, path, **kwds):
+def cli(ctx, paths, **kwds):
     """Produce diff between local repository and Tool Shed contents.
 
     By default, this will produce a diff between this repository and what
@@ -58,5 +53,5 @@ def cli(ctx, path, **kwds):
     def diff(realized_repository):
         return shed.diff_repo(ctx, realized_repository, **kwds)
 
-    exit_code = shed.for_each_repository(ctx, diff, path, **kwds)
+    exit_code = shed.for_each_repository(ctx, diff, paths, **kwds)
     sys.exit(exit_code)

planemo/commands/cmd_shed_download.py

@@ -16,7 +16,7 @@
 
 
 @click.command("shed_download")
-@options.shed_project_arg()
+@options.shed_read_options()
 @click.option(
     '--destination',
     default="shed_download.tar.gz",
@@ -28,13 +28,8 @@
          "created as shed_download_<name>.tar.gz by default for instance, "
          "simpler repositories will just be downloaded to the specified file."
 )
-@options.shed_owner_option()
-@options.shed_name_option()
-@options.shed_target_option()
-@options.recursive_shed_option()
-@options.shed_fail_fast_option()
 @pass_context
-def cli(ctx, path, **kwds):
+def cli(ctx, paths, **kwds):
     """Download a tool repository as a tarball from the tool shed and extract
     to the specified directory.
     """
@@ -43,5 +38,5 @@ def cli(ctx, path, **kwds):
     def download(realized_repository):
         return shed.download_tarball(ctx, tsi, realized_repository, **kwds)
 
-    exit_code = shed.for_each_repository(ctx, download, path, **kwds)
+    exit_code = shed.for_each_repository(ctx, download, paths, **kwds)
     sys.exit(exit_code)

planemo/commands/cmd_shed_init.py

@@ -37,8 +37,7 @@
     help='Specify repository category for .shed.yml (may specify multiple).',
     type=click.Choice(shed.CURRENT_CATEGORIES)
 )
-@options.shed_owner_option()
-@options.shed_name_option()
+@options.shed_repo_options()
 @options.force_option()
 @pass_context
 def cli(ctx, path, **kwds):

planemo/commands/cmd_shed_lint.py

@@ -8,7 +8,7 @@
 
 
 @click.command('shed_lint')
-@options.shed_project_arg()
+@options.shed_realization_options()
 @options.report_level_option()
 @options.fail_level_option()
 @options.click.option(
@@ -18,15 +18,13 @@
     help=("Lint tools discovered in the process of linting repositories.")
 )
 @options.lint_xsd_option()
-@options.recursive_shed_option()
-@options.shed_fail_fast_option()
 @pass_context
-def cli(ctx, path, **kwds):
+def cli(ctx, paths, **kwds):
     """Check a Tool Shed repository for common problems.
     """
     def lint(realized_repository):
         return shed_lint.lint_repository(ctx, realized_repository, **kwds)
 
     kwds["fail_on_missing"] = False
-    exit_code = shed.for_each_repository(ctx, lint, path, **kwds)
+    exit_code = shed.for_each_repository(ctx, lint, paths, **kwds)
     sys.exit(exit_code)

planemo/commands/cmd_shed_serve.py

@@ -0,0 +1,30 @@
+"""
+"""
+import time
+import click
+
+from planemo.cli import pass_context
+from planemo import options
+from planemo import galaxy_serve
+from planemo import shed
+from planemo import io
+
+
+@click.command("shed_serve")
+@options.shed_read_options()
+@options.galaxy_run_options()
+@click.option(
+    "--skip_dependencies",
+    is_flag=True,
+    help="Do not install shed dependencies as part of repository installation."
+)
+@pass_context
+def cli(ctx, paths, **kwds):
+    """ Serve a transient Galaxy instance after installing repositories
+    from a remote Tool Shed.
+    """
+    install_args_list = shed.install_arg_lists(ctx, paths, **kwds)
+    with galaxy_serve.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)

planemo/commands/cmd_shed_test.py

@@ -0,0 +1,51 @@
+"""
+"""
+import socket
+import sys
+
+import click
+
+from planemo.cli import pass_context
+from planemo import options
+from planemo import galaxy_serve
+from planemo import shed
+from planemo import galaxy_test
+
+
+@click.command("shed_test")
+@options.shed_read_options()
+@options.galaxy_target_options()
+@options.test_options()
+@click.option(
+    "--skip_dependencies",
+    is_flag=True,
+    help="Do not install shed dependencies as part of repository installation."
+)
+@pass_context
+def cli(ctx, paths, **kwds):
+    """ Serve a transient Galaxy instance after installing repositories
+    from a remote Tool Shed.
+    """
+    galaxy_test.process_defaults(ctx, kwds)
+    install_args_list = shed.install_arg_lists(ctx, paths, **kwds)
+    port = get_free_port()
+    kwds["port"] = port
+    return_code = 1
+    with galaxy_serve.shed_serve(ctx, install_args_list, **kwds) as config:
+        config.kill()
+        return_code = galaxy_test.run_in_config(
+            ctx,
+            config,
+            installed=True,
+            **kwds
+        )
+    if return_code:
+        sys.exit(return_code)
+
+
+def get_free_port():
+    sock = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
+    sock.bind(('localhost', 0))
+    port = sock.getsockname()[1]
+    sock.close()
+    return port

planemo/commands/cmd_shed_upload.py

@@ -18,18 +18,12 @@
 
 
 @click.command("shed_upload")
-@options.shed_project_arg()
+@options.shed_publish_options()
 @click.option(
     '-m',
     '--message',
     help="Commit message for tool shed upload."
 )
-@options.shed_owner_option()
-@options.shed_name_option()
-@options.shed_target_option()
-@options.shed_key_option()
-@options.shed_email_option()
-@options.shed_password_option()
 @click.option(
     '--tar_only',
     is_flag=True,
@@ -56,14 +50,12 @@
          "'difference' (only attributes populated by the shed would would "
          "be updated.)"
 )
-@options.recursive_shed_option()
-@options.shed_fail_fast_option()
 @pass_context
-def cli(ctx, path, **kwds):
+def cli(ctx, paths, **kwds):
     """Handle possible recursion through paths for uploading files to a toolshed
     """
     def upload(realized_repository):
         return shed.upload_repository(ctx, realized_repository, **kwds)
 
-    exit_code = shed.for_each_repository(ctx, upload, path, **kwds)
+    exit_code = shed.for_each_repository(ctx, upload, paths, **kwds)
     sys.exit(exit_code)