Allow URIs to be used instead of paths for a couple operations.

jmchilton · jmchilton · commit ce0dc4e31ef2 · 2017-03-15T10:15:30.000-04:00
Depends on galaxy-lib enhancements from galaxyproject/galaxy-lib#52.
diff --git a/planemo/commands/cmd_lint.py b/planemo/commands/cmd_lint.py
@@ -8,7 +8,7 @@
 
 
 @click.command('lint')
-@options.optional_tools_arg(multiple=True)
+@options.optional_tools_arg(multiple=True, allow_uris=True)
 @options.report_level_option()
 @options.report_xunit()
 @options.fail_level_option()
@@ -46,12 +46,12 @@
 # default=False,
 # )
 @command_function
-def cli(ctx, paths, **kwds):
+def cli(ctx, uris, **kwds):
     """Check for common errors and best practices."""
     lint_args = build_lint_args(ctx, **kwds)
     exit_code = lint_tools_on_path(
         ctx,
-        paths,
+        uris,
         lint_args,
         recursive=kwds["recursive"]
     )
diff --git a/planemo/commands/cmd_run.py b/planemo/commands/cmd_run.py
@@ -9,10 +9,11 @@
 from planemo.cli import command_function
 from planemo.engine import engine_context
 from planemo.io import conditionally_captured_io, warn
+from planemo.tools import uri_to_path
 
 
 @click.command('run')
-@options.required_tool_arg()
+@options.required_tool_arg(allow_uris=True)
 @options.required_job_arg()
 @options.galaxy_run_options()
 @options.galaxy_config_options()
@@ -22,12 +23,13 @@
 @options.run_output_json_option()
 @options.engine_options()
 @command_function
-def cli(ctx, path, job_path, **kwds):
+def cli(ctx, uri, job_path, **kwds):
     """Planemo command for running tools and jobs.
 
     \b
         % planemo run cat1-tool.cwl cat-job.json
     """
+    path = DEFAULT_TOOL_LOCATION_FETCHER.to_tool_path(uri)
     kwds["cwl"] = path.endswith(".cwl")
     conformance_test = kwds.get("conformance_test", False)
 
diff --git a/planemo/commands/cmd_serve.py b/planemo/commands/cmd_serve.py
@@ -5,15 +5,16 @@
 from planemo.cli import command_function
 from planemo.galaxy import galaxy_serve
 from planemo.runnable import for_paths
+from planemo.tools import uris_to_paths
 
 
 @click.command('serve')
-@options.optional_tools_arg(multiple=True)
+@options.optional_tools_arg(multiple=True, allow_uris=True)
 @options.galaxy_serve_options()
 @options.enable_cwl_option()
 @options.galaxy_cwl_root_option()
 @command_function
-def cli(ctx, paths, **kwds):
+def cli(ctx, uris, **kwds):
     """Launch Galaxy instance with specified tools.
 
     The Galaxy tool panel will include just the referenced tool or tools (by
@@ -36,5 +37,6 @@ def cli(ctx, paths, **kwds):
     proof yet, so please be careful and do not try this against a production
     Galaxy instance.
     """
+    paths = uris_to_paths(ctx, uris)
     runnables = for_paths(paths)
     galaxy_serve(ctx, runnables, **kwds)
diff --git a/planemo/cwl/run.py b/planemo/cwl/run.py
@@ -71,6 +71,8 @@ def run_cwltool(ctx, path, job_path, **kwds):
     if kwds.get("no_container", False):
         args.append("--no-container")
 
+    args.append("--non-strict")
+
     args.extend([path, job_path])
     ctx.vlog("Calling cwltool with arguments %s" % args)
     with tempfile.NamedTemporaryFile() as tmp_stdout, \
@@ -81,7 +83,7 @@ def run_cwltool(ctx, path, job_path, **kwds):
             ret_code = main.main(
                 args,
                 stdout=tmp_stdout,
-                stderr=tmp_stderr
+                stderr=tmp_stderr,
             )
         tmp_stdout.flush()
         tmp_stderr.flush()
diff --git a/planemo/options.py b/planemo/options.py
@@ -509,17 +509,24 @@ def conda_global_option():
     )
 
 
-def required_tool_arg():
+def required_tool_arg(allow_uris=False):
     """ Decorate click method as requiring the path to a single tool.
     """
-    arg_type = click.Path(
+    arg_type_class = click.Path if not allow_uris else UriLike
+    arg_type = arg_type_class(
         exists=True,
         file_okay=True,
         dir_okay=False,
         readable=True,
         resolve_path=True,
     )
-    return click.argument("path", metavar="TOOL_PATH", type=arg_type)
+    if allow_uris:
+        name = "uri"
+        metavar = "TOOL_URI"
+    else:
+        name = "path"
+        metavar = "TOOL_PATH"
+    return click.argument(name, metavar=metavar, type=arg_type)
 
 
 def required_job_arg():
@@ -536,7 +543,7 @@ def required_job_arg():
 
 
 def _optional_tools_default(ctx, param, value):
-    if param.name == "paths" and len(value) == 0:
+    if param.name in ["paths", "uris"] and len(value) == 0:
         return [os.path.abspath(os.getcwd())]
     else:
         return value
@@ -556,19 +563,32 @@ def optional_tools_or_packages_arg(multiple=False):
     )
 
 
-def optional_tools_arg(multiple=False):
+class UriLike(click.Path):
+
+    def convert(self, value, param, ctx):
+        if "://" in value:
+            return value
+        else:
+            return super(UriLike, self).convert(value, param, ctx)
+
+
+def optional_tools_arg(multiple=False, allow_uris=False):
     """ Decorate click method as optionally taking in the path to a tool
     or directory of tools. If no such argument is given the current working
     directory will be treated as a directory of tools.
     """
-    arg_type = click.Path(
+    arg_type_class = click.Path if not allow_uris else UriLike
+    arg_type = arg_type_class(
         exists=True,
         file_okay=True,
         dir_okay=True,
         readable=True,
         resolve_path=True,
     )
-    name = "paths" if multiple else "path"
+    if allow_uris:
+        name = "uris" if multiple else "uri"
+    else:
+        name = "paths" if multiple else "path"
     nargs = -1 if multiple else 1
     return click.argument(
         name,
diff --git a/planemo/tools.py b/planemo/tools.py
@@ -6,6 +6,7 @@
 import traceback
 
 from galaxy.tools import loader_directory
+from galaxy.tools.fetcher import ToolLocationFetcher
 
 from planemo.io import error, info
 
@@ -14,6 +15,20 @@
 SHED_FILES = ["tool_dependencies.xml", "repository_dependencies.xml"]
 
 
+def uri_to_path(ctx, uri):
+    fetcher = ToolLocationFetcher()
+    return fetcher.to_tool_path(uri)
+
+
+def uris_to_paths(ctx, uris):
+    fetcher = ToolLocationFetcher()
+    paths = []
+    for uri in uris:
+        path = fetcher.to_tool_path(uri)
+        paths.append(path)
+    return paths
+
+
 def yield_tool_sources_on_paths(ctx, paths, recursive=False):
     for path in paths:
         for (tool_path, tool_source) in yield_tool_sources(ctx, path, recursive):
diff --git a/requirements.txt b/requirements.txt
@@ -13,6 +13,6 @@ virtualenv
 lxml
 gxformat2>=0.1.1
 ephemeris>=0.2.0
-galaxy-lib>=17.5.6
+galaxy-lib>=17.5.7
 html5lib>=0.9999999,!=0.99999999,!=0.999999999,!=1.0b10,!=1.0b09 ; python_version == '2.7'
 cwltool==1.0.20170224141733 ; python_version == '2.7'
diff --git a/tests/test_lint.py b/tests/test_lint.py
@@ -18,6 +18,10 @@ def test_ok_tools(self):
             lint_cmd = ["lint", "--urls", ok_tool]
             self._check_exit_code(lint_cmd)
 
+    def test_ok_http(self):
+        lint_cmd = ["lint", "https://raw.githubusercontent.com/galaxyproject/planemo/master/tests/data/tools/ok_conditional.xml"]
+        self._check_exit_code(lint_cmd)
+
     def test_fail_tools(self):
         fail_tools = glob.glob("%s/fail_*" % TEST_TOOLS_DIR)
         for fail_tool in fail_tools:
