diff env/lib/python3.9/site-packages/planemo/tool_lint.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/planemo/tool_lint.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,82 @@
+from __future__ import absolute_import
+
+from os.path import basename
+
+from galaxy.tool_util.lint import lint_tool_source
+
+import planemo.linters.biocontainer_registered
+import planemo.linters.conda_requirements
+import planemo.linters.doi
+import planemo.linters.urls
+import planemo.linters.xsd
+from planemo.exit_codes import (
+    EXIT_CODE_GENERIC_FAILURE,
+    EXIT_CODE_OK,
+)
+from planemo.io import (
+    coalesce_return_codes,
+    error,
+    info,
+)
+from planemo.lint import build_lint_args
+from planemo.tools import (
+    is_tool_load_error,
+    yield_tool_sources_on_paths,
+)
+
+LINTING_TOOL_MESSAGE = "Linting tool %s"
+
+
+def build_tool_lint_args(ctx, **kwds):
+    lint_args = build_lint_args(ctx, **kwds)
+    extra_modules = _lint_extra_modules(**kwds)
+    lint_args["extra_modules"] = extra_modules
+    return lint_args
+
+
+def lint_tools_on_path(ctx, paths, lint_args, **kwds):
+    assert_tools = kwds.get("assert_tools", True)
+    recursive = kwds.get("recursive", False)
+    exit_codes = []
+    for (tool_path, tool_xml) in yield_tool_sources_on_paths(ctx, paths, recursive):
+        if handle_tool_load_error(tool_path, tool_xml):
+            exit_codes.append(EXIT_CODE_GENERIC_FAILURE)
+            continue
+        info("Linting tool %s" % tool_path)
+        if not lint_tool_source(tool_xml, name=basename(tool_path), **lint_args):
+            error("Failed linting")
+            exit_codes.append(EXIT_CODE_GENERIC_FAILURE)
+        else:
+            exit_codes.append(EXIT_CODE_OK)
+    return coalesce_return_codes(exit_codes, assert_at_least_one=assert_tools)
+
+
+def _lint_extra_modules(**kwds):
+    linters = []
+    if kwds.get("xsd", True):
+        linters.append(planemo.linters.xsd)
+
+    if kwds.get("doi", False):
+        linters.append(planemo.linters.doi)
+
+    if kwds.get("urls", False):
+        linters.append(planemo.linters.urls)
+
+    if kwds.get("conda_requirements", False):
+        linters.append(planemo.linters.conda_requirements)
+
+    if kwds.get("biocontainer", False):
+        linters.append(planemo.linters.biocontainer_registered)
+
+    return linters
+
+
+def handle_tool_load_error(tool_path, tool_xml):
+    """ Return True if tool_xml is tool load error (invalid XML), and
+    print a helpful error message.
+    """
+    is_error = False
+    if is_tool_load_error(tool_xml):
+        info("Could not lint %s due to malformed xml." % tool_path)
+        is_error = True
+    return is_error