Merge pull request #1420 from bernt-matthias/linting-news

Tool linting add `--skip_file` and remove lxml schema validation

planemo/commands/cmd_lint.py

@@ -15,8 +15,7 @@
 @options.report_level_option()
 @options.report_xunit()
 @options.fail_level_option()
-@options.skip_option()
-@options.lint_xsd_option()
+@options.skip_options()
 @options.recursive_option()
 @click.option(
     "--urls",

planemo/commands/cmd_shed_lint.py

@@ -14,11 +14,10 @@
 @options.shed_realization_options()
 @options.report_level_option()
 @options.fail_level_option()
-@options.skip_option()
+@options.skip_options()
 @options.click.option(
     "--tools", is_flag=True, default=False, help=("Lint tools discovered in the process of linting repositories.")
 )
-@options.lint_xsd_option()
 @options.click.option(
     "--ensure_metadata",
     is_flag=True,

planemo/lint.py

@@ -4,7 +4,10 @@
 from urllib.request import urlopen
 
 import requests
-from galaxy.tool_util.lint import LintContext
+from galaxy.tool_util.lint import (
+    LintContext,
+    Linter,
+)
 
 from planemo.io import error
 from planemo.shed import find_urls_for_xml
@@ -20,8 +23,21 @@ def build_lint_args(ctx, **kwds):
         skip = ctx.global_config.get("lint_skip", "")
         if isinstance(skip, list):
             skip = ",".join(skip)
-
     skip_types = [s.strip() for s in skip.split(",")]
+
+    for skip_file in kwds.get("skip_file", []):
+        with open(skip_file) as f:
+            for line in f.readlines():
+                line = line.strip()
+                if not line or line.startswith("#"):
+                    continue
+                skip_types.append(line)
+
+    linters = Linter.list_listers()
+    invalid_skip_types = list(set(skip_types) - set(linters))
+    if len(invalid_skip_types):
+        error(f"Unknown linter type(s) {invalid_skip_types} in list of linters to be skipped. Known linters {linters}")
+
     lint_args = dict(
         level=report_level,
         fail_level=fail_level,

planemo/options.py

@@ -1375,12 +1375,6 @@ def shed_fail_fast_option():
     )
 
 
-def lint_xsd_option():
-    return planemo_option(
-        "--xsd/--no_xsd", is_flag=True, default=True, help=("Include tool XSD validation in linting process.")
-    )
-
-
 def lint_biocontainers_option():
     return planemo_option(
         "biocontainer",
@@ -1409,6 +1403,13 @@ def report_xunit():
     )
 
 
+def skip_options():
+    return _compose(
+        skip_option(),
+        skip_file_option(),
+    )
+
+
 def skip_option():
     return planemo_option(
         "-s",
@@ -1422,6 +1423,15 @@ def skip_option():
     )
 
 
+def skip_file_option():
+    return planemo_option(
+        "--skip_file",
+        type=click.Path(exists=True, file_okay=True, dir_okay=False, resolve_path=True),
+        multiple=True,
+        help=("File containing a list of lint tests to skip"),
+    )
+
+
 def fail_level_option():
     return planemo_option("--fail_level", type=click.Choice(["warn", "error"]), default="warn")
 

planemo/tool_lint.py

@@ -51,8 +51,6 @@ def lint_tools_on_path(ctx, paths, lint_args, **kwds):
 
 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)

tests/data/lint_skip_list.txt

@@ -0,0 +1,4 @@
+# check that comments work
+xml_order
+# check the white spaces are ignored
+ citations 

tests/test_lint.py

@@ -5,6 +5,7 @@
     CliTestCase,
     PROJECT_TEMPLATES_DIR,
     skip_if_environ,
+    TEST_DATA_DIR,
     TEST_REPOS_DIR,
     TEST_TOOLS_DIR,
 )
@@ -61,6 +62,11 @@ def test_skips(self):
         lint_cmd = ["lint", "--skip", "xml_order, citations", fail_citation]
         self._check_exit_code(lint_cmd, exit_code=0)
 
+        # Check skip_file (containing the same skips)
+        skip_file = os.path.join(TEST_DATA_DIR, "lint_skip_list.txt")
+        lint_cmd = ["lint", "--skip_file", skip_file, fail_citation]
+        self._check_exit_code(lint_cmd, exit_code=0)
+
     def test_recursive(self):
         nested_dir = os.path.join(TEST_REPOS_DIR, "multi_repos_nested")
 

tests/test_utils.py

@@ -55,7 +55,6 @@
 TEST_DIR = os.path.dirname(__file__)
 TEST_DATA_DIR = os.path.join(TEST_DIR, "data")
 TEST_AUTOPYGEN_DATA = os.path.join(TEST_DATA_DIR, "autopygen")
-TEST_DATA_DIR = os.path.join(TEST_DIR, "data")
 TEST_REPOS_DIR = os.path.join(TEST_DATA_DIR, "repos")
 TEST_TOOLS_DIR = os.path.join(TEST_DATA_DIR, "tools")
 PROJECT_TEMPLATES_DIR = os.path.join(TEST_DIR, os.path.pardir, "project_templates")