From f322c97829a297e39348a0b5470df06530e8d89f Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Fri, 15 Dec 2023 14:32:35 +0100
Subject: [PATCH] planemo lint: add --skip_file

new option allowing to specify one or more files
listing linters to skip
---
 planemo/commands/cmd_lint.py      |  2 +-
 planemo/commands/cmd_shed_lint.py |  2 +-
 planemo/lint.py                   | 10 +++++++++-
 planemo/options.py                | 18 ++++++++++++++++++
 4 files changed, 29 insertions(+), 3 deletions(-)

diff --git a/planemo/commands/cmd_lint.py b/planemo/commands/cmd_lint.py
index 23dcf4e06..2c22b5710 100644
--- a/planemo/commands/cmd_lint.py
+++ b/planemo/commands/cmd_lint.py
@@ -14,7 +14,7 @@
 @options.report_level_option()
 @options.report_xunit()
 @options.fail_level_option()
-@options.skip_option()
+@options.skip_options()
 @options.lint_xsd_option()
 @options.recursive_option()
 @click.option(
diff --git a/planemo/commands/cmd_shed_lint.py b/planemo/commands/cmd_shed_lint.py
index beb413580..2571ac417 100644
--- a/planemo/commands/cmd_shed_lint.py
+++ b/planemo/commands/cmd_shed_lint.py
@@ -13,7 +13,7 @@
 @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.")
 )
diff --git a/planemo/lint.py b/planemo/lint.py
index 25a0a9c7f..a8df3504a 100644
--- a/planemo/lint.py
+++ b/planemo/lint.py
@@ -20,8 +20,16 @@ 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)
+
     lint_args = dict(
         level=report_level,
         fail_level=fail_level,
diff --git a/planemo/options.py b/planemo/options.py
index b64d9c4e3..7050aed8a 100644
--- a/planemo/options.py
+++ b/planemo/options.py
@@ -1384,6 +1384,13 @@ def report_xunit():
     )
 
 
+def skip_options():
+    return _compose(
+        skip_option(),
+        skip_file_option(),
+    )
+
+
 def skip_option():
     return planemo_option(
         "-s",
@@ -1397,6 +1404,17 @@ 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")