From 28a47959bca2d135f82f9d8901b2b0aa228f30cb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20K=C3=B6ster?= <johannes.koester@tu-dortmund.de>
Date: Fri, 20 May 2022 10:30:42 +0200
Subject: [PATCH] fix: fix errors occurring when refering to input func via
 rules.<rulename>.input (#1669)

* fix: fix errors occurring when refering to input func via rules.<rulename>.input

* skip win

* fix for cases when a prefix is provided
---
 snakemake/io.py                                |  3 +++
 snakemake/rules.py                             | 18 +++++++++++++++++-
 tests/test_module_input_func/Snakefile         | 14 ++++++++++++++
 .../expected-results/test/results/C.txt        |  1 +
 tests/test_module_input_func/module1/Snakefile | 15 +++++++++++++++
 tests/tests.py                                 |  5 +++++
 6 files changed, 55 insertions(+), 1 deletion(-)
 create mode 100644 tests/test_module_input_func/Snakefile
 create mode 100644 tests/test_module_input_func/expected-results/test/results/C.txt
 create mode 100644 tests/test_module_input_func/module1/Snakefile

diff --git a/snakemake/io.py b/snakemake/io.py
index 182b1d1d0..ffd144e78 100755
--- a/snakemake/io.py
+++ b/snakemake/io.py
@@ -1443,6 +1443,9 @@ def git_content(git_file):
 
 def strip_wildcard_constraints(pattern):
     """Return a string that does not contain any wildcard constraints."""
+    if is_callable(pattern):
+        # do not apply on e.g. input functions
+        return pattern
 
     def strip_constraint(match):
         return "{{{}}}".format(match.group("name"))
diff --git a/snakemake/rules.py b/snakemake/rules.py
index 151b36a95..0e2891b54 100644
--- a/snakemake/rules.py
+++ b/snakemake/rules.py
@@ -1270,7 +1270,23 @@ def output(self):
 
     @lazy_property
     def input(self):
-        return self.rule.input._stripped_constraints()
+        def modify_callable(item):
+            if is_callable(item):
+                # For callables ensure that the rule's original path modifier is applied as well.
+
+                def inner(wildcards):
+                    return self.rule.apply_path_modifier(
+                        item(wildcards), self.rule.input_modifier, property="input"
+                    )
+
+                return inner
+            else:
+                # For strings, the path modifier has been already applied.
+                return item
+
+        return InputFiles(
+            toclone=self.rule.input, strip_constraints=True, custom_map=modify_callable
+        )
 
     @lazy_property
     def params(self):
diff --git a/tests/test_module_input_func/Snakefile b/tests/test_module_input_func/Snakefile
new file mode 100644
index 000000000..0b2e8fb10
--- /dev/null
+++ b/tests/test_module_input_func/Snakefile
@@ -0,0 +1,14 @@
+module mod1:
+    snakefile:
+        "module1/Snakefile"
+    prefix:
+        "test/"
+
+
+use rule * from mod1 as mod1_*
+
+
+rule all:
+    input:
+        rules.mod1_all.input,
+    default_target: True
diff --git a/tests/test_module_input_func/expected-results/test/results/C.txt b/tests/test_module_input_func/expected-results/test/results/C.txt
new file mode 100644
index 000000000..3cc58df83
--- /dev/null
+++ b/tests/test_module_input_func/expected-results/test/results/C.txt
@@ -0,0 +1 @@
+C
diff --git a/tests/test_module_input_func/module1/Snakefile b/tests/test_module_input_func/module1/Snakefile
new file mode 100644
index 000000000..cdd7386ba
--- /dev/null
+++ b/tests/test_module_input_func/module1/Snakefile
@@ -0,0 +1,15 @@
+def txt_output(wildcards):
+    return ["results/C.txt"]
+
+
+rule all:
+    input:
+        txt_output
+
+
+rule txt:
+    output:
+        "results/C.txt"
+    shell:
+        "echo 'C' "
+        ">{output} "
diff --git a/tests/tests.py b/tests/tests.py
index 82ec9052b..a5bd71143 100644
--- a/tests/tests.py
+++ b/tests/tests.py
@@ -1646,6 +1646,11 @@ def test_retries():
     run(dpath("test_retries"))
 
 
+@skip_on_windows  # OS agnostic
+def test_module_input_func():
+    run(dpath("test_module_input_func"))
+
+
 @skip_on_windows  # the testcase only has a linux-64 pin file
 def test_conda_pin_file():
     run(dpath("test_conda_pin_file"), use_conda=True)