fix: fix string resource definition in CLI and profile (#2627)

### Description

The PR is related to the[ issue described for the slurm submit
executor](snakemake/snakemake-executor-plugin-slurm#18)
plugin to not correctly hand over arguments.

The test folder is named `test_slurm_resource_propagation meesters` and
may not be complete, as it covers multiple related scenarios to provoke
the error.

Note, that the tests were carried out when using a cluster:

- `$ snakemake --executor slurm -j2 --workflow-profile ./profiles/
--default-resources slurm_account=<account>`
  yields
  ``Error:
  WorkflowError:
Failed to evaluate default resources value '<function
eval_resource_expression.<locals>.callable at 0x7f5c19ed0e00>'.```
    
when the patition is defined at the rule level in a profile. (see the
directory of the test case)
    
- likewise `$ snakemake --executor slurm -j2 --workflow-profile
./profiles/ --default-resources slurm_account=<account> --set-resources
slurm_extra="--nice=150"`
  yields
```ValueError: Invalid resource definition: entries have to be defined
as RULE:RESOURCE=VALUE, with VALUE being a positive integer a quoted
string, or a Python expression (e.g. min(max(2*input.size_mb, 1000),
8000)).```
  
These errors can both be triggered on the command line and in the config
file, of course.


### QC

* [x] The PR contains a test case for the changes or the changes are
already covered by an existing test case.
* [ ] The documentation (`docs/`) is updated to reflect the changes or
this is not necessary (e.g. if the change does neither modify the
language nor the behavior or functionalities of Snakemake).

---------

Co-authored-by: Johannes Koester <johannes.koester@uni-due.de>
Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>

snakemake/cli.py

@@ -81,7 +81,7 @@ def parse_set_resources(args):
     assignments = defaultdict(dict)
     if args is not None:
         for entry in args:
-            key, value = parse_key_value_arg(entry, errmsg=errmsg)
+            key, value = parse_key_value_arg(entry, errmsg=errmsg, strip_quotes=False)
             key = key.split(":")
             if len(key) != 2:
                 raise ValueError(errmsg)

snakemake/common/__init__.py

@@ -60,12 +60,13 @@ def mb_to_mib(mb):
     return int(math.ceil(mb * 0.95367431640625))
 
 
-def parse_key_value_arg(arg, errmsg):
+def parse_key_value_arg(arg, errmsg, strip_quotes=True):
     try:
         key, val = arg.split("=", 1)
     except ValueError:
         raise ValueError(errmsg + f" (Unparseable value: {repr(arg)})")
-    val = val.strip("'\"")
+    if strip_quotes:
+        val = val.strip("'\"")
     return key, val
 
 

snakemake/resources.py

@@ -532,10 +532,10 @@ def generic_callable(val, threads_arg, **kwargs):
             if not is_file_not_found_error(e, kwargs["input"]):
                 # Missing input files are handled by the caller
                 raise WorkflowError(
-                    "Failed to evaluate default resources value "
+                    "Failed to evaluate resources value "
                     f"'{val}'.\n"
                     "    String arguments may need additional "
-                    "quoting. Ex: --default-resources "
+                    "quoting. E.g.: --default-resources "
                     "\"tmpdir='/home/user/tmp'\".",
                     e,
                 )

tests/test_resource_string_in_cli_or_profile/Snakefile

@@ -0,0 +1,9 @@
+# fails when submitted as
+# $ snakemake --executor slurm -j2 --workflow-profile ./profiles/ --default-resources slurm_account=m2_zdvhpc
+
+rule all:
+     input: "a.out"
+
+rule test1:
+     output: "a.out"
+     shell: "touch {output}"

tests/test_resource_string_in_cli_or_profile/profiles/config.yaml

@@ -0,0 +1,4 @@
+set-resources:
+    test1:
+        slurm_partition: "smp"
+        slurm_extra: "'--nice=150'"

tests/tests.py

@@ -1969,6 +1969,17 @@ def test_issue1256():
     assert "line 9" in stderr
 
 
+def test_resource_string_in_cli_or_profile():
+    test_path = dpath("test_resource_string_in_cli_or_profile")
+    profile = os.path.join(test_path, "profiles")
+    # workflow profile is loaded by default
+    run(
+        test_path,
+        snakefile="Snakefile",
+        shellcmd=f"snakemake --workflow-profile {profile} -c1 --default-resources slurm_account=foo other_resource='--test'",
+    )
+
+
 def test_queue_input():
     run(dpath("test_queue_input"))