Shell quote user-provided subsampling options

Many (most?) of the subsampling config a user can specify takes the form
of command-line options to `augur filter`.  Previously the values were
passed through unmodified, leaving shell features like variable
interpolation and command substitution as tripping hazards for the user,
who would have to know to escape those in their YAML build config.  This
change preserves the shell-like semantics of single and double quotes
and backslashes in subsampling values, but renders the tripping hazards
inert by re-quoting each word in the value.

This assumes that we don't need to support those shell features within
subsampling config values (e.g. a user subsampling config doesn't need
to refer to an environment variable), or at least that their cost in
complexity for all users outweighs their benefit to a few users.

There are many other places in the workflow which blindly interpolate,
without quoting, user-provided values into shell commands.  This change
demonstrates a pattern we can use to handle them more robustly if we
choose.

Relatedly, we should consider a) explicitly using Snakemake's built in
{foo:q} interpolation syntax by default for single-word values, or b)
coercing Snakemake to always apply quoting unless asked otherwise with
{foo:u} (currently requires a monkeypatch).

workflow/snakemake_rules/common.smk

@@ -1,8 +1,24 @@
 """Small, shared functions used to generate inputs and parameters.
 """
 import datetime
+from shlex import (
+    quote as shquote,       # shquote() is used in this file and also other workflow files
+    split as shsplitwords,
+)
 from urllib.parse import urlsplit
 
+def shquotewords(s: str) -> str:
+    """
+    Split string *s* into (POSIX) shell words, quote each word, and join them
+    back into a string.
+
+    This is suitable for properly quoting multi-word, user-defined values which
+    should follow shell quoting and escaping semantics (e.g. to allow spaces in
+    single words) but not allow shell features like variable interpolation,
+    command substition, redirection, piping, etc.
+    """
+    return " ".join(shquote(word) for word in shsplitwords(s))
+
 def numeric_date(dt=None):
     """
     Convert datetime object to the numeric date.
@@ -73,15 +89,12 @@ def _get_filter_min_length_query(wildcards):
             # as recommended by pandas:
             #
             # https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.query.html
-            #
-            # We escape the backticks with backslashes to prevent the bash shell
-            # from expanding the contents between the backticks as a subprocess.
-            query_parts.append(f"(\`{input_name}\` == 'yes' & _length >= {min_length})")
+            query_parts.append(f"(`{input_name}` == 'yes' & _length >= {min_length})")
         else:
             query_parts.append(f"(_length >= {min_length})")
 
     query = " | ".join(query_parts)
-    return f"--query \"{query}\""
+    return f"--query {shquote(query)}"
 
 def _get_filter_value(wildcards, key):
     for input_name in config["inputs"].keys():

workflow/snakemake_rules/main_workflow.smk

@@ -160,9 +160,9 @@ def get_priority_argument(wildcards):
         return ""
 
     if subsampling_settings["priorities"]["type"] == "proximity":
-        return "--priority " + get_priorities(wildcards)
+        return "--priority " + shquote(get_priorities(wildcards))
     elif subsampling_settings["priorities"]["type"] == "file" and "file" in subsampling_settings["priorities"]:
-        return "--priority " + subsampling_settings["priorities"]["file"]
+        return "--priority " + shquote(subsampling_settings["priorities"]["file"])
     else:
         return ""
 
@@ -199,15 +199,15 @@ def _get_specific_subsampling_setting(setting, optional=False):
             elif setting == 'max_sequences':
                 value = f"--subsample-max-sequences {value}"
 
-            return value
+            return shquotewords(value)
         else:
             value = ""
 
         # Check format strings that haven't been resolved.
         if re.search(r'\{.+\}', value):
             raise Exception(f"The parameters for the subsampling scheme '{wildcards.subsample}' of build '{wildcards.build_name}' reference build attributes that are not defined in the configuration file: '{value}'. Add these build attributes to the appropriate configuration file and try again.")
 
-        return value
+        return shquotewords(value)
 
     return _get_setting