Merge pull request #80 from seqeralabs/bash_specific_constructs

Support for bash specific syntax and sys.argv

seqerakit/cli.py

@@ -19,6 +19,7 @@
 """
 import argparse
 import logging
+import sys
 
 from pathlib import Path
 from seqerakit import seqeraplatform, helper, overwrite
@@ -28,7 +29,7 @@
 logger = logging.getLogger(__name__)
 
 
-def parse_args():
+def parse_args(args=None):
     parser = argparse.ArgumentParser()
     parser.add_argument(
         "-l",
@@ -61,7 +62,7 @@ def parse_args():
         help="Additional arguments to pass to Seqera Platform"
         " CLI enclosed in double quotes (e.g. '--cli=\"--insecure\"')",
     )
-    return parser.parse_args()
+    return parser.parse_args(args if args is not None else sys.argv[1:])
 
 
 class BlockParser:
@@ -122,8 +123,8 @@ def handle_block(self, block, args, destroy=False):
             logger.error(f"Unrecognized resource block in YAML: {block}")
 
 
-def main():
-    options = parse_args()
+def main(args=None):
+    options = parse_args(args)
     logging.basicConfig(level=options.log_level)
 
     # Parse CLI arguments into a list
@@ -146,7 +147,6 @@ def main():
     # Parse the YAML file(s) by blocks
     # and get a dictionary of command line arguments
     cmd_args_dict = helper.parse_all_yaml(options.yaml, destroy=options.delete)
-
     for block, args_list in cmd_args_dict.items():
         for args in args_list:
             try:

seqerakit/seqeraplatform.py

@@ -72,8 +72,11 @@ def _construct_command(self, cmd, *args, **kwargs):
     # Checks environment variables to see that they are set accordingly
     def _check_env_vars(self, command):
         full_cmd_parts = []
+        shell_constructs = ["|", ">", "<", "$(", "&", "&&", "`"]
         for arg in command:
-            if "$" in arg:
+            if any(construct in arg for construct in shell_constructs):
+                full_cmd_parts.append(arg)
+            elif "$" in arg:
                 for env_var in re.findall(r"\$\{?[\w]+\}?", arg):
                     if re.sub(r"[${}]", "", env_var) not in os.environ:
                         raise EnvironmentError(