2 files changed, 71 insertions, 0 deletions
diff --git a/gn3/commands.py b/gn3/commands.py
new file mode 100644
index 0000000..50b6d29
--- /dev/null
+++ b/gn3/commands.py
@@ -0,0 +1,42 @@
+"""Procedures used to work with the various bio-informatics cli
+commands"""
+from typing import Dict
+from typing import List
+from typing import Optional
+
+from gn3.file_utils import lookup_file
+from gn3.file_utils import jsonfile_to_dict
+
+
+# pylint: disable=locally-disabled, too-many-arguments
+def compose_gemma_cmd(
+        token: str,
+        metadata_filename: str,
+        gemma_wrapper_cmd: str = "gemma-wrapper",
+        gemma_wrapper_kwargs: Optional[Dict] = None,
+        gemma_kwargs: Optional[Dict] = None,
+        gemma_args: Optional[List] = None) -> str:
+    """Compose a valid GEMMA command given the correct values"""
+    cmd = f"{gemma_wrapper_cmd} --json"
+    if gemma_wrapper_kwargs:
+        cmd += (" "  # Add extra space between commands
+                " ".join([f" --{key} {val}" for key, val
+                          in gemma_wrapper_kwargs.items()]))
+    data = jsonfile_to_dict(lookup_file("TMPDIR",
+                                        token,
+                                        metadata_filename))
+    geno_file = lookup_file(environ_var="TMPDIR",
+                            root_dir="genotype",
+                            file_name=data.get("geno", ""))
+    pheno_file = lookup_file(environ_var="TMPDIR",
+                             root_dir=token,
+                             file_name=data.get("geno", ""))
+    cmd += f" -- -g {geno_file} -p {pheno_file}"
+    if gemma_kwargs:
+        cmd += (" "
+                " ".join([f" -{key} {val}"
+                          for key, val in gemma_kwargs.items()]))
+    if gemma_args:
+        cmd += (" "
+                " ".join([f" {arg}" for arg in gemma_args]))
+    return cmd
diff --git a/tests/unit/test_commands.py b/tests/unit/test_commands.py
new file mode 100644
index 0000000..a319332
--- /dev/null
+++ b/tests/unit/test_commands.py
@@ -0,0 +1,29 @@
+"""Test cases for procedures defined in commands.py"""
+import os
+import unittest
+
+from unittest import mock
+from gn3.commands import compose_gemma_cmd
+
+
+class TestCommands(unittest.TestCase):
+    """Test cases for commands.py"""
+
+    @mock.patch("gn3.commands.lookup_file")
+    def test_compose_gemma_cmd_no_extra_args(self, mock_lookup_file):
+        """Test that thhe gemma cmd is composed correctly"""
+        metadata_file = os.path.join(os.path.dirname(__file__),
+                                     "test_data/metadata.json")
+        mock_lookup_file.side_effect = [metadata_file,
+                                        "/tmp/genofile.txt",
+                                        "/tmp/gf13Ad0tRX/phenofile.txt"]
+        self.assertEqual(compose_gemma_cmd("gf13Ad0t",
+                                           "metadata.json",
+                                           gemma_wrapper_cmd="gemma-wrapper",
+                                           gemma_wrapper_kwargs=None,
+                                           gemma_kwargs=None,
+                                           gemma_args=["-gk"]),
+                         ("gemma-wrapper --json -- "
+                          "-g /tmp/genofile.txt "
+                          "-p /tmp/gf13Ad0tRX/phenofile.txt"
+                          " -gk"))