Merge pull request #121 from seqeralabs/114-support-stdin

feat: add support for stdin to cli

README.md

@@ -109,6 +109,18 @@ Use `--version` or `-v` to retrieve the current version of your seqerakit instal
 ```bash
 seqerakit --version
 ```
+### Input
+`seqerakit` supports input through either file paths to YAMLs or directly from standard input (stdin).
+
+#### Using File Path
+```bash
+seqerakit /path/to/file.yaml
+```
+#### Using stdin
+```console
+$ cat file.yaml | seqerakit -
+```
+See the [Defining your YAML file using CLI options](#defining-your-yaml-file-using-cli-options) section for guidance on formatting your input YAML file(s).
 
 ### Dryrun
 

seqerakit/cli.py

@@ -21,7 +21,6 @@
 import logging
 import sys
 
-from pathlib import Path
 from seqerakit import seqeraplatform, helper, overwrite
 from seqerakit.seqeraplatform import ResourceExistsError, ResourceCreationError
 from seqerakit import __version__
@@ -66,7 +65,6 @@ def parse_args(args=None):
     yaml_processing = parser.add_argument_group("YAML Processing Options")
     yaml_processing.add_argument(
         "yaml",
-        type=Path,
         nargs="*",
         help="One or more YAML files with Seqera Platform resource definitions.",
     )
@@ -154,10 +152,14 @@ def main(args=None):
         return
 
     if not options.yaml:
-        logging.error(
-            " No YAML(s) provided. Please provide atleast one YAML configuration file."
-        )
-        sys.exit(1)
+        if sys.stdin.isatty():
+            logging.error(
+                " No YAML(s) provided and no input from stdin. Please provide "
+                "at least one YAML configuration file or pipe input from stdin."
+            )
+            sys.exit(1)
+        else:
+            options.yaml = [sys.stdin]
 
     # Parse CLI arguments into a list
     cli_args_list = options.cli_args.split() if options.cli_args else []

seqerakit/helper.py

@@ -19,6 +19,7 @@
 """
 import yaml
 from seqerakit import utils
+import sys
 
 
 def parse_yaml_block(yaml_data, block_name):
@@ -57,24 +58,48 @@ def parse_all_yaml(file_paths, destroy=False):
     # If multiple yamls, merge them into one dictionary
     merged_data = {}
 
-    for file_path in file_paths:
-        with open(file_path, "r") as f:
-            data = yaml.safe_load(f)
-
-            # Check if the YAML file is empty or contains no valid data
-            if data is None or not data:
-                raise ValueError(
-                    f" The file '{file_path}' is empty or does not contain valid data."
-                )
+    # Special handling for stdin represented by "-"
+    if not file_paths or "-" in file_paths:
+        # Read YAML directly from stdin
+        data = yaml.safe_load(sys.stdin)
+        if not data:
+            raise ValueError(
+                " The input from stdin is empty or does not contain valid YAML data."
+            )
+        merged_data.update(data)
 
-            for key, value in data.items():
+    for file_path in file_paths:
+        if file_path == "-":
+            continue
+        try:
+            with open(file_path, "r") as f:
+                data = yaml.safe_load(f)
+                if not data:
+                    raise ValueError(
+                        f" The file '{file_path}' is empty or "
+                        "does not contain valid data."
+                    )
+
+            for key, new_value in data.items():
                 if key in merged_data:
-                    try:
-                        merged_data[key].extend(value)
-                    except AttributeError:
-                        merged_data[key] = [merged_data[key], value]
+                    if isinstance(new_value, list) and all(
+                        isinstance(i, dict) for i in new_value
+                    ):
+                        # Handle list of dictionaries & merge without duplication
+                        existing_items = {
+                            tuple(sorted(d.items())) for d in merged_data[key]
+                        }
+                        for item in new_value:
+                            if tuple(sorted(item.items())) not in existing_items:
+                                merged_data[key].append(item)
+                    else:
+                        # override if not list of dictionaries
+                        merged_data[key] = new_value
                 else:
-                    merged_data[key] = value
+                    merged_data[key] = new_value
+        except FileNotFoundError:
+            print(f"Error: The file '{file_path}' was not found.")
+            sys.exit(1)
 
     block_names = list(merged_data.keys())
 
@@ -95,7 +120,7 @@ def parse_all_yaml(file_paths, destroy=False):
         "launch",
     ]
 
-    # Reverse the order of resources if destroy is True
+    # Reverse the order of resources to delete if destroy is True
     if destroy:
         resource_order = resource_order[:-1][::-1]
 

tests/unit/test_helper.py

@@ -1,7 +1,8 @@
-from unittest.mock import mock_open
+from unittest.mock import patch, mock_open
 from seqerakit import helper
 import yaml
 import pytest
+from io import StringIO
 
 
 # Fixture to mock a YAML file
@@ -48,8 +49,8 @@ def test_create_mock_organization_yaml(mock_yaml_file):
             "overwrite": True,
         }
     ]
-
     file_path = mock_yaml_file(test_data)
+    print(f"debug - file_path: {file_path}")
     result = helper.parse_all_yaml([file_path])
 
     assert "organizations" in result
@@ -343,6 +344,53 @@ def test_empty_yaml_file(mock_yaml_file):
     )
 
 
+def test_empty_stdin_file():
+    # Prepare the mock to simulate empty stdin
+    with patch("sys.stdin", StringIO("")):
+        # Use '-' to indicate that stdin should be read
+        with pytest.raises(ValueError) as e:
+            helper.parse_all_yaml(["-"])
+        assert (
+            "The input from stdin is empty or does not contain valid YAML data."
+            in str(e.value)
+        )
+
+
+def test_stdin_yaml_file():
+    # Prepare the mock to simulate stdin
+    yaml_data = """
+compute-envs:
+  - name: test_computeenv
+    config-mode: forge
+    workspace: my_organization/my_workspace
+    credentials: my_credentials
+    type: aws-batch
+    wait: AVAILABLE
+        """
+    with patch("sys.stdin", StringIO(yaml_data)):
+        result = helper.parse_all_yaml(["-"])
+
+    expected_block_output = [
+        {
+            "cmd_args": [
+                "aws-batch",
+                "forge",
+                "--name",
+                "test_computeenv",
+                "--workspace",
+                "my_organization/my_workspace",
+                "--credentials",
+                "my_credentials",
+                "--wait",
+                "AVAILABLE",
+            ],
+            "overwrite": False,
+        }
+    ]
+    assert "compute-envs" in result
+    assert result["compute-envs"] == expected_block_output
+
+
 def test_error_type_yaml_file(mock_yaml_file):
     test_data = {
         "compute-envs": [