NF: tools/text2filetree.py helper to convert some indented text into our filetree example spec

tools/text2filetree.py

@@ -0,0 +1,287 @@
+#!/usr/bin/env python3
+import argparse
+import json
+import sys
+
+
+def parse_file_tree(input_data, tab_width=4):
+    """
+    Parse a file tree hierarchy from an input stream and convert it to a nested dictionary.
+
+    :param input_data: Input string or file-like object representing the file tree
+    :param tab_width: Number of spaces to replace tabs with
+    :return: A nested dictionary representing the file tree
+    """
+    # If input is a string, convert to a list of lines
+    if isinstance(input_data, str):
+        lines = input_data.splitlines()
+    else:
+        lines = [line.rstrip() for line in input_data.readlines()]
+
+    def _parse_tree(lines):
+        # Create main tree dictionary
+        tree = {}
+
+        # Stack to keep track of nested dictionaries and their indentation levels
+        dict_stack = [(tree, -1)]
+
+        for i, line in enumerate(lines):
+            # Skip empty lines
+            if not line.strip():
+                continue
+
+            # Replace tabs with specified number of spaces
+            line = line.replace("\t", " " * tab_width).rstrip()
+
+            # Compute indentation and clean name
+            indent_level = len(line) - len(line.lstrip())
+            current_name = line.strip()
+
+            # Find the correct parent dictionary based on indentation
+            while dict_stack and dict_stack[-1][1] >= indent_level:
+                dict_stack.pop()
+
+            # If stack is empty, something went wrong with indentation
+            if not dict_stack:
+                raise ValueError(f"Invalid indentation for line: {line}")
+
+            # Get the current parent dictionary
+            parent_dict, _ = dict_stack[-1]
+
+            # Determine if it's a directory
+            # 1. Explicitly marked with '/'
+            # 2. Has children on next lines with more indentation
+            is_dir = current_name.endswith("/") or (
+                i < len(lines) - 1
+                and len(lines[i + 1]) - len(lines[i + 1].lstrip()) > indent_level
+            )
+
+            # Normalize directory name
+            if is_dir and not current_name.endswith("/"):
+                current_name += "/"
+
+            # Add item to the dictionary
+            if is_dir:
+                # Create a new nested dictionary for directories
+                new_dict = {}
+                parent_dict[current_name] = new_dict
+                # Push new dictionary and its indentation to the stack
+                dict_stack.append((new_dict, indent_level))
+            else:
+                # Add files with empty string value
+                parent_dict[current_name] = ""
+
+        return tree
+
+    # Call the internal parsing function and return its result
+    return _parse_tree(lines)
+
+
+def decorate_output(output_str, decoration_type):
+    """
+    Decorate the output based on the specified decoration type
+
+    :param output_str: JSON string to be decorated
+    :param decoration_type: Type of decoration to apply
+    :return: Decorated output string
+    """
+    if decoration_type == "bids-filetree":
+        return f"{{{{ MACROS___make_filetree_example(\n\n{output_str}\n\n) }}}}"
+    return output_str
+
+
+def main():
+    # Set up argument parsing
+    parser = argparse.ArgumentParser(
+        description="Parse file tree hierarchy into a nested dictionary."
+    )
+    parser.add_argument(
+        "input_file",
+        nargs="?",
+        type=argparse.FileType("r"),
+        default=sys.stdin,
+        help="Input file to parse (default: stdin)",
+    )
+    parser.add_argument(
+        "--tab-width",
+        type=int,
+        default=4,
+        help="Number of spaces to replace tabs with (default: 4)",
+    )
+    parser.add_argument(
+        "--output-file",
+        type=str,
+        default=None,
+        help="Output file to write the parsed dictionary (default: stdout)",
+    )
+    parser.add_argument(
+        "--indent", type=int, default=2, help="Indentation for JSON output (default: 2)"
+    )
+    parser.add_argument(
+        "-D",
+        "--decorate",
+        type=str,
+        choices=["bids-filetree"],
+        default=None,
+        help="Decorate the output with a specific format",
+    )
+
+    # Parse arguments
+    args = parser.parse_args()
+
+    # Parse the file tree
+    result = parse_file_tree(args.input_file, args.tab_width)
+
+    # Prepare output using json.dumps with specified indent
+    output_str = json.dumps(result, indent=args.indent)
+
+    # Decorate output if specified
+    if args.decorate:
+        output_str = decorate_output(output_str, args.decorate)
+
+    # Determine output destination
+    if args.output_file:
+        # Write to file
+        with open(args.output_file, "w") as f:
+            f.write(output_str)
+    else:
+        # Print to stdout
+        print(output_str)
+
+
+def test_example1():
+    """
+    Test parsing a file tree with nested directories
+    """
+    input_tree = """file1
+a.dat
+sub-1
+  subsub
+    file.dat
+  filehere
+anotherfile"""
+
+    expected_output = {
+        "file1": "",
+        "a.dat": "",
+        "sub-1/": {"subsub/": {"file.dat": ""}, "filehere": ""},
+        "anotherfile": "",
+    }
+
+    # Parse the input tree
+    result = parse_file_tree(input_tree)
+
+    # Use deep comparison to check the result
+    assert result == expected_output, f"Expected {expected_output}, but got {result}"
+
+
+def test_decorations():
+    """
+    Test the output decoration functionality
+    """
+    dummy_json = '{"test": "value"}'
+
+    # Test bids-filetree decoration
+    decorated = decorate_output(dummy_json, "bids-filetree")
+    assert (
+        decorated == '{{ MACROS___make_filetree_example(\n\n{"test": "value"}\n\n) }}'
+    )
+
+    # Test no decoration
+    undecorated = decorate_output(dummy_json, None)
+    assert undecorated == dummy_json
+
+
+def test_more_complex_tree():
+    """
+    Test a more complex nested directory structure
+    """
+    input_tree = """root
+  subdir1
+    file1.txt
+    subsubdir
+      file2.txt
+  subdir2
+    file3.txt"""
+
+    expected_output = {
+        "root/": {
+            "subdir1/": {"file1.txt": "", "subsubdir/": {"file2.txt": ""}},
+            "subdir2/": {"file3.txt": ""},
+        }
+    }
+
+    # Parse the input tree
+    result = parse_file_tree(input_tree)
+
+    # Use deep comparison to check the result
+    assert result == expected_output, f"Expected {expected_output}, but got {result}"
+
+
+def test_neuroimaging_dataset():
+    """
+    Test parsing a complex neuroimaging dataset file structure
+    """
+    input_tree = """dataset_description.json
+tasks.tsv
+tasks.json
+participants.tsv
+sub-A/
+  ses-20220101/
+    ephys/
+        sub-A_ses-20220101_task-nosepoke_ephys.nix
+        sub-A_ses-20220101_task-nosepoke_ephys.json
+        sub-A_ses-20220101_task-nosepoke_events.tsv
+        sub-A_ses-20220101_task-rest_ephys.nix
+        sub-A_ses-20220101_task-rest_ephys.json
+        sub-A_ses-20220101_channels.tsv
+        sub-A_ses-20220101_electrodes.tsv
+        sub-A_ses-20220101_probes.tsv
+  ses-20220102/
+    ephys/
+        sub-A_ses-20220102_task-rest_ephys.nix
+        sub-A_ses-20220102_task-rest_ephys.json
+        sub-A_ses-20220102_channels.tsv
+        sub-A_ses-20220102_electrodes.tsv
+        sub-A_ses-20220102_probes.tsv"""
+
+    expected_output = {
+        "dataset_description.json": "",
+        "tasks.tsv": "",
+        "tasks.json": "",
+        "participants.tsv": "",
+        "sub-A/": {
+            "ses-20220101/": {
+                "ephys/": {
+                    "sub-A_ses-20220101_task-nosepoke_ephys.nix": "",
+                    "sub-A_ses-20220101_task-nosepoke_ephys.json": "",
+                    "sub-A_ses-20220101_task-nosepoke_events.tsv": "",
+                    "sub-A_ses-20220101_task-rest_ephys.nix": "",
+                    "sub-A_ses-20220101_task-rest_ephys.json": "",
+                    "sub-A_ses-20220101_channels.tsv": "",
+                    "sub-A_ses-20220101_electrodes.tsv": "",
+                    "sub-A_ses-20220101_probes.tsv": "",
+                }
+            },
+            "ses-20220102/": {
+                "ephys/": {
+                    "sub-A_ses-20220102_task-rest_ephys.nix": "",
+                    "sub-A_ses-20220102_task-rest_ephys.json": "",
+                    "sub-A_ses-20220102_channels.tsv": "",
+                    "sub-A_ses-20220102_electrodes.tsv": "",
+                    "sub-A_ses-20220102_probes.tsv": "",
+                }
+            },
+        },
+    }
+
+    # Parse the input tree
+    result = parse_file_tree(input_tree)
+
+    # Use deep comparison to check the result
+    assert result == expected_output, f"Expected {expected_output}, but got {result}"
+
+
+if __name__ == "__main__":
+    # If run directly, execute main
+    main()