diff iscc_similarity_parse_output.py @ 0:9fee6d81910d draft default tip

planemo upload for repository https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/iscc-sum commit 6db86b8b65a0e05b7f3541d505fbe900633fc72a

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/iscc_similarity_parse_output.py	Fri Dec 19 15:02:49 2025 +0000
@@ -0,0 +1,158 @@
+#!/usr/bin/env python
+"""
+Parse ISCC similarity output into tabular format with unique identifiers.
+
+Input format (from iscc-sum --similar):
+    ISCC:K4AOMG... *file1.txt
+      ~08 ISCC:K4AOMG... *file2.txt
+      ~10 ISCC:K4AOMG... *file3.txt
+    ISCC:K4AGSPO... *file4.txt
+
+Output format (tabular with 7 columns, bidirectional):
+    file_id      filename    iscc_code    match_id     match_filename    match_iscc_hash    distance
+    23  file1.txt   K4AOMG...    24  file2.txt         K4AOMG...          8
+    24  file2.txt   K4AOMG...    23  file1.txt         K4AOMG...          8
+    25  file4.txt   K4AGSPO...                                                      -1
+"""
+import argparse
+
+
+def clean_filename(filename):
+    """Remove directory prefix from filename."""
+    # Remove 'input_files/' prefix if present
+    if filename.startswith('input_files/'):
+        filename = filename[len('input_files/'):]
+
+    return filename
+
+
+def load_id_mapping(mapping_file):
+    """Load filename to element_identifier mapping.
+
+    Returns: dict mapping cleaned filename -> element_identifier
+    """
+    mapping = {}
+    with open(mapping_file, 'r') as f:
+        for line in f:
+            parts = line.strip().split('\t')
+            if len(parts) == 2:
+                filename, element_id = parts
+                # Clean the filename the same way as in parse
+                cleaned = clean_filename(filename)
+                mapping[cleaned] = element_id
+    return mapping
+
+
+def parse_iscc_line(line):
+    """Parse ISCC line and extract code and filename.
+
+    Format: "ISCC:CODE *filename" or "  ~NN ISCC:CODE *filename"
+    Returns: (code, filename) or (None, None) if parse fails
+    """
+    # Find the * separator
+    if ' *' not in line:
+        return None, None
+
+    # Split on ' *' to get code part and filename
+    parts = line.split(' *', 1)
+    code_part = parts[0].strip()
+    filename = clean_filename(parts[1].strip())
+
+    # Extract CODE (after 'ISCC:')
+    if 'ISCC:' in code_part:
+        code = code_part.split('ISCC:', 1)[1].strip()
+    else:
+        code = ''
+
+    return code, filename
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        description='Parse ISCC similarity output into tabular format'
+    )
+    parser.add_argument(
+        'similarity_raw',
+        help='Raw similarity output from iscc-sum --similar'
+    )
+    parser.add_argument(
+        'id_mapping',
+        help='TSV file mapping filenames to element identifiers'
+    )
+    parser.add_argument(
+        'output_file',
+        help='Tabular output file'
+    )
+    args = parser.parse_args()
+
+    # Load ID mapping
+    id_map = load_id_mapping(args.id_mapping)
+
+    # Parse similarity output
+    file_codes = {}  # filename -> code mapping
+    matches = []  # List of (file1, code1, file2, code2, distance)
+    current_ref = None
+    current_code = None
+
+    with open(args.similarity_raw, 'r') as f:
+        for line in f:
+            line = line.rstrip()
+            if not line:
+                continue
+
+            if line.startswith('ISCC:'):
+                # Reference file: "ISCC:CODE *filename"
+                code, filename = parse_iscc_line(line)
+                if code and filename:
+                    current_ref = filename
+                    current_code = code
+                    file_codes[filename] = code
+
+            elif line.startswith(' ') and current_ref:
+                # Similar file: "  ~NN ISCC:CODE *filename"
+                parts = line.strip().split(None, 1)  # Split on first whitespace
+                if len(parts) == 2:
+                    dist_str = parts[0].replace('~', '')
+                    distance = int(dist_str)
+
+                    # Parse the rest of the line for ISCC and filename
+                    code, filename = parse_iscc_line(parts[1])
+
+                    if code and filename:
+                        matches.append((current_ref, current_code, filename, code, distance))
+                        file_codes[filename] = code
+    # Write output with identifiers
+    with open(args.output_file, 'w') as out:
+        # Write header (7 columns)
+        out.write("file_id\tfilename\tiscc_code\tmatch_id\tmatch_filename\tmatch_iscc_code\tdistance\n")
+
+        # Track which files have matches
+        files_with_matches = set()
+
+        # Write similarity matches in both directions
+        for file1, code1, file2, code2, distance in matches:
+            # Get element identifiers
+            file1_name = id_map[file1]
+            file2_name = id_map[file2]
+            file1_id = str.split(file1, '_', 1)[0]  # Extract ID from filename
+            file2_id = str.split(file2, '_', 1)[0]  # Extract ID from filename
+
+            # Write A -> B (file_id is the numeric ID, filename is the element_identifier)
+            out.write(f"{file1_id}\t{file1_name}\t{code1}\t{file2_id}\t{file2_name}\t{code2}\t{distance}\n")
+            # Write B -> A (bidirectional)
+            out.write(f"{file2_id}\t{file2_name}\t{code2}\t{file1_id}\t{file1_name}\t{code1}\t{distance}\n")
+
+            files_with_matches.add(file1)
+            files_with_matches.add(file2)
+
+        # Write files with no matches (distance = -1, empty match columns)
+        for filename in sorted(file_codes.keys()):
+            if filename not in files_with_matches:
+                file_id = str.split(filename, '_', 1)[0]  # Extract ID from filename
+                element_name = id_map[filename]
+                code_val = file_codes[filename]
+                out.write(f"{file_id}\t{element_name}\t{code_val}\t\t\t\t-1\n")
+
+
+if __name__ == '__main__':
+    main()