From 4e5406c221e91ede93d9d8036110da62c86cca66 Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Tue, 14 Dec 2021 12:58:25 +0100
Subject: [PATCH] Add helper script to find duplicate test YAML md5s (#1167)

* Add helper script to find duplicate test YAML md5s

* Count how many modules the duplicates affect
---
 .github/check_duplicate_md5s.py | 82 +++++++++++++++++++++++++++++++++
 1 file changed, 82 insertions(+)
 create mode 100644 .github/check_duplicate_md5s.py

diff --git a/.github/check_duplicate_md5s.py b/.github/check_duplicate_md5s.py
new file mode 100644
index 00000000..60506ab5
--- /dev/null
+++ b/.github/check_duplicate_md5s.py
@@ -0,0 +1,82 @@
+#!/usr/bin/env python
+
+from rich import print
+from rich.table import Table
+import click
+import glob
+import os
+import yaml
+
+
+@click.command()
+@click.option(
+    "--min_dups",
+    default=5,
+    show_default=True,
+    help="Minimum number of duplicates to report",
+)
+@click.option(
+    "--search_dir",
+    default=f"{os.path.dirname(__file__)}/../tests/**/test.yml",
+    show_default=True,
+    help="Glob directory pattern used to find test YAML files",
+)
+def find_duplicate_md5s(min_dups, search_dir):
+    """
+    Find duplicate file MD5 sums in test YAML files.
+    """
+    md5_filenames = {}
+    md5_output_fn_counts = {}
+    module_counts = {}
+
+    # Loop through all files in tests/ called test.yml
+    for test_yml in glob.glob(search_dir, recursive=True):
+        # Open file and parse YAML
+        with open(test_yml, "r") as fh:
+            test_config = yaml.safe_load(fh)
+            # Loop through tests and check for duplicate md5s
+            for test in test_config:
+                for test_file in test.get("files", []):
+                    if "md5sum" in test_file:
+                        md5 = test_file["md5sum"]
+                        md5_filenames[md5] = md5_filenames.get(md5, []) + [
+                            os.path.basename(test_file.get("path"))
+                        ]
+                        md5_output_fn_counts[md5] = md5_output_fn_counts.get(md5, 0) + 1
+                        # Log the module that this md5 was in
+                        modname = os.path.basename(os.path.dirname(test_yml))
+                        # If tool/subtool show the whole thing
+                        # Ugly code but trying to stat os-agnostic
+                        if os.path.basename(
+                            os.path.dirname(os.path.dirname(test_yml))
+                        ) not in ["modules", "config", "subworkflows"]:
+                            modname = "{}/{}".format(
+                                os.path.basename(
+                                    os.path.dirname(os.path.dirname(test_yml))
+                                ),
+                                os.path.basename(os.path.dirname(test_yml)),
+                            )
+                        module_counts[md5] = module_counts.get(md5, []) + [modname]
+
+    # Set up rich table
+    table = Table(title="Duplicate MD5s", row_styles=["dim", ""])
+    table.add_column("MD5", style="cyan", no_wrap=True)
+    table.add_column("Count", style="magenta", justify="right")
+    table.add_column("Num modules", style="blue", justify="right")
+    table.add_column("Filenames", style="green")
+
+    # Add rows - sort md5_output_fn_counts by value
+    for md5 in sorted(md5_output_fn_counts, key=md5_output_fn_counts.get):
+        if md5_output_fn_counts[md5] >= min_dups:
+            table.add_row(
+                md5,
+                str(md5_output_fn_counts[md5]),
+                str(len(set(module_counts[md5]))),
+                ", ".join(set(md5_filenames[md5])),
+            )
+
+    print(table)
+
+
+if __name__ == "__main__":
+    find_duplicate_md5s()