Commit ef2397f4 authored by Vincent Stehlé's avatar Vincent Stehlé
Browse files identify the sequence file

We add a database of the sequence files we know about with their sha256,
and we try to identify the input sequence file among those.

A `--seq-db' option is added to allow specifying the database.

Update documentation accordingly. While at it, fix spacing.
Signed-off-by: Vincent Stehlé's avatarVincent Stehlé <>
parent 126803b3
......@@ -265,13 +265,29 @@ override the result of some tests with the following ones:
filesystem implementation limitations and they do
not prevent an OS to boot.
`KNOWN ACS LIMITATION` Genuine bugs, which are fixed in a more recent version
of the ACS or which must ultimately be fixed and which
we know about.
`KNOWN ACS LIMITATION` Genuine bugs, which are fixed in a more recent
version of the ACS or which must ultimately be fixed
and which we know about.
Some of the rules just add a `comments` field with some help text.
### Database of sequence files
The `seq.db` file contains a list of known sequence files, which allows to
identify the input sequence file.
This database file contains lines describing each known sequence file in turn,
in the following format:
sha256 description
Everything appearing after a '#' sign is treated as a comment and ignored.
The database filename can be specified with the `--seq-db` option.
## Notes
### Known Issues:
* "comment" is currently not implemented, as formatting is not currently consistent, should reflect the comments from the test.
......@@ -8,6 +8,8 @@ import csv
import logging
import json
import re
import hashlib
import os
from packaging import version
......@@ -600,6 +602,50 @@ def combine_dbs(db1, db2):
return cross_check
# Load the database of known sequence files.
def load_known_seq(seq_db):
known_seqs = {}
with open(seq_db, 'r') as f:
for line in f:
line = line.rstrip()
line = re.sub(r'#.*', '', line)
m = re.match(r'\s*([0-9a-fA-F]+)\s+(.*)', line)
if not m:
kh =
d =
assert(kh not in known_seqs)
logging.debug(f'{kh} {d}')
known_seqs[kh] = d
logging.debug(f'{len(known_seqs)} known seq file(s)')
return known_seqs
# Try to identify the .seq file in a list of known versions using its sha256.
def ident_seq(seq_file, seq_db):
known_seqs = load_known_seq(seq_db)
# Hash seq file
hm = 'sha256'
hl =
with open(seq_file, 'rb') as f:
h = hl.hexdigest()
logging.debug(f'{hm} {h} {seq_file}')
# Try to identify the seq file
if h in known_seqs:"""Identified `{seq_file}' as "{known_seqs[h]}".""")
logging.debug(f"Could not identify `{seq_file}'...")
# Read the .ekl log file and the .seq file and combine them into a single
# database, which we return.
def read_log_and_seq(log_file, seq_file):
......@@ -717,6 +763,8 @@ def read_md(input_md):
if __name__ == '__main__':
me = os.path.realpath(__file__)
here = os.path.dirname(me)
parser = argparse.ArgumentParser(
description='Process SCT results.'
' This program takes the SCT summary and sequence files,'
......@@ -743,6 +791,9 @@ if __name__ == '__main__':
'--print', action='store_true', help='Print results to stdout')
parser.add_argument('--input-md', help='Input .md filename')
'--seq-db', help='Known sequence files database filename',
parser.add_argument('log_file', help='Input .ekl filename')
parser.add_argument('seq_file', help='Input .seq filename')
parser.add_argument('find_key', nargs='?', help='Search key')
......@@ -768,6 +819,10 @@ if __name__ == '__main__':
# Command line argument 1 is the ekl file to open.
# Command line argument 2 is the seq file to open.
# Try to identify the sequence file
ident_seq(args.seq_file, args.seq_db)
# Read both and combine them into a single cross_check database.
cross_check = read_log_and_seq(args.log_file, args.seq_file)
# List of known sequence files and their sha256
6a381192057c511b2b69282c58d6107c1daeaf0b95038605d4c58383eb5cc88b Test sample.seq
6ae5a92f0b83b3a1469c89f6a02b0771ae3818a424e7118a28bba053be394078 Supplied SBBR.seq
6b83dbfbd1f07fc61a918297f02f449591a72131b64ac746f969a4210f97aee8 ACS-IR v21.05_0.8_BETA-0 EBBR.seq
c06684b3f8b35871e37b9447f609f9aab6070a7ca1c4ba63a52e029c018c9b73 ACS-IR v21.07_0.9_BETA EBBR.seq
ec730fd81eada415278b39533fe7cc21147b39183447dc11fa77ad4419d13969 Supplied EBBR.seq
f7793d53c10106c1c275a4992e1710ce9863e210dd07581a3d783c4f4cf2312b ACS-IR v21.07_0.9_BETA EBBR_manual.seq
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