Commit 995a6b69 authored by Mathieu Giraud's avatar Mathieu Giraud Committed by Vidjil Team
Browse files

scripts/ option -w, list raw file names

parent f5c0b8b8
......@@ -4,16 +4,22 @@ import vidjil_utils
import argparse
parser = argparse.ArgumentParser(description='Link sequences and/or results file from the DB.',
parser = argparse.ArgumentParser(description='Output shell commands to link sequences and/or results file from the DB to human-readable names',
epilog='At least -s or -r should be used')
parser.add_argument('--sequences', '-s', action='store_true', help='link sequence files')
parser.add_argument('--results', '-r', action='store_true', help='link results files')
parser.add_argument('--diag', '-d', action='store_true', help='link only diagnosis results (first sample per patient)')
parser.add_argument('--filter', '-f', type=str, default='', help='filter on patient name or info (%(default)s), only for -s or -d')
parser.add_argument('--raw', '-w', action='store_true', help='do not link, only display the list of raw files')
args = parser.parse_args()
our_id = 0
def link(from_name, to_name, comments, link):
if link:
print "ln -s %s %s \t# %s" % (from_name, to_name, comments)
print from_name
if args.sequences:
print "### Sequences"
......@@ -25,11 +31,12 @@ if args.sequences:
our_id += 1
print "ln -s %s/%-20s %5s.fa" % (defs.DIR_SEQUENCES, res.sequence_file.data_file, our_id),
print "\t", "# seq-%04d" %, "%-20s" % res.sequence_file.filename,
print "\t", "# pat-%04d (%s %s)" % (, res.patient.first_name, res.patient.last_name)
link("%s/%-20s" % (defs.DIR_SEQUENCES, res.sequence_file.data_file),
"%5s.fa" % our_id,
"seq-%04d %-20s" % (, res.sequence_file.filename)
+ "\t# pat-%04d (%s %s)" % (, res.patient.first_name, res.patient.last_name),
not args.raw)
def last_result_by_file():
for seq in db(db.sequence_file).select():
......@@ -84,9 +91,11 @@ if gen_results:, seq.sampling_date)
our_id = our_id.replace(' ', '-')
print "ln -s %s/%-20s %5s.vidjil" % (defs.DIR_RESULTS, res.results_file.data_file, our_id),
print "\t", "# seq-%04d" %, "%-20s" % seq.filename, "%-10s" % seq.sampling_date,
print "\t", "# pat-%04d (%s %s) - %s" % (, res.patient.first_name, res.patient.last_name,'\n', ' '))
link("%s/%-20s" % (defs.DIR_RESULTS, res.results_file.data_file),
"%5s.vidjil" % our_id,
"seq-%04d %-20s %-10s" % (, seq.filename, seq.sampling_date)
+ "\t# pat-%04d (%s %s) - %s" % (, res.patient.first_name, res.patient.last_name,'\n', ' ')),
not args.raw)
log.debug("=== completed ===")
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