From 26174557d40f4643b8c506c0cdfa66503b18544e Mon Sep 17 00:00:00 2001 From: Tom Clegg Date: Tue, 25 Jun 2013 11:57:20 -0400 Subject: [PATCH] fix permissions and bugs, use decompressed_name in output --- crunch_scripts/grep | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) mode change 100644 => 100755 crunch_scripts/grep diff --git a/crunch_scripts/grep b/crunch_scripts/grep old mode 100644 new mode 100755 index 6392e0c9e7..908cea2048 --- a/crunch_scripts/grep +++ b/crunch_scripts/grep @@ -1,20 +1,21 @@ #!/usr/bin/env python import arvados +import string arvados.job_setup.one_task_per_input_file(if_sequence=0, and_end_task=True) this_job = arvados.current_job() this_task = arvados.current_task() this_task_input = this_task['parameters']['input'] -search_string = this_task['parameters']['pattern'] +search_string = this_job['script_parameters']['pattern'] input_file = list(arvados.CollectionReader(this_task_input).all_files())[0] out = arvados.CollectionWriter() -out.set_current_file_name(input_file.name()) +out.set_current_file_name(input_file.decompressed_name()) out.set_current_stream_name(input_file.stream_name()) for line in input_file.readlines(): - if string.find(line, search_string): + if 0 <= string.find(line, search_string): out.write(line) this_task.set_output(out.finish()) -- 2.30.2