<commit_before>#!/bin/bash
#set -o errexit

# testing decoding run.json in awsem
# CWL
python awsf/aws_decode_run_json.py tests/awsf/bqLd8oa7Tdzq.run.json
python awsf/aws_decode_run_json.py tests/awsf/qD9zkkqAWjnE.run.json  # double-nested

# WDL
python awsf/aws_decode_run_json.py tests/awsf/wdl/pzn3Us98y21I.run.json   # nested
python awsf/aws_decode_run_json.py tests/awsf/wdl/uGeIte1giKxt.run.json  # double-nested

# shell
python awsf/aws_decode_run_json.py tests/awsf/bqLd8oa7Tdzr.run.json
if [[ $(grep COMMAND env_command_list.txt | wc -l) != "1" ]]
then
    exit 1
fi


## testing output upload / postrun json creation
# test for cwl
python awsf/aws_upload_output_update_json.py tests/awsf/bqLd8oa7Tdzq.run.json tests/awsf/bqLd8oa7Tdzq.log.json tests/awsf/bqLd8oa7Tdzq.LOG tests/awsf/bqLd8oa7Tdzq.md5sum.txt tests/awsf/bqLd8oa7Tdzq.postrun.json.out

# test for shell
python awsf/aws_upload_output_update_json.py tests/awsf/bqLd8oa7Tdzr.run.json - tests/awsf/bqLd8oa7Tdzr.log tests/awsf/bqLd8oa7Tdzq.md5sum.txt tests/awsf/bqLd8oa7Tdzq.postrun.json.out shell

# test for wdl
# commented out since they will produce 'file not found error'. They work only if the files to upload exist.
#python awsf/aws_upload_output_update_json.py tests/awsf/wdl/a3T0RlZ09WuR.run.json tests/awsf/wdl/a3T0RlZ09WuR.log.json tests/awsf/wdl/a3T0RlZ09WuR.log tests/awsf/wdl/a3T0RlZ09WuR.md5sum.txt tests/awsf/wdl/a3T0RlZ09WuR.postrun.json.out wdl
#python awsf/aws_upload_output_update_json.py tests/awsf/wdl/a3T0RlZ09WuS.run.json tests/awsf/wdl/a3T0RlZ09WuS.log.json tests/awsf/wdl/a3T0RlZ09WuS.log tests/awsf/wdl/a3T0RlZ09WuS.md5sum.txt tests/awsf/wdl/a3T0RlZ09WuS.postrun.json.out wdl  # test for alt_cond_output_argnames
<commit_msg>very minor typo<commit_after>#!/bin/bash
#set -o errexit

# testing decoding run.json in awsem
# CWL
python awsf/aws_decode_run_json.py tests/awsf/bqLd8oa7Tdzq.run.json
python awsf/aws_decode_run_json.py tests/awsf/qD9zkkqAWjnE.run.json  # double-nested

# WDL
python awsf/aws_decode_run_json.py tests/awsf/wdl/pzn3Us98y21I.run.json   # nested
python awsf/aws_decode_run_json.py tests/awsf/wdl/uGeIte1giKxt.run.json  # double-nested

# shell
python awsf/aws_decode_run_json.py tests/awsf/bqLd8oa7Tdzr.run.json
if [[ $(grep COMMAND env_command_list.txt | wc -l) != "1" ]]
then
    exit 1
fi


## testing output upload / postrun json creation
# test for cwl
python awsf/aws_upload_output_update_json.py tests/awsf/bqLd8oa7Tdzq.run.json tests/awsf/bqLd8oa7Tdzq.log.json tests/awsf/bqLd8oa7Tdzq.LOG tests/awsf/bqLd8oa7Tdzq.md5sum.txt tests/awsf/bqLd8oa7Tdzq.postrun.json.out

# test for shell
python awsf/aws_upload_output_update_json.py tests/awsf/bqLd8oa7Tdzr.run.json - tests/awsf/bqLd8oa7Tdzr.log tests/awsf/bqLd8oa7Tdzq.md5sum.txt tests/awsf/bqLd8oa7Tdzr.postrun.json.out shell

# test for wdl
# commented out since they will produce 'file not found error'. They work only if the files to upload exist.
#python awsf/aws_upload_output_update_json.py tests/awsf/wdl/a3T0RlZ09WuR.run.json tests/awsf/wdl/a3T0RlZ09WuR.log.json tests/awsf/wdl/a3T0RlZ09WuR.log tests/awsf/wdl/a3T0RlZ09WuR.md5sum.txt tests/awsf/wdl/a3T0RlZ09WuR.postrun.json.out wdl
#python awsf/aws_upload_output_update_json.py tests/awsf/wdl/a3T0RlZ09WuS.run.json tests/awsf/wdl/a3T0RlZ09WuS.log.json tests/awsf/wdl/a3T0RlZ09WuS.log tests/awsf/wdl/a3T0RlZ09WuS.md5sum.txt tests/awsf/wdl/a3T0RlZ09WuS.postrun.json.out wdl  # test for alt_cond_output_argnames

{'fraction_non_alphanumeric': 0.10116279069767442, 'fraction_numerical': 0.0436046511627907, 'mean_word_length': 5.090265486725664, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4509818', 'n_tokens_mistral': 1662, 'n_tokens_neox': 1603, 'n_words': 218}