<commit_before>#!/bin/bash

set -e

export ARASTURL=192.168.127.12
export PATH=/kb/deployment/bin:$PATH

TEST_DIR="test_${$}"

function message {
    echo
    echo
    echo
    echo
    echo "##########################"
    echo "#"
    echo "# $1"
    echo "#"
    echo "##########################"
    echo
    echo
    echo
    echo
}


message "Check queue status"
arast -s $ARASTURL stat

message "Download synthetic metagenome (200MB)"
rm -f smg.fa
# curl -OL http://www.mcs.anl.gov/~fangfang/test/smg.fa
wget http://www.mcs.anl.gov/~fangfang/test/smg.fa

message "Submit synthetic  metagenome for kiki assembly and bwa mapping validation"
arast -s $ARASTURL run -a kiki -f smg.fa --bwa

message "Check job status"
sleep 2
arast -s $ARASTURL stat
sleep 5

message "Check random data status"
arast -s $ARASTURL stat --data 1
sleep 5

message "Wait 90s for job to finish and download results"
sleep 90
arast -s $ARASTURL get

message "Tests Complete: PASSED"<commit_msg>minor update<commit_after>#!/bin/bash

set -e

export ARASTURL=192.168.127.12
export PATH=/kb/deployment/bin:$PATH

TEST_DIR="test_${$}"

function message {
    echo
    echo
    echo
    echo
    echo "##########################"
    echo "#"
    echo "# $1"
    echo "#"
    echo "##########################"
    echo
    echo
    echo
    echo
}


message "Check queue status"
arast -s $ARASTURL stat

message "Download synthetic metagenome (200MB)"
rm -f smg.fa
# curl -OL http://www.mcs.anl.gov/~fangfang/test/smg.fa
wget http://www.mcs.anl.gov/~fangfang/test/smg.fa

message "Submit synthetic  metagenome for kiki assembly and bwa mapping validation"
$jobid=`arast -s $ARASTURL run -a kiki -f smg.fa --bwa`

message "Check job status"
sleep 2
arast -s $ARASTURL stat
sleep 5

message "Check random data status"
arast -s $ARASTURL stat --data 1
sleep 5

message "Wait 90s for job to finish and download results"
sleep 90
arast -s $ARASTURL get $jobid

message "Tests Complete: PASSED"
{'fraction_non_alphanumeric': 0.15843097300050943, 'fraction_numerical': 0.023433520122261846, 'mean_word_length': 3.354767184035477, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 4, 'xml': 0}, 'pii_count': 2, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 4, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4530476', 'n_tokens_mistral': 742, 'n_tokens_neox': 697, 'n_words': 221}