code stringlengths 1 1.96M | language stringclasses 1
value |
|---|---|
rm -f *.ma.*
| Shell |
source ../testsupport.sh
run test.txt
grep -q "Stage world" test.out || err "Failed to execute stage world"
exists test.txt.hello test1.world.xml test*.world.tsv
true
| Shell |
rm -rf test.txt.hello test1.csv test1.world.*
| Shell |
source ../testsupport.sh
run
grep -q "Variable or parameter 'planet' was not specified" test.out || err "Failed to find expected error message when parameter not specified"
bpipe run -p planet=mars test.groovy > test.out
grep -q "hello mars" test.out || err "did not find expected message 'hello mars' in output"
| Shell |
source ../testsupport.sh
run test.txt
exists test.hello.csv
# Note: used to be test.hello.world.csv
# However the refernece to $output2.csv without $output1 referenced is difficult to handle.
# we used to default to naming $output2 the same as $output1 if $output1 was not referenced
# anywhere. However this is trick... | Shell |
rm -f *.csv *.hello
| Shell |
source ../testsupport.sh
run test.txt
exists test.txt.hello test.txt.csv
| Shell |
rm -f *.csv test.txt.*
| Shell |
source ../testsupport.sh
run input*.txt
#grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
#grep -q "Stage world" test.out || err "Failed to find expected stage world"
#grep -q "Stage world2" test.out || err "Failed to find expected stage world2"
#grep -q "Stage end" test.out || err "Failed ... | Shell |
rm -f *.hello *.hello.*
| Shell |
source ../testsupport.sh
rm -f *align*
run
grep -q "An input pattern was specified '.*' but no inputs were given when Bpipe was run" test.out || err "Failed to find expected error message"
true
| Shell |
source ../testsupport.sh
. ./cleanup.sh
run
grep -q "Stage there" test.out || err "Failed to find expected stage there"
grep -q "Stage world" test.out || err "Failed to find expected stage world"
grep -q "Stage buddy" test.out || err "Failed to find expected stage buddy"
grep -q "Stage foo" test.out && err "Observe... | Shell |
rm -f test.world.txt test.there.txt test.buddy.txt
| Shell |
source ../testsupport.sh
run
grep -q "It failed" test.out || err "Failed to find expected text 'It Failed' in output"
bpipe override hello > test.out
run
grep -q "It failed" test.out && err "Found unexpected text 'It Failed' in output"
true
| Shell |
rm -rf .bpipe
| Shell |
source ../testsupport.sh
bpipe run -L chr2 test.groovy test.txt > test.out
exists test.chr2.hello.csv
notexists test.chr1.hello.csv
true
| Shell |
rm -f *.csv
| Shell |
#!/bin/bash
TESTS=${@:-`find . -maxdepth 1 -type d | grep "[A-Za-z]"`}
source testsupport.sh
succ=0
fail=0
failures=""
for t in $TESTS;
do
echo "============== $t ================"
cd "$BASE"/"$t"
rm -rf .bpipe
if ./run.sh;
then
echo
echo "SUCCEEDED"
echo
let 'succ=succ+1'
else
echo
echo "FAILE... | Shell |
source ../testsupport.sh
rm -f test.txt.* test.hello.* test.bar
run test.txt
grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
grep -q "Stage world" test.out || err "Failed to find expected stage world"
run test.txt
grep -q "execute" test.out && err "Failed to find stage being skipped on ... | Shell |
rm -rf *.out *.csv *.xml test.*.txt doc
| Shell |
source ../testsupport.sh
run test.groovy test.csv test1.fastq.gz test2.fastq.gz
grep -q 'Stage hello' test.out || err "Failed to find stage hello in output"
exists test.xml test1_fastqc.zip test2_fastqc.zip test.tsv
| Shell |
rm -f *.xml *.zip *.tsv
| Shell |
source ../testsupport.sh
./cleanup.sh
run
grep -q "Stage init" test.out || err "Failed to find expected stage init"
grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
grep -q "Stage fail" test.out || err "Failed to find expected stage fail"
grep -q "Command failed with exit status" test.out... | Shell |
ls | grep '[0-9].*.txt' | xargs rm -f
rm -f dummy*.log.txt
| Shell |
# Add BPipe from the project root to the path
if [ -z "$BASE" ];
then
BASE=`pwd`
if [ ! -e $BASE/../bin/bpipe ] && [ -e $BASE/../../bin/bpipe ] ;
then
BASE=`pwd`/..
fi
fi
PATH="$BASE/../bin:$PATH"
#which bpipe
if [ $? -ne 0 ]; then
echo Cannot find the 'bpipe' launch script on the path. Please make sure that... | Shell |
source ../testsupport.sh
run
exists foo.txt bar.txt
grep -q "Stage async_stuff" test.out || err "Failed to find expected stage async_stuff in output"
grep -q "Command.*failed" test.out || err "Failed to find expected failed command in output"
grep -q "Exit status = 1" test.out || err "Failed to find expected exit s... | Shell |
rm -f foo.txt bar.txt
| Shell |
source ../testsupport.sh
source ./cleanup.sh
run *.chr*.*vcf *.chr*bam
grep -c chr14 test.out | grep -q 1 || err "Unexpected number of references to chr14 - should be only 1"
grep -c chr15 test.out | grep -q 1 || err "Unexpected number of references to chr15 - should be only 1"
true
| Shell |
rm -f hello.txt
| Shell |
source ../testsupport.sh
run 11D*.txt
[ `grep -c "Stage hello" test.out` == 3 ] || err "Incorrect number of parallel stages from file split: expected 3"
true
| Shell |
rm -f *.hello.txt
| Shell |
source ../testsupport.sh
. cleanup.sh
run test.txt
grep -q "Stage folder" test.out || err "Failed to find expected stage hello"
grep -q "Stage after" test.out || err "Failed to find expected stage world"
[ `grep -c "execute" test.out` == 2 ] || err "Skipped steps incorrectly on first run"
[ ! -f thefolder/output.... | Shell |
rm -rf thefolder *.after.xml .bpipe/outputs
| Shell |
source ../testsupport.sh
run test.bed test.bam
grep Stage test.out | head -2 | grep -q align && err "Found align stage too early"
true
| Shell |
rm -f test.*.*
| Shell |
source ../testsupport.sh
rm -f test.*vcf
run test.txt
grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
grep -q "Stage filter_with_ext" test.out || err "Failed to find expected stage filter_with_ext"
[ ! -f test.vcf ] && err "Failed to find expected output test.vcf"
[ ! -f test.fix.vcf ] &... | Shell |
source ../testsupport.sh
run test.txt
grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
grep -q "Stage world" test.out || err "Failed to find expected stage world"
[ ! -f test.csv ] && err "Failed to find expected output test.csv"
[ ! -f test.xml ] && err "Failed to find expected output tes... | Shell |
rm -f test.xml test.csv
| Shell |
source ../testsupport.sh
rm -f *.csv *.xml
run test.txt
grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
grep -q "Stage world" test.out || err "Failed to find expected stage world"
grep -q "Inputs are test.csv test[0-9].xml test[0-9].xml test[0-9].xml" test.out || err "Failed to find expec... | Shell |
source ../testsupport.sh
run test1.fastq test2.fastq ref.fa
exists test1.paired.bam
grep -q "cat test1.fastq test2.fastq ref.fa" commandlog.txt || err "Failed to find correct command in commandlog.txt"
true
| Shell |
rm -f *.bam
| Shell |
source ../testsupport.sh
run test.txt test1.xml test2.xml
# Both stages should have executed and printed "executing"
grep -q "executing1" test.out || err "Failed to find command 1 executing"
grep -q "executing2" test.out || err "Failed to find command 2 executing"
# Necessary on Macs and others with only 1 second ... | Shell |
rm -f *.csv qcstats.*
| Shell |
source ../testsupport.sh
rm -f test.txt.hello test.csv.world *.hello *.world
run test.txt test.csv
grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
grep -q "Stage world" test.out || err "Failed to find expected stage world"
[ ! -f test.txt.hello ] && err "Failed to find expected output te... | Shell |
source ../testsupport.sh
bpipe run -d outdir test.groovy test.txt
exists outdir/hello.output.world.xml outdir/hello.output.csv
true
| Shell |
rm -rf outdir
| Shell |
source ../testsupport.sh
rm -f test.foo.txt test.foo.bar.txt
run test.txt
grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
grep -q "Stage world" test.out || err "Failed to find expected stage world"
[ ! -f test.foo.txt ] && err "Failed to find expected output test.foo.txt"
[ ! -f test.foo... | Shell |
rm -f test.foo.txt test.foo.bar.txt
| Shell |
source ../testsupport.sh
run
exists test2.csv
| Shell |
rm -rf *.csv .bpipe
| Shell |
source ../testsupport.sh
run test*.txt
exists test_1.world.xml test_2.world.xml
true
| Shell |
rm -f *.csv *.xml
| Shell |
source ../testsupport.sh
run test.txt
exists out/test.hello.csv
bpipe query out/test.hello.csv > test.out 2>&1
grep -q "Command:" test.out || err "Failed to find expected output of query command"
true
| Shell |
rm -rf .bpipe *.csv out
| Shell |
source ../testsupport.sh
run
grep -q "Bpipe test module success once!" test.out || err "Failed to load module"
grep -q "Bpipe test module success again!" test.out || err "Failed to load module"
true
| Shell |
rm -rf .bpipe/outputs
rm -f test.out
rm -f commandlog.txt
rm -fr doc
| Shell |
source ../testsupport.sh
run *.chr14.*vcf *.chr14.*bam
grep -q "MUW09_C0R8HACXX_ATCACG_L001_R1.fastq.merge.dedupe.merge.reorder.rg.recal.chr14.realign.bam => MUW09_C0R8HACXX_ATCACG_L001_R1.fastq.merge.dedupe.merge.reorder.rg.recal.chr14.realign.test.bam" test.out || err "Expected MUW09_C0R8HACXX_ATCACG_L001_R1.fast... | Shell |
source ../testsupport.sh
rm -f test.world.txt test.txt
run *.fastq
grep -q "SureSelect_Capture_11MG2107_AD0AN0ACXX_GATCAG_L002_R1.fastq SureSelect_Capture_11MG2107_AD0AN0ACXX_GATCAG_L002_R2.fastq" test.out || err "Failed to find expected GATCAG files R1 and R2"
grep -q "SureSelect_Capture_11MG2108_AD0AN0ACXX_TAGCTT_... | Shell |
source ../testsupport.sh
rm -f test.txt.*
run test.txt
grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
grep -q "Stage world" test.out || err "Failed to find expected stage world"
grep -q "Stage world2" test.out || err "Failed to find expected stage world2"
grep -q "Stage end" test.out || ... | Shell |
source ../testsupport.sh
run test.txt
exists foo/test.out.txt
| Shell |
rm -rf foo test.out.txt
| Shell |
source ../testsupport.sh
run test*.txt
grep -q "inputs are.*test1.txt.*test2.txt" test.out || err "Failed to find references to split files in output"
true
| Shell |
source ../testsupport.sh
run foo.txt bar.txt
exists foo.txt.hello
| Shell |
rm -f foo.txt.hello
| Shell |
source ../testsupport.sh
. ./cleanup.sh
run test.txt
grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
grep -q "Stage world" test.out || err "Failed to find expected stage world"
[ ! -f test.txt.hello ] && err "Failed to find expected output test.txt"
[ ! -f test.txt.hello.world ] && err "... | Shell |
rm -f test.txt.*
| Shell |
source ../testsupport.sh
run test.vcf test.bam
exists test.extract.bam
true
| Shell |
rm -f *.extract.* test.bed
| Shell |
source ../testsupport.sh
run s_*.txt
grep -q "Stage dedupe" test.out || err "Failed to find expected stage dedupe"
grep -q "Stage align" test.out || err "Failed to find expected stage align"
[ ! -f s_2_1.foo.txt ] && err "Failed to find expected output s_2_1.foo.txt"
[ ! -f s_3_1.foo.txt ] && err "Failed to find ex... | Shell |
rm -f *align* *foo*
| Shell |
source ../testsupport.sh
rm check.txt
run
grep -q "Stage check" test.out || err "Failed to find expected stage check"
[ ! -f check.txt ] && err "Failed to find expected output check.txt"
true
| Shell |
source ../testsupport.sh
# Remove files produced by previous run (if any)
rm -f test.out_1 test.out_2
# Run the test
run test.txt
# Check for valid result
grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
grep -q "Stage world" test.out || err "Failed to find expected stage world"
[ ! -f te... | Shell |
rm test.f*
| Shell |
source ../testsupport.sh
. ./clean.sh
run test.txt
grep -q "Stage hello" test.out || err "Failed to find expected stage hello"
grep -q "Stage world" test.out || err "Failed to find expected stage world"
[ ! -f test.f1.txt ] && err "Failed to find expected output test.f1.txt"
[ ! -f test.f1.f2.txt ] && err "Failed t... | Shell |
source ../testsupport.sh
run test.txt
exists test.hello.world.xml
exists test.hello.world_with_filter.xml
exists test.hello.world_with_mismatch_filter.xml
exists test.hello.csv
bpipe cleanup -y >> test.out
notexists test.hello.world.xml
notexists test.hello.csv
notexists test.hello.world_with_filter.xml
# Because ... | Shell |
rm -rf .bpipe *.xml *.csv
| Shell |
source ../testsupport.sh
run *.txt *.csv
exists "result.out"
exists test1.csv.there.xls test2.csv.there.xls
exists test1.txt.me.xml test2.txt.me.xml
wc result.out | grep -q "4[^0-9]*4" || err "Failed to find correct number of files in result.out"
for i in test1.csv.there.xls test2.csv.there.xls test1.txt.me.xml te... | Shell |
rm -rf *.hello* *.help* *world *.xml *.xls commandlog.txt
| Shell |
source ../testsupport.sh
bpipe run -p planet=Mars test.groovy > test.out 2>&1
exists test.output.txt
grep -q "Hello Mars, from Earth" test.output.txt || err "Expected message not found in file generated from template"
true
| Shell |
rm -rf .bpipe test.output.txt notifications
| Shell |
source ../testsupport.sh
run test.txt test.csv
exists test.over.csv
true
| Shell |
rm -f *.over.*
| Shell |
source ../testsupport.sh
run test.bam test.vcf
exists test.clean.vcf
true
| Shell |
rm -f *.hello.* *.clean.*
| Shell |
source ../testsupport.sh
run test.txt test_*.xsl
exists test.hello.world.there.xml test_1.greetings.bed test_2.greetings.bed
[ `grep -c bar test.hello.world.there.xml` == 2 ] || err "Failed to find 2 lines with bar in test.hello.world.there.xml"
grep -q bar test_1.greetings.bed || err "Failed to find bar in outpu... | Shell |
rm -f *.csv *.tsv *.xml
| Shell |
source ../testsupport.sh
run test1.txt test2.txt
# Note: this used to be test1.hello.goo.txt,
# but since the output is not derived from any input passing through the
# 'hello' stage, it actually makes more sense to be test1.goo.txt.
# That change happened when another bug related to filters
# was fixed - see filt... | Shell |
rm -rf *.goo.txt *.csv *.xml .bpipe
| Shell |
source ../testsupport.sh
run test.txt
exists test.html
grep -q "Oh dear, it failed" test.html || err "Did not find expected message in test.html"
grep -q "Failed" test.html || err "Did not find expected message in test.html"
true
| Shell |
rm -rf .bpipe test.html
| Shell |
source ../testsupport.sh
source ./cleanup.sh
# note option -n 1 is important for this test
bpipe run -n 1 test.groovy s_1.txt > test.out 2>&1
grep -q "Stage how_are_you" test.out || err "Failed to find expected stage how_are_you"
grep -q "Stage take_me_to_your_leader" test.out || err "Failed to find expected stage ... | Shell |
rm -f s_1.txt.*
| Shell |
source ../testsupport.sh
# Run first time - should create files
bpipe run test.groovy > test.out
exists output_dir/test1.foo test*.txt
# Run second time - should SKIP creating files
rm commandlog.txt
echo "============" >> test.out
echo "============ RUN 2" >> test.out
echo "============" >> test.out
bpipe run tes... | Shell |
rm -rf output_dir *.foo *.txt
| Shell |
ant clean; ant release; adb install -r bin/MetaTracker-release.apk
| Shell |
#!/bin/sh
adb shell cat /data/data/com.google.android.apps.iosched/shared_prefs/com.google.android.apps.iosched_preferences.xml | xmllint --format - | Shell |
#!/bin/sh
#
# Copyright 2013 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed ... | Shell |
#!/bin/sh
adb shell pm clear com.google.android.apps.iosched | Shell |
#!/bin/sh
if [[ -z $ADB ]]; then ADB=adb; fi
MAC_UNAME="Darwin"
if [[ "`uname`" == ${MAC_UNAME} ]]; then
DATE_FORMAT="%Y-%m-%dT%H:%M:%S"
else
DATE_FORMAT="%Y-%m-%d %H:%M:%S"
fi
if [ -z "$1" ]; then
NOW_DATE=$(date "+${DATE_FORMAT}")
echo Please provide a mock time in the format \"${NOW_DATE}\" or \"d\" to del... | Shell |
#!/bin/sh
# Remember VERBOSE only works on debug builds of the app
adb shell setprop log.tag.iosched_SyncHelper VERBOSE
adb shell setprop log.tag.iosched_SessionsHandler VERBOSE
adb shell setprop log.tag.iosched_BitmapCache VERBOSE
| Shell |
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