Commit 0ef7e348 authored by Dillenn Terumalai's avatar Dillenn Terumalai
Browse files

Merge branch 'dev' into 'master'

Version 1.7.0

See merge request !9
parents 828ea393 acaba857
Pipeline #1700 passed with stage
in 22 seconds
# SPSP Transfer Tool CI/CD
stages:
- test
- deploy
......@@ -25,6 +24,8 @@ centos test:
- logs/spsp*.log
expire_in: 1 week
when: on_failure
only:
- merge_requests
debian test:
image: debian:10
......@@ -33,7 +34,6 @@ debian test:
- apt-get install -y netcat
- apt-get install -y gpg
- apt-get install -y openssh-client
- apt-get install -y gpg
- mkdir -p ~/.ssh
- echo "$SSH_PRIVATE_KEY" >> ~/.ssh/id_ed25519
- chmod 600 ~/.ssh/id_ed25519
......@@ -43,14 +43,39 @@ debian test:
script:
- ./spsp init --without-env
- ./spsp test --without-env
inherit:
default: false
artifacts:
paths:
- logs/error.log
- logs/spsp*.log
expire_in: 1 week
when: on_failure
only:
- merge_requests
ubuntu test:
image: ubuntu:20.04
before_script:
- apt-get update
- apt-get install -y netcat
- apt-get install -y gnupg2
- apt-get install -y openssh-client
- mkdir -p ~/.ssh
- echo "$SSH_PRIVATE_KEY" >> ~/.ssh/id_ed25519
- chmod 600 ~/.ssh/id_ed25519
- echo -e "Host *\n\tStrictHostKeyChecking no\n\n" > ~/.ssh/config
stage: test
script:
- ./spsp init --without-env
- ./spsp test --without-env
artifacts:
paths:
- logs/error.log
- logs/spsp*.log
expire_in: 1 week
when: on_failure
only:
- merge_requests
release:
stage: deploy
......
......@@ -2,7 +2,7 @@
# SPSP transfer-tool is developed and maintained by SIB. For more information, please contact spsp-support@sib.swiss
VERSION="1.6.0" # bumped to support spsp --help, spsp --version
VERSION="1.7.0" # bumped to support spsp --help, spsp --version
# Define colors that are used in the help screen
......@@ -234,7 +234,7 @@ autoMode() {
if [ -d "$DIRECTORY" ] && [ "$DIRECTORY" != $OUTBOX ] && [ "$DIRECTORY" != $SENT ] && [ "$DIRECTORY" != $LOGS ]; then
if ls "$DIRECTORY"/*.fastq* 1> /dev/null 2>&1 && ls "$DIRECTORY"/*.xlsx 1> /dev/null 2>&1; then
if ls "$DIRECTORY"/*.fast* 1> /dev/null 2>&1 && ls "$DIRECTORY"/*.xlsx 1> /dev/null 2>&1; then
if [[ "$*" == *--fake* ]] || [[ "$*" == *-F* ]]; then
compressFolder "$DIRECTORY"
......@@ -273,8 +273,8 @@ autoMode() {
else
((ERRORS=ERRORS+1))
((STEP_ERRORS=STEP_ERRORS+1))
echo "[$(date +"%T")] local.ERROR: Missing files (*.fastq/.fastq.gz and/or *.xlsx) inside $DIRECTORY of $VIRUSES DIRECTORY" >> "../$LOGFILE"
echo "[$(date +"%F %T")] local.ERROR: Missing files (*.fastq/.fastq.gz and/or *.xlsx) inside $DIRECTORY of $VIRUSES DIRECTORY" >> "../$ERRORLOGFILE"
echo "[$(date +"%T")] local.ERROR: Missing files (*.fasta/.fastq/.fastq.gz and/or *.xlsx) inside $DIRECTORY of $VIRUSES DIRECTORY" >> "../$LOGFILE"
echo "[$(date +"%F %T")] local.ERROR: Missing files (*.fasta/.fastq/.fastq.gz and/or *.xlsx) inside $DIRECTORY of $VIRUSES DIRECTORY" >> "../$ERRORLOGFILE"
fi
fi
......@@ -288,7 +288,7 @@ autoMode() {
if [ -d "$DIRECTORY" ] && [ "$DIRECTORY" != $OUTBOX ] && [ "$DIRECTORY" != $SENT ] && [ "$DIRECTORY" != $LOGS ]; then
if ls "$DIRECTORY"/*.fastq* 1> /dev/null 2>&1 && ls "$DIRECTORY"/*.xlsx 1> /dev/null 2>&1; then
if ls "$DIRECTORY"/*.fast* 1> /dev/null 2>&1 && ls "$DIRECTORY"/*.xlsx 1> /dev/null 2>&1; then
if [[ "$*" == *--fake* ]] || [[ "$*" == *-F* ]]; then
compressFolder "$DIRECTORY"
......@@ -327,8 +327,8 @@ autoMode() {
else
((ERRORS=ERRORS+1))
((STEP_ERRORS=STEP_ERRORS+1))
echo "[$(date +"%T")] local.ERROR: Missing files (*.fastq/.fastq.gz and/or *.xlsx) inside $DIRECTORY of $BACTERIA DIRECTORY" >> "../$LOGFILE"
echo "[$(date +"%F %T")] local.ERROR: Missing files (*.fastq/.fastq.gz and/or *.xlsx) inside $DIRECTORY of $BACTERIA DIRECTORY" >> "../$ERRORLOGFILE"
echo "[$(date +"%T")] local.ERROR: Missing files (*.fasta/.fastq/.fastq.gz and/or *.xlsx) inside $DIRECTORY of $BACTERIA DIRECTORY" >> "../$LOGFILE"
echo "[$(date +"%F %T")] local.ERROR: Missing files (*.fasta/.fastq/.fastq.gz and/or *.xlsx) inside $DIRECTORY of $BACTERIA DIRECTORY" >> "../$ERRORLOGFILE"
fi
fi
done
......@@ -494,9 +494,15 @@ generateFakeFiles() {
rm -rf ./$VIRUSES/fake-viruses/*
truncate -s 5M ./$VIRUSES/fake-viruses/fake-viruses.xlsx
for i in {1..10}; do
for i in {1..3}; do
truncate -s 1G ./$VIRUSES/fake-viruses/fake-virus${i}.fastq.gz
done
for i in {1..3}; do
truncate -s 1G ./$VIRUSES/fake-viruses/fake-virus${i}.fastq
done
for i in {1..3}; do
truncate -s 1G ./$VIRUSES/fake-viruses/fake-virus${i}.fasta
done
if [ ! -d "$BACTERIA/fake-bacteria" ]; then
mkdir -p $BACTERIA/fake-bacteria
......@@ -505,9 +511,15 @@ generateFakeFiles() {
rm -rf ./$BACTERIA/fake-bacteria/*
truncate -s 5M ./$BACTERIA/fake-bacteria/bacteria.xlsx
for i in {1..10}; do
for i in {1..3}; do
truncate -s 1G ./$BACTERIA/fake-bacteria/bacteria${i}.fastq.gz
done
for i in {1..3}; do
truncate -s 1G ./$BACTERIA/fake-bacteria/bacteria${i}.fastq
done
for i in {1..3}; do
truncate -s 1G ./$BACTERIA/fake-bacteria/bacteria${i}.fasta
done
autoMode --fake --no-archive
......
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