Merge branch 'dev' into 'master'

Version 1.7.0

See merge request SPSP/transfer-tool!9

.gitlab-ci.yml

-# 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

spsp

@@ -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