Demo docker system and bug fixing

Dockerfile

@@ -10,7 +10,7 @@ RUN apt-get update && apt-get upgrade -y
 RUN apt-get install -y \
     git wget lsb-core lsb-release
 
-RUN git clone https://github.com/BU-ISCIII/iskylims.git /srv/iskylims
+RUN git clone https://github.com/saramonzon/iskylims.git /srv/iskylims
 WORKDIR /srv/iskylims
 RUN git checkout develop
 
@@ -23,4 +23,4 @@ ENV PYTHONPATH="/opt/iskylims/virtualenv/lib/python3.10/site-packages:${PYTHONPA
 # Expose
 EXPOSE 8001
 # Start the application
-CMD ["python3", "/opt/iskylims/manage.py", "runserver", "0:8001"]
+CMD ["python3", "/opt/iskylims/manage.py", "runserver", "0:8001"]

conf/first_install_tables.json

@@ -1333,48 +1333,6 @@
         "generated_at": "2023-01-23T17:15:24.556"
     }
 },
-{
-    "model": "drylab.resolutionstates",
-    "pk": 1,
-    "fields": {
-        "state_value": "Recorded"
-    }
-},
-{
-    "model": "drylab.resolutionstates",
-    "pk": 2,
-    "fields": {
-        "state_value": "In Progress"
-    }
-},
-{
-    "model": "drylab.resolutionstates",
-    "pk": 3,
-    "fields": {
-        "state_value": "Delivery"
-    }
-},
-{
-    "model": "drylab.resolutionstates",
-    "pk": 4,
-    "fields": {
-        "state_value": "Cancelled"
-    }
-},
-{
-    "model": "drylab.resolutionstates",
-    "pk": 5,
-    "fields": {
-        "state_value": "Rejected"
-    }
-},
-{
-    "model": "drylab.resolutionstates",
-    "pk": 6,
-    "fields": {
-        "state_value": "Queued"
-    }
-},
 {
     "model": "wetlab.poolstates",
     "pk": 1,
@@ -1803,12 +1761,20 @@
 },
 {
     "model": "wetlab.runconfigurationtest",
-    "pk": 4,
+    "pk": 2,
     "fields": {
-        "run_test_name": "NextSeq_Test",
+        "run_test_name": "NextSeq_Test_001",
         "run_test_folder": "NextSeq_Test"
     }
 },
+{
+    "model": "wetlab.runconfigurationtest",
+    "pk": 3,
+    "fields": {
+        "run_test_name": "NovaSeq_Test_001",
+        "run_test_folder": "NovaSeq_Test"
+    }
+},
 {
     "model": "wetlab.configsetting",
     "pk": 1,
@@ -20050,10 +20016,82 @@
     "model": "drylab.servicestate",
     "pk": 8,
     "fields": {
-        "state_value": "waiting_information",
-        "state_display": "Waiting Information",
+        "state_value": "on_hold",
+        "state_display": "On hold",
         "description": "Service is on hold, waiting for user provides more information",
         "show_in_stats": true
     }
+},
+{
+    "model": "drylab.resolutionstates",
+    "pk": 1,
+    "fields": {
+        "state_value": "recorded",
+        "state_display": "Recorded",
+        "description": "Resolution has been successful recorded in iSkyLIMS"
+    }
+},
+{
+    "model": "drylab.resolutionstates",
+    "pk": 2,
+    "fields": {
+        "state_value": "approved",
+        "state_display": "Approved",
+        "description": "Resolution request has been accepted"
+    }
+},
+{
+    "model": "drylab.resolutionstates",
+    "pk": 3,
+    "fields": {
+        "state_value": "rejected",
+        "state_display": "Rejected",
+        "description": "Resolution can not be handle because is not in porfoloio or for any other reason"
+    }
+},
+{
+    "model": "drylab.resolutionstates",
+    "pk": 4,
+    "fields": {
+        "state_value": "queued",
+        "state_display": "Queued",
+        "description": "Resolution is the the list, waiting for a bioinformatic to be handled"
+    }
+},
+{
+    "model": "drylab.resolutionstates",
+    "pk": 5,
+    "fields": {
+        "state_value": "in_progress",
+        "state_display": "In Progress",
+        "description": "Bioinformatic is working on the Resolution"
+    }
+},
+{
+    "model": "drylab.resolutionstates",
+    "pk": 6,
+    "fields": {
+        "state_value": "delivered",
+        "state_display": "Delivered",
+        "description": "Resolution wascompleted and results were sent to the user"
+    }
+},
+{
+    "model": "drylab.resolutionstates",
+    "pk": 7,
+    "fields": {
+        "state_value": "archived",
+        "state_display": "Archived",
+        "description": null
+    }
+},
+{
+    "model": "drylab.resolutionstates",
+    "pk": 8,
+    "fields": {
+        "state_value": "on_hold",
+        "state_display": "On hold",
+        "description": "Resolution is on hold, waiting for user provides more information"
+    }
 }
 ]

docker-compose.yml

@@ -35,7 +35,7 @@ services:
             - /etc/localtime:/etc/localtime:ro
             - /usr/share/zoneinfo:/usr/share/zoneinfo
             - ngs_data_vol:/mnt
-        command: '-S -s "ngs_data;/mnt;yes;yes;no;samba_user;none;none;ngs data samba share" -u "samba_user;sambapasswd" -p'
+        command: '-S -s "ngs_data;/mnt/test_ngs_data;yes;yes;no;samba_user;none;none;ngs data samba share" -u "samba_user;sambapasswd" -p'
 
     app:
         build: .

docker_install.sh

@@ -1,5 +1,81 @@
 #!/usr/bin/bash
 
+ISKYLIMS_VERSION="3.0.0"
+
+usage() {
+cat << EOF
+This script install and upgrade the iskylims app.
+
+usage : $0 --demo_data
+    Optional input data:
+    --demo_data  | provide already dowloaded demo data from zenodo
+
+
+Examples:
+    Install demo docker system
+    bash $0 
+
+    Provide already downloaded data from zenodo (compressed)
+    bash $0 --demo_data /path/to/iskylims_demo_data.tar.gz 
+EOF
+}
+
+# translate long options to short
+reset=true
+
+for arg in "$@"
+do
+    if [ -n "$reset" ]; then
+      unset reset
+      set --      # this resets the "$@" array so we can rebuild it
+    fi
+    case "$arg" in
+    # OPTIONAL
+        --demo_data)     set -- "$@" -d ;;
+
+    # ADITIONAL
+        --help)          set -- "$@" -h ;;
+        --version)       set -- "$@" -v ;;
+    # PASSING VALUE IN PARAMETER
+        *)               set -- "$@" "$arg" ;;
+    esac
+done
+
+# SETTING DEFAULT VALUES
+demo_data=false
+
+# PARSE VARIABLE ARGUMENTS WITH getops
+options=":d:vh"
+while getopts $options opt; do
+    case $opt in
+        d)
+            demo_data=$OPTARG
+            ;;
+        h )
+            usage
+            exit 1
+            ;;
+        v )
+            echo $ISKYLIMS_VERSION
+            exit 1
+            ;;
+        \?)
+            echo "Invalid Option: -$OPTARG" 1>&2
+            usage
+            exit 1
+            ;;
+        : )
+            echo "Option -$OPTARG requires an argument." >&2
+            exit 1
+            ;;
+        * )
+            echo "Unimplemented option: -$OPTARG" >&2;
+            exit 1
+            ;;
+    esac
+done
+shift $((OPTIND-1))
+
 echo "Deploying test containers..."
 docker compose build --no-cache 
 docker compose up -d
@@ -12,22 +88,30 @@ docker exec -it iskylims_app python3 manage.py migrate
 docker exec -it iskylims_app python3 manage.py makemigrations django_utils core wetlab drylab
 docker exec -it iskylims_app python3 manage.py migrate
 
-echo "Loading in database initial data"
-docker exec -it iskylims_app python3 manage.py loaddata conf/first_install_tables.json
-
 echo "Creating super user "
 docker exec -it iskylims_app python3 manage.py createsuperuser
 
+echo "Loading in database initial data"
+docker exec -it iskylims_app python3 manage.py loaddata conf/first_install_tables.json
+docker exec -it iskylims_app python3 manage.py loaddata test/test_data.json
+
 echo "Download testing files and copy it to samba container"
-wget https://zenodo.org/record/8091169/files/iskylims_demo_data.tar.gz
-docker cp iskylims_demo_data.tar.gz samba:/mnt
+if [ "$demo_data" == "false" ];then
+    wget https://zenodo.org/record/8091169/files/iskylims_demo_data.tar.gz
+    demo_data="./iskylims_demo_data.tar.gz"
+fi
+docker cp $demo_data samba:/mnt
 docker exec -it samba tar -xf  /mnt/iskylims_demo_data.tar.gz -C /mnt
 
 echo "deleting compress testing file"
 docker exec -it samba rm /mnt/iskylims_demo_data.tar.gz
-rm  iskylims_demo_data.tar.gz
 
+if [ "$demo_data" == "false" ];then
+    rm -f $demo_data
+fi
 
 echo "Running crontab"
 docker exec -it iskylims_app python3 manage.py crontab add
+docker exec -it iskylims_app cron
+
 echo "You can now access iskylims via: http://localhost:8001"