fixing bugs in migration script for issue #180

install.sh

@@ -382,6 +382,7 @@ if [ $upgrade == true ]; then
     fi
 
     if [ "$upgrade_type" = "full" ] || [ "$upgrade_type" = "app" ]; then
+        # Fetch the information from LibraryPool for run_process_id, before the migration
 
         # update installation by sinchronize folders
         echo "Copying files to installation folder"
@@ -390,6 +391,11 @@ if [ $upgrade == true ]; then
               --exclude "logs" --exclude "documents" --exclude "migrations" --exclude "__pycache__" \
               README.md LICENSE test conf core drylab clinic wetlab django_utils $INSTALL_PATH
 
+        # Fetch the values of LibraryPool for run_process_is
+        mkdir -p $SCRIPT_DIR/tmp
+        lib_pool_f_name=$SCRIPT_DIR/tmp/library_pool_info.tsv
+        mysql --user=$DB_USER --password=$DB_PASS --host=$DB_SERVER_IP --port=$DB_PORT iskylims -e "SELECT * FROM wetlab_library_pool" > $lib_pool_f_name
+
         # update the settings.py and the main urls
         echo "Update settings and url file."
         # update_settings_and_urls
@@ -416,11 +422,6 @@ if [ $upgrade == true ]; then
         echo "activate the virtualenv"
         source virtualenv/bin/activate
 
-        # Fetch the values of LibraryPool for run_process_is
-        mkdir -p $SCRIPT_DIR/tmp
-        lib_pool_f_name=$SCRIPT_DIR/tmp/my_test.csv
-        upgrade_to_lib_pool_db
-
         # Update the database
         echo "checking for database changes"
         if python manage.py makemigrations | grep -q "No changes"; then
@@ -438,15 +439,17 @@ if [ $upgrade == true ]; then
         fi   
 
         # Restore the values in LibraryPool for run_process on the new structure
+        echo "Restore the values in LibraryPool for run_process on the new structure"
         upgrade_to_lib_pool_db
         # remove the tmp folder
-        # rm -rf $SCRIPT_DIR/tmp
+        rm  -f $lib_pool_f_name
+
 
         # Collect static files
         echo "Running collect statics..."
         python manage.py collectstatic
         echo "Done collect statics"
-         rm -rf $SCRIPT_DIR/tmp
+
         if [ $tables == true ] ; then
             echo "Loading pre-filled tables..."
             python manage.py loaddata conf/first_install_tables.json

wetlab/admin.py

@@ -38,7 +38,6 @@ class LibraryPoolAdmin(admin.ModelAdmin):
         "platform",
         "pool_code_id",
         "register_user",
-        "run_process_id",
     )
 
 

wetlab/models.py

@@ -1310,7 +1310,11 @@ class LibraryPool(models.Model):
     register_user = models.ForeignKey(User, on_delete=models.CASCADE)
     pool_state = models.ForeignKey(PoolStates, on_delete=models.CASCADE)
     # To be deleted in release 3.2.0 or higher
-    # replace by run_process_id from foreign key to many to many
+    # replace by run_process_id
+    """run_process_id = models.ForeignKey(
+        RunProcess, on_delete=models.CASCADE, null=True, blank=True
+    )
+    """
     run_process = models.ManyToManyField(RunProcess, blank=True)
     # rum_proc = models.ManyToManyField(RunProcess, blank=True)
     platform = models.ForeignKey(

wetlab/scripts/library_pool_to_many_relation.py

@@ -10,17 +10,20 @@ def run(f_name):
         The second part of the script fetch the data from the file and add the
         run_process_pk to the run_process field of the LibraryPool instance
     """
-    if hasattr(wetlab.models.LibraryPool, "run_process_id"):
-        with open (f_name, "w") as fo:
-            for library_pool in wetlab.models.LibraryPool.objects.all():
-                # if library_pool.run_process_id:
-                #    library_pool.run_process.add(library_pool.run_process_id)
-                if library_pool.run_process_id is not None:
-                    fo.write(str(library_pool.id) + "," + str(library_pool.run_process_id.id) + "\n")
     if hasattr(wetlab.models.LibraryPool, "run_process"):
         with open (f_name, "r") as fh:
-            for line in fh:
-                library_pool_pk, run_process_pk = line.strip().split(",")
+            lines = fh.readlines()
+        heading = lines[0].strip().split("\t")
+        if  "run_process_id_id" in heading:
+            r_proc_idx = heading.index("run_process_id_id")
+            pk_idx = 0
+            for line in lines[1:]:
+                l_data = line.strip().split("\t")
+                if l_data[r_proc_idx] == "NULL":
+                    continue
+                library_pool_pk = l_data[pk_idx]
+                run_process_pk = l_data[r_proc_idx]
+
                 try:
                     library_pool = wetlab.models.LibraryPool.objects.get(id=library_pool_pk)
                     run_process = wetlab.models.RunProcess.objects.get(id=run_process_pk)
@@ -29,6 +32,11 @@ def run(f_name):
                     continue
                 if not library_pool.run_process.filter(id=run_process_pk).exists():
                     library_pool.run_process.add(run_process)
+                    print(f"LibraryPool: {library_pool_pk} added run_process: {run_process_pk}")
+        else:
+            print("Data migration for LibraryPool was already done")
+    else:
+        print("LibraryPool model does not have run_process field")