diff --git a/README.md b/README.md
index 6ea3b4c8..55504068 100644
--- a/README.md
+++ b/README.md
@@ -1,16 +1,15 @@
-# Code-generator
+<h1 align=center>Code Generator</h1>
 
-Command line utility to auto-generate the structure files that [this server](https://github.com/ScienceDb/graphql-server)
-will use to perform CRUD operations for each model created.
+Command line utility to generate the structure files that Zendro [graphql-server](https://github.com/Zendro-dev/graphql-server) will use to perform CRUD operations for each model created.
 
-## Set up:
+## Set up
 Clone the repository and run:
 ```
 $ npm install -g
 ```
 If you only want to install it locally run `npm install` instead
 
-## Usage:
+## Usage
 
 To run the unit-test case:
 ```
@@ -22,82 +21,103 @@ To run the integration-test case
 $ npm run test-integration [-- OPTIONS]
 ```
 Note:
-Intergation-test case creates a docker-compose ambient with three servers:
+Integration-test case creates a docker-compose environment with three servers:
 
-    gql_postgres
-    gql_science_db_graphql_server
-    gql_ncbi_sim_srv
-
-By default, after the test run, all corresponding Docker images will be completely removed from the docker, this cleanup step can be skiped with __-k__ option.
+```
+gql_postgres
+gql_science_db_graphql_server
+gql_ncbi_sim_srv
+```
 
-Please run this utility with __-h__ option to see the full documentation in manpage style.
+### Examples of use - Test integration
 
-## Examples of use - Test integration:
 To see full test-integration info:
-```
+```bash
 $ npm run test-integration -- -h
 ```
-To restart containers:
-```
-$ npm run test-integration -- -r
+
+To execute a default test run:
+```bash
+$ npm run test-integration
 ```
-To generate code and start containers:
+
+To test a specific `graphql-server` branch:
+```bash
+$ npm run test-integration -- b <branch_name>
 ```
+
+To generate code:
+```bash
 $ npm run test-integration -- -g
 ```
-To do the tests only and keep the containers running at end:
-```
-$ npm run test-integration -- -t -k
-```
+
 To generate code and do the tests, removing all Docker images at end:
-```
-$ npm run test-integration -- -T
-```
-To do a full clean up (removes containers, images and code):
-```
+```bash
 $ npm run test-integration -- -T
 ```
 
-
-And to generate the structure files:
+To generate code, do the tests, and keep the containers running at end:
+```bash
+$ npm run test-integration -- -T -k
 ```
-$ code-generator -f <input-json-files> -o <output-directory>
+
+To do the tests only and keep the containers running at end:
+```bash
+$ npm run test-integration -- -t -k
 ```
+
+To restart containers:
+```bash
+$ npm run test-integration -- -r
 ```
-INPUT:
-<input-json-files> - directory where json models are stored
-<output-directory> - directory where the generated code will be written
+
+To clean generated code, remove containers and volumes:
+```bash
+$ npm run test-integration -- -C
 ```
-This command will create(if doesn't exist) four folders containing the generated files for each model in the ```input-json-files```:
 
-* models ----> sequelize model
-* schemas ----> graphQL schema
-* resolvers ----> basic CRUD resolvers
-* migrations ----> create and delete table migration file
+To do a full clean up (removes containers, images and code):
+```bash
+$ npm run test-integration -- -c
+```
 
+### Examples of use - Code Generator
 
-## Examples of use - Code generator:
 In the same directory of this repository run:
 
-```
+```bash
+# -f <input-json-files>   directory where json models are stored
+# -o <output-directory>   directory where the generated code will be written
 $ code-generator -f ./example_json_files -o /your_path_directory
 ```
-If you want to complete the example with the [server](https://github.com/ScienceDb/graphql-server)
-make ```/your_path_directory``` the same directory where the server repository is stored.
 
-NOTE: For displaying the explanation about usage we can run the help flag:
-```
+For help using this command:
+
+```bash
 $ code-generator -h
+
+# Code generator for the GraphQL server
+#
+# Options:
+#
+#   -f, --jsonFiles <filesFolder>      Folder containing one json file for each model
+#   -o, --outputDirectory <directory>  Directory where generated code will be written
+#   -h, --help                         output usage information
 ```
-```
-Code generator for GraphQL server
 
- Options:
+This command will create four sub-folders within the `output-directory` folder, containing the generated files for each model:
+
 
-   -f, --jsonFiles <filesFolder>      Folder containing one json file for each model
-   -o, --outputDirectory <directory>  Directory where generated code will be written
-   -h, --help                         output usage information
 ```
+models/      -> sequelize model
+schemas/     -> graphQL schema
+resolvers/   -> basic CRUD resolvers
+migrations/  -> create and delete table migration file
+```
+
+To use the code generator with the [graphql-server](https://github.com/Zendro-dev/graphql-server),
+use its path in the `output-directory`.
+
 
 ## JSON files Spec
 
@@ -107,15 +127,15 @@ For each model we need to specify the following fields in the json file:
 
 Name | Type | Description
 ------- | ------- | --------------
-*model* | String | Name of the model (it is recommended uppercase for the initial character).
-*storageType* | String | Type of storage where the model is stored. So far can be one of __sql__ or __Webservice__ or __zendro\_server__
-*url* | String | This field is only mandatory for __zendro\_server__ stored models. Indicates the url where the zendro server storing the model is runnning. 
-*attributes* | Object | The key of each entry is the name of the attribute and theres two options for the value . Either can be a string indicating the type of the attribute or an object where the user can indicates the type of the attribute(in the _type_ field) but also can indicates an attribute's description (in the _description_ field). See the [table](#types-spec) below for allowed types. Example of option one: ```{ "attribute1" : "String", "attribute2: "Int" }``` Example of option two: ``` { "attribute1" : {"type" :"String", "description": "Some description"}, "attribute2: "Int ```
+*model*       | String | Name of the model (it is recommended to Capitalize the name).
+*storageType* | String | Type of storage where the model is stored. Currently supported types are __sql__, __Webservice__, and __zendro\_server__
+*url*         | String | This field is only mandatory for __zendro\_server__ stored models. Indicates the URL of the Zendro server storing the model.
+*attributes*  | Object | The key of each entry is the name of the attribute. There are two options for the value: a string indicating the type of the attribute, or an object with two properties: _type_ (the type of the attribute) and _description_ (attribute description). See [types-spec](#types-spec) table below for allowed types. Example of option one: ```{ "attribute1" : "String", "attribute2: "Int" }``` Example of option two: ``` { "attribute1" : {"type" :"String", "description": "Some description"}, "attribute2: "Int ```
 *associations* | Object | The key of each entry is the name of the association and the value should be an object describing the associations. See [Associations Spec](associations-spec) section below for the specifications of the associations.
 
 EXAMPLES OF VALID JSON FILES
 
-```
+```jsonc
 //Dog.json
 {
   "model" : "Dog",
@@ -139,7 +159,7 @@ EXAMPLES OF VALID JSON FILES
 
 ```
 
-```
+```jsonc
 //Publisher.json
 {
   "model" : "Publisher",
@@ -175,7 +195,7 @@ Date |
 Time |
 DateTime |
 
-For more info about `Date`, `Time`, and `DateTime` types, please see this [info](https://github.com/excitement-engineer/graphql-iso-date/blob/HEAD/rfc3339.txt).
+For more info about `Date`, `Time`, and `DateTime` types, please see the [graphql-iso-date/rfc3339.txt](https://github.com/excitement-engineer/graphql-iso-date/blob/HEAD/rfc3339.txt).
 
 Example:
 * Date: A date string, such as `2007-12-03`.
@@ -211,7 +231,7 @@ name | Type | Description
 ## NOTE:
 Be aware that in the case of this type of association the user is required to describe the cross table used in the field _keysIn_ as a model in its own. For example, if we have a model `User` and a model `Role` and they are associated in a _manytomany_ way, then we also need to describe the `role_to_user` model:
 
-```
+```jsonc
 //User model
 {
   "model" : "User",
@@ -235,7 +255,7 @@ Be aware that in the case of this type of association the user is required to de
 }
 ```
 
-```
+```jsonc
 //Role model
 {
   "model" : "Role",
@@ -258,7 +278,7 @@ Be aware that in the case of this type of association the user is required to de
 }
 ```
 
-```
+```jsonc
 //role_to_user model
 {
   "model" : "role_to_user",
@@ -275,7 +295,7 @@ Be aware that in the case of this type of association the user is required to de
  It's important to notice that when a model involves a foreign key for the association, this key should be explicitly written into the attributes field of the given local model.
 
 Example:
-```
+```jsonc
 {
   "model" : "book",
   "storageType" : "sql",
@@ -301,7 +321,7 @@ THE SAME DATA MODELS DESCRIPTION(.json files) WILL BE USEFUL FOR GENERATING BOTH
 
 Fields *`label`* and *`sublabel`* in the specification are only needed by the GUI generator, but backend generator will only read required information, therefore extra fields such as *`label`* and *`sublabel`* will be ignored by the backend generator.
 Example:
-```
+```jsonc
 //book.json
 {
  "model" : "Book",
@@ -329,27 +349,3 @@ Example:
 ## Testing
 
 For relevant files see `package.json` (section scripts), directories `.test` and `docker`. Test framework is `mocha` and `chai`.
-
-### Unit tests
-
-Run all existing unit tests with
-```
-npm run test-unit
-```
-
-### Integration tests
-
-#### Requirements
-
-You need to be on a \*nix operating system, and have bash and Docker installed and running.
-
-Integration tests are carried out using Docker to setup a GraphQL web server and generate code for example data models. The last step of the setup is to create databases and migrate schemas. After that the server is started using `localhost:3000`, which can than be accessed using HTTP. Solely via such HTTP connections the generated API (GraphQL web server) is tested, just as a user might be doing with e.g. `curl`.
-
-All related Docker files are stored in `./docker`; especially `docker-compose-test.yml`.
-
-The test pipeline is defined and executed in `./test/integration-test.bash` for reasons of simplicity. The actual integration tests are written using `mocha` and can be found in `./test/mocha_integration_test.js`, which is invoked by the above bash script.
-
-To ecexute the integration tests run
-```
-npm run test-integration
-```
diff --git a/docker/Dockerfile.graphql_server b/docker/Dockerfile.graphql_server
index 31b2046e..ae0318b1 100644
--- a/docker/Dockerfile.graphql_server
+++ b/docker/Dockerfile.graphql_server
@@ -3,10 +3,9 @@ FROM node:14.3.0-stretch-slim
 # Create app directory
 WORKDIR /usr/src/app
 
+ENV JQ_PATH=/usr/bin/jq
+
 # Clone the skeleton project and install dependencies
-RUN apt-get update && apt-get install -y git procps autoconf libtool make &&\
-  git clone --branch master https://github.com/ScienceDb/graphql-server.git . && \
-  chmod u+x ./migrateDbAndStartServer.sh && \
-  npm install --save
+RUN apt-get update && apt-get install -y git procps autoconf libtool make jq
 
 EXPOSE 3000
diff --git a/docker/data_models_storage_config1.json b/docker/data_models_storage_config1.json
new file mode 100644
index 00000000..9711932e
--- /dev/null
+++ b/docker/data_models_storage_config1.json
@@ -0,0 +1,11 @@
+{
+  "default-sql": {
+    "storageType": "sql",
+    "username": "sciencedb",
+    "password": "sciencedb",
+    "database": "sciencedb_development",
+    "host": "gql_postgres1",
+    "dialect": "postgres",
+    "operatorsAliases": false
+  }
+}
\ No newline at end of file
diff --git a/docker/data_models_storage_config2.json b/docker/data_models_storage_config2.json
new file mode 100644
index 00000000..d1c582e4
--- /dev/null
+++ b/docker/data_models_storage_config2.json
@@ -0,0 +1,11 @@
+{
+  "default-sql": {
+    "storageType": "sql",
+    "username": "sciencedb",
+    "password": "sciencedb",
+    "database": "sciencedb_development",
+    "host": "gql_postgres2",
+    "dialect": "postgres",
+    "operatorsAliases": false
+  }
+}
\ No newline at end of file
diff --git a/docker/docker-compose-test.yml b/docker/docker-compose-test.yml
index bf0bde1c..5839664c 100644
--- a/docker/docker-compose-test.yml
+++ b/docker/docker-compose-test.yml
@@ -17,27 +17,16 @@ services:
     build:
       context: .
       dockerfile: Dockerfile.graphql_server
-
     volumes:
-      - ./integration_test_run/instance1/models/adapters:/usr/src/app/models/adapters
-      - ./integration_test_run/instance1/schemas:/usr/src/app/schemas
-      - ./integration_test_run/instance1/resolvers:/usr/src/app/resolvers
-      - ./integration_test_run/instance1/models/sql:/usr/src/app/models/sql
-      - ./integration_test_run/instance1/models/distributed:/usr/src/app/models/distributed
-      - ./integration_test_run/instance1/models/zendro-server:/usr/src/app/models/zendro-server
-      - ./integration_test_run/instance1/models/generic:/usr/src/app/models/generic
-      - ./integration_test_run/instance1/migrations:/usr/src/app/migrations
-      - ./integration_test_run/instance1/validations:/usr/src/app/validations
-      - ./integration_test_run/instance1/patches:/usr/src/app/patches
-      - ./sequelize_config_instance1.json:/usr/src/app/config/config.json
-
+      - ./integration_test_run/servers/instance1:/usr/src/app
+      - ./data_models_storage_config1.json:/usr/src/app/config/data_models_storage_config.json
     ports:
       - "3000:3000"
-
     environment:
       PORT: 3000
       REQUIRE_SIGN_IN: "false"
       LIMIT_RECORDS: 25
+      JQ_PATH: /usr/bin/jq
     # Await POSTGRES role and DB creation, migrate schema, then start web server:
     networks:
       - integrationtest
@@ -47,7 +36,6 @@ services:
       - /bin/sh
       - -c
       - |
-        npm install
         ./migrateDbAndStartServer.sh
 
   gql_ncbi_sim_srv1:
@@ -96,17 +84,8 @@ services:
       dockerfile: Dockerfile.graphql_server
 
     volumes:
-      - ./integration_test_run/instance2/models/adapters:/usr/src/app/models/adapters
-      - ./integration_test_run/instance2/schemas:/usr/src/app/schemas
-      - ./integration_test_run/instance2/resolvers:/usr/src/app/resolvers
-      - ./integration_test_run/instance2/models/sql:/usr/src/app/models/sql
-      - ./integration_test_run/instance2/models/distributed:/usr/src/app/models/distributed
-      - ./integration_test_run/instance2/models/zendro-server:/usr/src/app/models/zendro-server
-      - ./integration_test_run/instance2/models/generic:/usr/src/app/models/generic
-      - ./integration_test_run/instance2/migrations:/usr/src/app/migrations
-      - ./integration_test_run/instance2/validations:/usr/src/app/validations
-      - ./integration_test_run/instance2/patches:/usr/src/app/patches
-      - ./sequelize_config_instance2.json:/usr/src/app/config/config.json
+      - ./integration_test_run/servers/instance2:/usr/src/app
+      - ./data_models_storage_config2.json:/usr/src/app/config/data_models_storage_config.json
 
     ports:
       - "3030:3030"
@@ -115,6 +94,7 @@ services:
       PORT: 3030
       REQUIRE_SIGN_IN: "false"
       LIMIT_RECORDS: 25
+      JQ_PATH: /usr/bin/jq
     # Await POSTGRES role and DB creation, migrate schema, then start web server:
     networks:
       - integrationtest
@@ -123,7 +103,6 @@ services:
       - /bin/sh
       - -c
       - |
-        npm install
         ./migrateDbAndStartServer.sh
 
 networks:
diff --git a/docker/integration_test_run/.gitignore b/docker/integration_test_run/.gitignore
index ac0ae0d6..37c310a1 100644
--- a/docker/integration_test_run/.gitignore
+++ b/docker/integration_test_run/.gitignore
@@ -1,6 +1,2 @@
-# Ignore everything in this directory
-*
-# Except this file
-!.gitignore
-!instance1
-!instance2
+# graphql-server instances
+servers/
diff --git a/docker/integration_test_run/instance1/.gitignore b/docker/integration_test_run/instance1/.gitignore
deleted file mode 100644
index e69de29b..00000000
diff --git a/docker/integration_test_run/instance2/.gitignore b/docker/integration_test_run/instance2/.gitignore
deleted file mode 100644
index e69de29b..00000000
diff --git a/docker/integration_test_run/scripts/checkout-branch.sh b/docker/integration_test_run/scripts/checkout-branch.sh
new file mode 100644
index 00000000..20e956d8
--- /dev/null
+++ b/docker/integration_test_run/scripts/checkout-branch.sh
@@ -0,0 +1,35 @@
+#/usr/bin/env bash
+
+# This script assumes the initial working directory is "integration_test_run"
+
+TARGET_BRANCH=$1
+
+
+if [[ -d "servers" ]]; then
+
+  for instance in $(ls servers)
+  do
+
+    INSTANCE_PATH="servers/$instance"
+
+    if [[ -d "$INSTANCE_PATH" ]]; then
+
+      # Change into instance directory
+      cd $INSTANCE_PATH
+
+      # Forcefully checkout to target branch
+      # WARNING: discards all changes when switching branches!
+      git checkout --force $TARGET_BRANCH
+
+      # Synchronize with remote
+      git fetch --all
+      git reset --hard
+
+      # Return to previous working directory
+      cd - 1>/dev/null
+
+    fi
+
+  done
+
+fi
diff --git a/docker/integration_test_run/scripts/clean-workspace.sh b/docker/integration_test_run/scripts/clean-workspace.sh
new file mode 100644
index 00000000..43d1e282
--- /dev/null
+++ b/docker/integration_test_run/scripts/clean-workspace.sh
@@ -0,0 +1,41 @@
+#!/usr/bin/env bash
+
+PATHS=(
+  migrations
+  models/adapters
+  models/distributed
+  models/generic
+  models/sql
+  models/zendro-server
+  patches
+  resolvers
+  schemas
+  validations
+  acl_rules.js
+)
+
+for instance in servers/*
+do
+
+  # Change to graphql-server directory
+  if [ -d $instance ]
+  then
+
+    cd $instance
+
+    # Forcefully delete all generated files
+    for d in ${PATHS[@]}
+    do
+      echo $instance/${d}
+      rm -rf ${d}
+    done
+
+    # Checkout deleted static files
+    git checkout $(git diff --no-renames --name-only --diff-filter=D)
+
+    # Return to previous working directory
+    cd - 1>/dev/null
+
+  fi
+
+done
diff --git a/docker/sequelize_config_instance1.json b/docker/sequelize_config_instance1.json
deleted file mode 100644
index 9d3eb492..00000000
--- a/docker/sequelize_config_instance1.json
+++ /dev/null
@@ -1,26 +0,0 @@
-{
-  "development": {
-    "username": "sciencedb",
-    "password": "sciencedb",
-    "database": "sciencedb_development",
-    "host": "gql_postgres1",
-    "dialect": "postgres",
-    "operatorsAliases": false
-  },
-  "test": {
-    "username": "sciencedb",
-    "password": "sciencedb",
-    "database": "sciencedb_test",
-    "host": "gql_postgres1",
-    "dialect": "postgres",
-    "operatorsAliases": false
-  },
-  "production": {
-    "username": "sciencedb",
-    "password": "sciencedb",
-    "database": "sciencedb_production",
-    "host": "gql_postgres1",
-    "dialect": "postgres",
-    "operatorsAliases": false
-  }
-}
diff --git a/docker/sequelize_config_instance2.json b/docker/sequelize_config_instance2.json
deleted file mode 100644
index f3ebb6c4..00000000
--- a/docker/sequelize_config_instance2.json
+++ /dev/null
@@ -1,26 +0,0 @@
-{
-  "development": {
-    "username": "sciencedb",
-    "password": "sciencedb",
-    "database": "sciencedb_development",
-    "host": "gql_postgres2",
-    "dialect": "postgres",
-    "operatorsAliases": false
-  },
-  "test": {
-    "username": "sciencedb",
-    "password": "sciencedb",
-    "database": "sciencedb_test",
-    "host": "gql_postgres2",
-    "dialect": "postgres",
-    "operatorsAliases": false
-  },
-  "production": {
-    "username": "sciencedb",
-    "password": "sciencedb",
-    "database": "sciencedb_production",
-    "host": "gql_postgres2",
-    "dialect": "postgres",
-    "operatorsAliases": false
-  }
-}
diff --git a/funks.js b/funks.js
index 6d88626e..981937a7 100644
--- a/funks.js
+++ b/funks.js
@@ -2,10 +2,12 @@ let fs = require('fs');
 const ejs = require('ejs');
 const inflection = require('inflection');
 const jsb = require('js-beautify').js_beautify;
+const { join, parse } = require('path');
 const {promisify} = require('util');
 const ejsRenderFile = promisify( ejs.renderFile );
 const stringify_obj = require('stringify-object');
 const colors = require('colors/safe');
+const { getModelDatabase } = require('./lib/generators-aux');
 
 
 /**
@@ -495,28 +497,29 @@ convertToType = function(many, model_name){
  * @return {object}           Object with all extra info that will be needed to create files with templates.
  */
 module.exports.getOptions = function(dataModel){
-  
+
   let opts = {
-      name : dataModel.model,
-      nameCp: capitalizeString(dataModel.model),
-      storageType : getStorageType(dataModel),
-      table: inflection.pluralize(uncapitalizeString(dataModel.model)),
-      nameLc: uncapitalizeString(dataModel.model),
-      namePl: inflection.pluralize(uncapitalizeString(dataModel.model)),
-      namePlCp: inflection.pluralize(capitalizeString(dataModel.model)),
-      attributes: getOnlyTypeAttributes(dataModel.attributes),
-      jsonSchemaProperties: attributesToJsonSchemaProperties(getOnlyTypeAttributes(dataModel.attributes)),
-      associationsArguments: module.exports.parseAssociations(dataModel),
-      arrayAttributeString: attributesArrayString( getOnlyTypeAttributes(dataModel.attributes) ),
-      indices: dataModel.indices,
-      definitionObj : dataModel,
-      attributesDescription: getOnlyDescriptionAttributes(dataModel.attributes),
-      url: dataModel.url || "",
-      externalIds: dataModel.externalIds || [],
-      regex: dataModel.regex || "",
-      adapterName: dataModel.adapterName || "",
-      registry: dataModel.registry || [],
-      idAttribute: getIdAttribute(dataModel)
+    name : dataModel.model,
+    nameCp: capitalizeString(dataModel.model),
+    storageType : getStorageType(dataModel),
+    database: getModelDatabase(dataModel),
+    table: inflection.pluralize(uncapitalizeString(dataModel.model)),
+    nameLc: uncapitalizeString(dataModel.model),
+    namePl: inflection.pluralize(uncapitalizeString(dataModel.model)),
+    namePlCp: inflection.pluralize(capitalizeString(dataModel.model)),
+    attributes: getOnlyTypeAttributes(dataModel.attributes),
+    jsonSchemaProperties: attributesToJsonSchemaProperties(getOnlyTypeAttributes(dataModel.attributes)),
+    associationsArguments: module.exports.parseAssociations(dataModel),
+    arrayAttributeString: attributesArrayString( getOnlyTypeAttributes(dataModel.attributes) ),
+    indices: dataModel.indices,
+    definitionObj : dataModel,
+    attributesDescription: getOnlyDescriptionAttributes(dataModel.attributes),
+    url: dataModel.url || "",
+    externalIds: dataModel.externalIds || [],
+    regex: dataModel.regex || "",
+    adapterName: dataModel.adapterName || "",
+    registry: dataModel.registry || [],
+    idAttribute: getIdAttribute(dataModel)
   };
 
   opts['editableAttributesStr'] = attributesToString(getEditableAttributes(opts.attributes, getEditableAssociations(opts.associationsArguments), getIdAttribute(dataModel)));
@@ -709,7 +712,7 @@ generateAssociationsMigrations =  function( opts, dir_write){
     //       assoc["source"] = opts.table;
     //       assoc["cross"] = false;
     //       let generatedMigration = await module.exports.generateJs('create-association-migration',assoc);
-    //       let name_migration = createNameMigration(dir_write, 'z-column-'+assoc.targetKey+'-to-'+opts.table);
+    //       let name_migration = createNameMigration(dir_write, '', 'z-column-'+assoc.targetKey+'-to-'+opts.table);
     //       fs.writeFile( name_migration, generatedMigration, function(err){
     //         if (err)
     //         {
@@ -725,7 +728,7 @@ generateAssociationsMigrations =  function( opts, dir_write){
       if(assoc.targetStorageType === 'sql'){
           assoc["source"] = opts.table;
           let generatedMigration = await module.exports.generateJs('create-through-migration',assoc);
-          let name_migration = createNameMigration(dir_write, 'z-through-'+assoc.keysIn);
+          let name_migration = createNameMigration(dir_write, '', 'z-through-'+assoc.keysIn);
           fs.writeFile( name_migration, generatedMigration, function(err){
             if (err)
             {
@@ -746,11 +749,11 @@ generateAssociationsMigrations =  function( opts, dir_write){
  * @param  {string} model_name Name of the model.
  * @return {string}            Path where generated file will be written.
  */
-createNameMigration = function(dir_write, model_name){
+createNameMigration = function(rootDir, migrationsDir, model_name){
   let date = new Date();
-   date = date.toISOString().slice(0,19).replace(/[^0-9]/g, "");
+  date = date.toISOString().slice(0,19).replace(/[^0-9]/g, "");
   //return dir_write + '/migrations/' + date + '-create-'+model_name +'.js';
-  return dir_write + '/migrations/' + date + '-'+model_name +'.js';
+  return join(rootDir, migrationsDir, `${date}-${model_name}.js`);
 };
 
  /**
@@ -760,9 +763,15 @@ createNameMigration = function(dir_write, model_name){
   * @param  {object} opts      Object with options needed for the template that will generate the section
   * @param  {string} dir_write Path (including name of the file) where the generated section will be written as a file.
   */
-generateSection = async function(section, opts, dir_write ){
+generateSection = async function(section, opts, filePath ){
   let generatedSection = await module.exports.generateJs('create-'+section ,opts);
-  fs.writeFileSync(dir_write, generatedSection);
+
+  const parsedPath = parse(filePath);
+  if (!fs.existsSync(parsedPath.dir)) {
+    fs.mkdirSync(parsedPath.dir);
+  }
+
+  fs.writeFileSync(filePath, generatedSection);
 };
 
 /**
@@ -803,7 +812,7 @@ generateSections = async function(sections, opts, dir_write) {
         break;
       //migrations
       case 'migrations':
-        file_name = createNameMigration(dir_write, section.fileName);
+        file_name = createNameMigration(dir_write, section.dir, section.fileName);
         break;
       //validations & patches
       case 'validations':
@@ -846,7 +855,8 @@ generateSections = async function(sections, opts, dir_write) {
 writeCommons = async function(dir_write, models, adapters){
   writeSchemaCommons(dir_write);
   console.log(path.join(dir_write,'models'))
-  writeIndexAdapters(path.join(dir_write,'models'));
+  //deprecated due to static adapters index, to be removed
+  // writeIndexAdapters(path.join(dir_write,'models'));
   await writeIndexResolvers(dir_write, models);
   await writeAcls(dir_write, models, adapters);
   //deprecated due to static global index, to be removed
@@ -1042,15 +1052,16 @@ module.exports.generateCode = async function(json_dir, dir_write, options){
 
     //set sections
     let sections = []; //schemas, resolvers, models, migrations, validations, patches
+    const migrationsDir = join('migrations', opts.database);
     switch(opts.storageType) {
       case 'sql':
         sections = [
-          {dir: 'schemas',    template: 'schemas',    fileName: opts.nameLc},
-          {dir: 'resolvers',  template: 'resolvers',  fileName: opts.nameLc},
-          {dir: 'models/sql',     template: 'models',     fileName: opts.nameLc},
-          {dir: 'migrations', template: 'migrations', fileName: opts.nameLc},
+          {dir: 'schemas',     template: 'schemas',     fileName: opts.nameLc},
+          {dir: 'resolvers',   template: 'resolvers',   fileName: opts.nameLc},
+          {dir: 'models/sql',  template: 'models',      fileName: opts.nameLc},
+          {dir: migrationsDir, template: 'migrations',  fileName: opts.nameLc},
           {dir: 'validations', template: 'validations', fileName: opts.nameLc},
-          {dir: 'patches',    template: 'patches',    fileName:opts.nameLc},
+          {dir: 'patches',     template: 'patches',     fileName: opts.nameLc},
         ]
         break;
 
@@ -1099,9 +1110,9 @@ module.exports.generateCode = async function(json_dir, dir_write, options){
 
       case 'sql-adapter':
         sections = [
-          {dir: 'models/adapters',     template: 'sql-adapter',  fileName: opts.adapterName},
-          {dir: 'migrations',   template: 'migrations',   fileName: opts.nameLc},
-          {dir: 'patches',    template: 'patches',    fileName:opts.adapterName},
+          {dir: 'models/adapters', template: 'sql-adapter', fileName: opts.adapterName},
+          {dir: migrationsDir,     template: 'migrations',  fileName: opts.nameLc     },
+          {dir: 'patches',         template: 'patches',     fileName: opts.adapterName},
         ]
         break;
 
diff --git a/lib/generators-aux.js b/lib/generators-aux.js
new file mode 100644
index 00000000..e5d76438
--- /dev/null
+++ b/lib/generators-aux.js
@@ -0,0 +1,21 @@
+
+/**
+ * Get the default database key of a given model.
+ * @param {string} dataModel data model definition object
+ */
+exports.getModelDatabase = function (dataModel) {
+
+  // Sanity check: storageType is a required property, but database
+  // should be set only for supported storage types.
+  const validStorage = {
+    'sql': 'default-sql',
+    'sql-adapter': 'default-sql',
+  }
+
+  const storageType = dataModel.storageType.toLowerCase();
+
+  const defaultDb = validStorage[storageType];
+
+  return dataModel.database || defaultDb || '';
+
+}
\ No newline at end of file
diff --git a/package.json b/package.json
index 733155e4..b9d562d9 100644
--- a/package.json
+++ b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "graphql-server-model-codegen",
-  "version": "0.2.0",
+  "version": "0.3.0",
   "description": "Command line utility which auto-generates code to setup and run a Science-DB GraphQL web-server. See sciencedb.github.io.",
   "repository": {
     "type": "git",
diff --git a/test/mocha_integration_test.js b/test/mocha_integration_test.js
index 4a210da2..6cab55ed 100644
--- a/test/mocha_integration_test.js
+++ b/test/mocha_integration_test.js
@@ -777,7 +777,7 @@ describe(
     expect(trCounts).to.deep.equal([]);
 
     /**
-     * Check: 
+     * Check:
      * max_limit records validation
      */
     //Add another 30 individuals:
@@ -874,10 +874,10 @@ describe(
     res = itHelpers.request_graph_ql_post(individualAdding);
     expect(res.statusCode).to.equal(200);
     ids.push(JSON.parse(res.body.toString('utf8')).data.addIndividual.id);
-    
+
     //test 1: count = 30
     res = itHelpers.request_graph_ql_post(`{ countIndividuals(search:{field:name operator:eq value:{value:"${individualName}"}}) }`);
-    resBody = JSON.parse(res.body.toString('utf8'));    
+    resBody = JSON.parse(res.body.toString('utf8'));
     expect(res.statusCode).to.equal(200);
     expect(resBody.data.countIndividuals).equal(30);
 
@@ -930,16 +930,16 @@ describe(
     expect(resBody.errors[0].path).to.deep.equal(err3_path);
 
     //test 8: pagination (cursor-based): with first: 24
-    res = itHelpers.request_graph_ql_post(`{individualsConnection(pagination:{first:24}, search:{field:name operator:eq value:{value:"${individualName}"}}) 
+    res = itHelpers.request_graph_ql_post(`{individualsConnection(pagination:{first:24}, search:{field:name operator:eq value:{value:"${individualName}"}})
     {
       pageInfo {
         startCursor
         endCursor
         hasPreviousPage
         hasNextPage
-      } 
+      }
       edges{
-        cursor 
+        cursor
         node{id}
     }}}`);
     expect(res.statusCode).to.equal(200);
@@ -952,14 +952,14 @@ describe(
     res = itHelpers.request_graph_ql_post(`{individualsConnection(pagination:{first:5, after:"${cursor20}"}, search:{field:name operator:eq value:{value:"${individualName}"}}) {edges{cursor node{id}}}}`);
     expect(res.statusCode).to.equal(200);
     resBody = JSON.parse(res.body.toString('utf8'));
-    
+
     expect(ids).to.include.members(resBody.data.individualsConnection.edges.map((item) => item.node.id));
     expect(resBody.data.individualsConnection.edges.map((item) => item.node.id)).to.have.deep.members(ids.slice(-10, 25));
 
     //test 10: pagination (cursor-based): with : last:5
     res = itHelpers.request_graph_ql_post(`{individualsConnection(pagination:{last:5}, search:{field:name operator:eq value:{value:"${individualName}"}}) {edges{cursor node{id}}}}`);
     expect(res.statusCode).to.equal(200);
-    resBody = JSON.parse(res.body.toString('utf8'));      
+    resBody = JSON.parse(res.body.toString('utf8'));
     expect(ids).to.include.members(resBody.data.individualsConnection.edges.map((item) => item.node.id));
     expect(resBody.data.individualsConnection.edges.map((item) => item.node.id)).to.have.deep.members(ids.slice(-5));
 
@@ -990,7 +990,7 @@ describe(
     individuals = JSON.parse(res.body.toString('utf8')).data.individuals;
     expect(individuals).to.deep.equal([]);
 
-  }).timeout(5000);
+  }).timeout(10000);
 
   //one_to_one associations where foreignKey is in the target model
   it('22. one_to_one associations setup', function() {
diff --git a/test/sh_integration_test_run.sh b/test/sh_integration_test_run.sh
index 6955dfb0..144f9ec6 100755
--- a/test/sh_integration_test_run.sh
+++ b/test/sh_integration_test_run.sh
@@ -15,7 +15,7 @@
 #
 #   Execution via npm:
 #
-#     npm run test-integration [-- OPTIONS]
+#     npm run test-integration -- [-- OPTIONS]
 #
 #   cleaup:
 #     npm run test-integration-clear
@@ -25,29 +25,67 @@
 # DESCRIPTION
 #     Command line utility to perform graphql server's integration-test.
 #
-#     Intergation-test case creates a docker-compose ambient with three servers:
+#     The integration-test command creates a docker-compose environment with three servers:
 #
 #     gql_postgres
 #     gql_science_db_graphql_server
 #     gql_ncbi_sim_srv
 #
-#     By default, after the test run, all corresponding Docker images will be completely removed from the docker, this cleanup step can be skiped with -k option as described below.
+#     The default behavior performs the following actions:
 #
-#     Default behavior performs the following actions:
+#         0) Checks the local testing environment (./docker/integration_test_run) and performs an initial setup the first time the command is run.
+#         1) Stops and removes Docker containers with docker-compose down command. It also removes Docker images (--rmi) and volumes (-v) created in previous runs.
+#         2) Removes any previously generated code located on the project's testing environment: ./docker/integration_test_run.
+#         3) Generates the code using the test models located on the project's test directory: ./test/integration_test_models.
+#         4) Creates and starts containers with docker-compose up command.
+#         5) Execcutes integration tests.
+#         6) Do a cleanup as described on steps 1) and 2) (use -k option to skip this step).
 #
-#         1) Stop and removes Docker containers with docker-compose down command, also removes Docker images (--rmi) and named or anonymous volumes (-v).
-#         2) Removes any previously generated code located on current project's local directory: ./docker/integration_test_run.
+#     The options are as follows:
+#
+#     -b, --branch
+#
+#         This option changes the testing branch of the zendro server instances. Changing the branch is a permanent side effect.
+#
+#         It can be used alone to execute the default script, or in conjunction with -s or -T.
+#
+#         The default branch is set to "master". When running tests for the first time, make sure this option is set to the desired branch.
+#
+#     -c, --cleanup
+#
+#         This option performs the following actions:
+#
+#         1) Stops and removes Docker containers with docker-compose down command, also removes Docker images (--rmi) and named or anonymous volumes (-v).
+#         2) Removes the testing environment server instances: ./docker/integration_test_run/{graphql-server,servers}.
+#
+#     -C, --softCleanup
+#
+#         This option performs the following actions:
+#
+#         1) Stops and removes Docker containers and volumes with docker-compose down command.
+#         2) Removes any previously generated code located on the testing environment server instances: ./docker/integration_test_run/servers.
+#
+#     -g, --generate-code
+#
+#         This option performs the following actions:
+#
+#         1) Stop and removes containers with docker-compose down command (without removing images).
+#         2) Removes any previously generated code located on the testing environment server instances: ./docker/integration_test_run/servers.
 #         3) Re-generates the code from the test models located on current project's local directory: ./test/integration_test_models. The code is generated on local directory: ./docker/integration_test_run.
 #         4) Creates and start containers with docker-compose up command.
-#         5) Excecutes integration tests. The code should exists, otherwise the integration tests are not executed.
-#         6) Do cleanup as described on 1) and 2) steps (use -k option to skip this step).
-#
-#     The options are as follows:
 #
 #     -h, --help
 #
 #         Display this help and exit.
 #
+#     -k, --keep-running
+#
+#         This option skips the cleanup step at the end of the integration-test-suite and keeps the Docker containers running.
+#
+#         It can be used alone, or in conjunction with the options -t or -T.
+#
+#         If this option is not specified, then, by default, the cleanup step is performed at the end of the tests (see -c option).
+#
 #     -r, --restart-containers
 #
 #         This option performs the following actions:
@@ -57,14 +95,12 @@
 #
 #         Because the containers that manages the test-suite's databases do not use docker named volumes, but transient ones, the databases will be re-initialized by this command, too.
 #
-#     -g, --generate-code
+#     -s, --setup
 #
 #         This option performs the following actions:
 #
-#         1) Stop and removes containers with docker-compose down command (without removing images).
-#         2) Removes any previously generated code located on current project's local directory: ./docker/integration_test_run.
-#         3) Re-generates the code from the test models located on current project's local directory: ./test/integration_test_models. The code is generated on local directory: ./docker/integration_test_run.
-#         4) Creates and start containers with docker-compose up command.
+#         1) Clones the graphql-server repository, optionally switching to the specified "-b BRANCH".
+#         2) Uses the cloned repository to create the server instances necessary for the integration tests.
 #
 #     -t, --run-test-only
 #
@@ -88,21 +124,6 @@
 #
 #         If option -k is also specified, then cleanup step is skipped at the end of the integration-test-suite, otherwise, the cleanup step is performed at the end of the tests (see -c option).
 #
-#     -k, --keep-running
-#
-#         This option skips the cleanup step at the end of the integration-test-suite and keeps the Docker containers running.
-#
-#         This option can be used alone, or in conjunction with the options -t or -T.
-#
-#         If this option is not specified, then, by default, the cleanup step is performed at the end of the tests (see -c option).
-#
-#     -c, --cleanup
-#
-#         This option performs the following actions:
-#
-#         1) Stops and removes Docker containers with docker-compose down command, also removes Docker images (--rmi) and named or anonymous volumes (-v).
-#         2) Removes any previously generated code located on current project's local directory: ./docker/integration_test_run.
-#
 # EXAMPLES
 #     Command line utility to perform graphql server's integration-test.
 #
@@ -118,7 +139,7 @@
 #     To restart containers:
 #     $ npm run test-integration -- -r
 #
-#     To generate code and start containers:
+#     To generate code:
 #     $ npm run test-integration -- -g
 #
 #     To do the tests only and keep the containers running at end:
@@ -126,10 +147,15 @@
 #
 #     To generate code and do the tests, removing all Docker images at end:
 #     $ npm run test-integration -- -T
-
+#
 #     To do a full clean up (removes containers, images and code):
 #     $ npm run test-integration -- -c
 #
+#     To setup a new testing environment
+#     $ npm run test-integration -- -s [BRANCH]
+#
+#     To do a soft clean up (removes containers, volumes and code, but preserves images):
+#     $ npm run test-integration -- -C
 #
 
 # exit on first error
@@ -138,35 +164,21 @@ set -e
 #
 # Constants
 #
-DOCKER_SERVICES=(gql_postgres \
-                 gql_science_db_graphql_server \
-                 gql_ncbi_sim_srv)
+DOCKER_SERVICES=(
+  gql_postgres
+  gql_science_db_graphql_server
+  gql_ncbi_sim_srv
+)
+TARGET_BRANCH=master
+TARGET_DIR="./docker/integration_test_run"
+INSTANCE_DIRS=(
+  "servers/instance1"
+  "servers/instance2"
+)
 TEST_MODELS_INSTANCE1="./test/integration_test_models_instance1"
 TEST_MODELS_INSTANCE2="./test/integration_test_models_instance2"
-TARGET_DIR_INSTANCE1="./docker/integration_test_run/instance1"
-TARGET_DIR_INSTANCE2="./docker/integration_test_run/instance2"
-CODEGEN_DIRS=($TARGET_DIR_INSTANCE1"/models/adapters" \
-              $TARGET_DIR_INSTANCE1"/models/sql" \
-              $TARGET_DIR_INSTANCE1"/models/distributed" \
-              $TARGET_DIR_INSTANCE1"/models/generic" \
-              $TARGET_DIR_INSTANCE1"/models/zendro-server"
-              $TARGET_DIR_INSTANCE1"/migrations" \
-              $TARGET_DIR_INSTANCE1"/schemas" \
-              $TARGET_DIR_INSTANCE1"/resolvers" \
-              $TARGET_DIR_INSTANCE1"/validations" \
-              $TARGET_DIR_INSTANCE1"/patches" \
-              $TARGET_DIR_INSTANCE2"/models/adapters" \
-              $TARGET_DIR_INSTANCE2"/models/sql" \
-              $TARGET_DIR_INSTANCE2"/models/distributed" \
-              $TARGET_DIR_INSTANCE2"/models/generic" \
-              $TARGET_DIR_INSTANCE2"/models/zendro-server"
-              $TARGET_DIR_INSTANCE2"/migrations" \
-              $TARGET_DIR_INSTANCE2"/schemas" \
-              $TARGET_DIR_INSTANCE2"/resolvers" \
-              $TARGET_DIR_INSTANCE2"/validations" \
-              $TARGET_DIR_INSTANCE2"/patches")
 MANPAGE="./man/sh_integration_test_run.man"
-T1=180
+SERVER_CHECK_WAIT_TIME=60
 DO_DEFAULT=true
 KEEP_RUNNING=false
 NUM_ARGS=$#
@@ -181,195 +193,172 @@ NC='\033[0m'
 #
 
 #
-# Function: deleteGenCode()
+# Function: checkGqlServer()
 #
-# Delete generated code.
+# Check if Zendro GraphQL servers respond to requests.
 #
-deleteGenCode() {
-  # Msg
-  echo -e "\n${LGRAY}@@ ----------------------------${NC}"
-  echo -e "${LGRAY}@@ Removing generated code...${NC}"
+checkGqlServer() {
 
-  # Remove generated code.
-  for i in "${CODEGEN_DIRS[@]}"
+  host="localhost:${1}/graphql"
+
+  logTask msg "Testing GraphQL server connection @ $host"
+
+  elapsedTime=0
+  until curl "$host" > /dev/null 2>&1
   do
-    if [ -d $i ]; then
-      rm -rf $i
-      if [ $? -eq 0 ]; then
-          echo -e "@ Removed: $i ... ${LGREEN}done${NC}"
-      else
-          echo -e "!!${RED}ERROR${NC}: trying to remove: ${RED}$i${NC} fails ... ${YEL}exit${NC}"
-          exit 0
-      fi
+
+    # Exit with error code 1
+    if [ $elapsedTime == $SERVER_CHECK_WAIT_TIME ]; then
+
+      logTask error "zendro graphql web server does not start, the wait time limit was reached (${SERVER_CHECK_WAIT_TIME}s)"
+      return 1
+
     fi
+
+    # Wait 2s and rety
+    sleep 2
+    elapsedTime=$(expr $elapsedTime + 2)
   done
 
+  return 0
 
-  # Msg
-  echo -e "@@ All code removed ... ${LGREEN}done${NC}"
-  echo -e "${LGRAY}---------------------------- @@${NC}\n"
 }
 
 #
-# Function: checkCode()
+# Function: checkWorkspace()
 #
-# Check if generated code exists.
+# Check if graphql-server instance folders exist.
 #
-checkCode() {
-  # Msg
-  echo -e "\n${LGRAY}@@ ----------------------------${NC}"
-  echo -e "${LGRAY}@@ Check generated code...${NC}"
+checkWorkspace() {
 
-  # Remove generated code.
-  for i in "${CODEGEN_DIRS[@]}"
-  do
-    # Check if directory exists
-    if [ -d $i ]; then
-      echo -e "Code directory ${LGREEN}$i${NC} exists."
-
-      # Check if directory is empty
-      #if [ -n "$(ls -A ${i} 2>/dev/null)" ]; then
-      #  echo -e "@@ Code at: $i ... ${LGREEN}ok${NC}"
-      #else
-      #  echo -e "!!${RED}ERROR${NC}: Code directory: ${RED}$i${NC} exists but is empty!, please try -T option ... ${YEL}exit${NC}"
-      #  echo -e "${LGRAY}---------------------------- @@${NC}\n"
-      #  exit 0
-      #fi
+  logTask begin "Check graphql-server instances"
+
+  FAIL=false
+
+  for instance in ${INSTANCE_DIRS[@]}; do
+
+    instance_name=$(basename $instance)
+
+    if [[ ! -d "$TARGET_DIR/$instance" ]]; then
+
+      FAIL=true
+      logTask error "Server directory: ${RED}${instance_name}${NC} does not exist!"
     else
-      echo -e "!!${RED}ERROR${NC}: Code directory: ${RED}$i${NC} does not exists!, please try -T option ... ${YEL}exit${NC}"
-      echo -e "${LGRAY}---------------------------- @@${NC}\n"
-      exit 0
+      logTask msg "${instance_name} exists"
     fi
+
   done
 
-  # Msg
-  echo -e "@@ Code check ... ${LGREEN}done${NC}"
-  echo -e "${LGRAY}---------------------------- @@${NC}\n"
+  if [[ $FAIL == true ]]; then
+    logTask quit "One or more server instances were not installed. Please use ${YEL}-s${NC} or execute a full test run with ${YEL}-k${NC} before using this command."
+    exit 0
+  fi
+
+  logTask end "Instances check"
 }
 
 #
-# Function: restartContainers()
+# Function: consumeArgs()
 #
-# Downs and ups containers
+# Shift the remaining arguments on $# list, and sets the flag KEEP_RUNNING=true if
+# argument -k or --keep-running is found.
 #
-restartContainers() {
-  # Msg
-  echo -e "\n${LGRAY}@@ ----------------------------${NC}"
-  echo -e "${LGRAY}@@ Restarting containers...${NC}"
+consumeArgs() {
 
-  # Soft down
-  docker-compose -f ./docker/docker-compose-test.yml down
-  # Msg
-  echo -e "@@ Containers down ... ${LGREEN}done${NC}"
+  while [[ $NUM_ARGS -gt 0 ]]
+  do
+      a="$1"
 
-  # Install
-  npm install
-  # Msg
-  echo -e "@@ Installing ... ${LGREEN}done${NC}"
+      case $a in
+        -k|--keep-running)
 
-  # Up
-  docker-compose -f ./docker/docker-compose-test.yml up -d
-  # Msg
-  echo -e "@@ Containers up ... ${LGREEN}done${NC}"
+          # set flag
+          KEEP_RUNNING=true
 
-  # List
-  docker-compose -f ./docker/docker-compose-test.yml ps
+          logTask begin "Keep containers running at end: $KEEP_RUNNING"
 
-  # Msg
-  echo -e "@@ Containers restarted ... ${LGREEN}done${NC}"
-  echo -e "${LGRAY}---------------------------- @@${NC}\n"
+          # Remove last argument
+          shift
+          let "NUM_ARGS--"
+        ;;
+
+        *)
+          logTask msg "Discarding option: ${RED}$a${NC}"
+
+          # Remove last argument
+          shift
+          let "NUM_ARGS--"
+        ;;
+      esac
+  done
 }
 
 #
-# Function: cleanup()
+# Function: deleteDockerSetup()
 #
-# Default actions (without --keep-running):
-#   Remove docker items (containers, images, etc.).
-#   Remove generated code.
+# Removes docker containers, images, and volumes.
 #
-cleanup() {
-  # Msg
-  echo -e "\n${LGRAY}@@ ----------------------------${NC}"
-  echo -e "${LGRAY}@@ Starting cleanup...${NC}"
+deleteDockerSetup() {
+
+  logTask begin "Removing docker setup"
 
-  # Hard down
   docker-compose -f ./docker/docker-compose-test.yml down -v --rmi all
 
-  # Delete code
-  deleteGenCode
+  logTask end "Removed docker setup"
+
+}
+
+#
+# Function: deleteGenCode()
+#
+# Delete generated code.
+#
+deleteGenCode() {
+
+  logTask begin "Removing generated code"
+
+  # Change to workspace root
+  cd $TARGET_DIR
+
+  # Remove generated files
+  bash scripts/clean-workspace.sh
+
+  # Change to project root
+  cd - 1>/dev/null
 
-  # Msg
-  echo -e "@@ Cleanup ... ${LGREEN}done${NC}"
-  echo -e "${LGRAY}---------------------------- @@${NC}\n"
+  logTask end "All code removed"
 
 }
 
 #
-# Function: softCleanup()
+# Function: deleteServerSetup()
 #
-# restart & removeCodeGen
+# Delete testing environment.
 #
-softCleanup() {
-  # Msg
-  echo -e "\n${LGRAY}@@ ----------------------------${NC}"
-  echo -e "${LGRAY}@@ Starting soft cleanup...${NC}"
+deleteServerSetup() {
 
-  # Down
-  docker-compose -f ./docker/docker-compose-test.yml down
-  # Msg
-  echo -e "@@ Containers down ... ${LGREEN}done${NC}"
+  logTask begin "Removing Zendro instances"
+
+  # Remove workspace modules and server instances
+  rm -rf $TARGET_DIR/{graphql-server,servers}
 
-  # Delete code
-  deleteGenCode
+  logTask end "Zendro instances deleted"
 
-  # Msg
-  echo -e "@@ Soft cleanup ... ${LGREEN}done${NC}"
-  echo -e "${LGRAY}---------------------------- @@${NC}\n"
 }
 
 #
-# Function: waitForGql()
+# Function: doTests()
 #
-# Waits for GraphQL Server to start, for a maximum amount of T1 seconds.
+# Run integration tests using mocha.
 #
-waitForGql() {
-  # Msg
-  echo -e "\n${LGRAY}@@ ----------------------------${NC}"
-  echo -e "${LGRAY}@@ Waiting for GraphQL server to start...${NC}"
+doTests() {
 
-  # Wait until the Science-DB GraphQL web-server is up and running
-  waited=0
-  until curl 'localhost:3000/graphql' > /dev/null 2>&1
-  do
-    if [ $waited == $T1 ]; then
-      # Msg: error
-      echo -e "!!${RED}ERROR${NC}: science-db graphql web server does not start, the wait time limit was reached ($T1).\n"
-      echo -e "${LGRAY}---------------------------- @@${NC}\n"
-      exit 0
-    fi
-    sleep 2
-    waited=$(expr $waited + 2)
-  done
+  logTask begin "Starting mocha tests"
 
-  # Msg
-  echo -e "@@ First GraphQL server is up! ... ${LGREEN}done${NC}"
-  echo -e "${LGRAY}---------------------------- @@${NC}\n"
+  mocha ./test/mocha_integration_test.js
 
-  until curl 'localhost:3030/graphql' > /dev/null 2>&1
-  do
-    if [ $waited == $T1 ]; then
-      # Msg: error
-      echo -e "!!${RED}ERROR${NC}: science-db graphql web server does not start, the wait time limit was reached ($T1).\n"
-      echo -e "${LGRAY}---------------------------- @@${NC}\n"
-      exit 0
-    fi
-    sleep 2
-    waited=$(expr $waited + 2)
-  done
+  logTask end "Mocha tests"
 
-  # Msg
-  echo -e "@@ Second GraphQL server is up! ... ${LGREEN}done${NC}"
-  echo -e "${LGRAY}---------------------------- @@${NC}\n"
 }
 
 #
@@ -378,21 +367,18 @@ waitForGql() {
 # Generate code.
 #
 genCode() {
-  # Msg
-  echo -e "\n${LGRAY}@@ ----------------------------${NC}"
-  echo -e "${LGRAY}@@ Generating code...${NC}"
 
-  # Install
-  npm install
-  # Msg
-  echo -e "@@ Installing ... ${LGREEN}done${NC}"
+  logTask begin "Generating code"
 
-  # Generate
+  TARGET_DIR_INSTANCE1="${TARGET_DIR}/${INSTANCE_DIRS[0]}"
+  TARGET_DIR_INSTANCE2="${TARGET_DIR}/${INSTANCE_DIRS[1]}"
+
+  # Generate code
   node ./index.js -f ${TEST_MODELS_INSTANCE1} -o ${TARGET_DIR_INSTANCE1}
   node ./index.js -f ${TEST_MODELS_INSTANCE2} -o ${TARGET_DIR_INSTANCE2}
 
   # Patch the resolver for web-server
-  #patch -V never ${TARGET_DIR_INSTANCE1}/resolvers/aminoacidsequence.js ./docker/ncbi_sim_srv/amino_acid_sequence_resolver.patch
+  # patch -V never ${TARGET_DIR_INSTANCE1}/resolvers/aminoacidsequence.js ./docker/ncbi_sim_srv/amino_acid_sequence_resolver.patch
   patch -V never ${TARGET_DIR_INSTANCE1}/models/generic/aminoacidsequence.js ./docker/ncbi_sim_srv/model_aminoacidsequence.patch
   # Add monkey-patching validation with AJV
   patch -V never ${TARGET_DIR_INSTANCE1}/validations/individual.js ./test/integration_test_misc/individual_validate.patch
@@ -402,119 +388,227 @@ genCode() {
   # Add patch for sql model accession validation
   patch -V never ${TARGET_DIR_INSTANCE1}/validations/accession.js ./test/integration_test_misc/accession_validate_instance1.patch
 
-  # Msg
-  echo -e "@@ Code generated on ${TARGET_DIR_INSTANCE1} and ${TARGET_DIR_INSTANCE2}: ... ${LGREEN}done${NC}"
-  echo -e "${LGRAY}---------------------------- @@${NC}\n"
+  logTask end "Code generated on ${TARGET_DIR_INSTANCE1} and ${TARGET_DIR_INSTANCE2}"
+
 }
 
 #
-# Function: upContainers()
+# Function: logTask()
 #
-# Up docker containers.
+# Logs a task begin or end message to stdout.
 #
-upContainers() {
-  # Msg
-  echo -e "\n${LGRAY}@@ ----------------------------${NC}"
-  echo -e "${LGRAY}@@ Starting up containers...${NC}"
+# USAGE:
+#
+#   $ logTask <mode> "<task message>"
+#
+# <mode> = begin | check | end | msg | quit
+#
+logTask() {
 
-  # Install
-  npm install
-  # Msg
-  echo -e "@@ Installing ... ${LGREEN}done${NC}"
+  case $1 in
+    begin)
+      echo -e "\n${LGRAY}@@ ----------------------------${NC}"
+      echo -e "${LGRAY}@@ $2...${NC}"
+    ;;
+    check)
+      echo -e "@@ $2 ... ${LGREEN}done${NC}"
+    ;;
+    end)
+      echo -e "@@ $2 ... ${LGREEN}done${NC}"
+      echo -e "${LGRAY}---------------------------- @@${NC}\n"
+    ;;
+    error)
+      echo -e "!!${RED}ERROR${NC}: $2"
+    ;;
+    msg)
+      echo -e "@@ $2"
+    ;;
+    quit)
+      echo -e "@@ $2 ... ${YEL}exit${NC}"
+    ;;
+  esac
+
+}
+
+#
+# Function: man()
+#
+# Show man page of this script.
+#
+man() {
+  # Show
+  more ${MANPAGE}
+}
+
+#
+# Function: restartContainers()
+#
+# Downs and ups containers
+#
+restartContainers() {
+
+  logTask begin "Restarting containers"
+
+  # Soft down
+  docker-compose -f ./docker/docker-compose-test.yml down
+  logTask check "Containers down"
 
   # Up
-  docker-compose -f ./docker/docker-compose-test.yml up -d --no-recreate
-  # Msg
-  echo -e "@@ Containers up ... ${LGREEN}done${NC}"
+  docker-compose -f ./docker/docker-compose-test.yml up -d
+  logTask check "Containers up"
 
   # List
   docker-compose -f ./docker/docker-compose-test.yml ps
 
-  # Msg
-  echo -e "@@ Containers up ... ${LGREEN}done${NC}"
-  echo -e "${LGRAY}---------------------------- @@${NC}\n"
+  logTask end "Containers restarted"
+
 }
 
 #
-# Function: doTests()
+# Function: resetDockerSetup()
 #
-# Do the mocha integration tests.
+# Stops docker-compose testing environment, removes containers and volumes.
 #
-doTests() {
- # Msg
-  echo -e "\n${LGRAY}@@ ----------------------------${NC}"
-  echo -e "${LGRAY}@@ Starting mocha tests...${NC}"
+resetDockerSetup() {
 
-  # Wait for graphql server
-  waitForGql
+  logTask begin "Removing docker containers and volumes"
 
-  # Do tests
-  mocha ./test/mocha_integration_test.js
+  docker-compose -f ./docker/docker-compose-test.yml down -v
+
+  logTask end "Containers down"
 
-  # Msg
-  echo -e "@@ Mocha tests ... ${LGREEN}done${NC}"
-  echo -e "${LGRAY}---------------------------- @@${NC}\n"
 }
 
 #
-# Function: consumeArgs()
+# Function: setupTestingEnvironment
 #
-# Shift the remaining arguments on $# list, and sets the flag KEEP_RUNNING=true if
-# argument -k or --keep-running is found.
+# Clones and initializes a two-server environment workspace.
 #
-consumeArgs() {
+setupTestingEnvironment() {
 
-  while [[ $NUM_ARGS -gt 0 ]]
-  do
-      a="$1"
+  # Remove any existing setup
+  deleteServerSetup
 
-      case $a in
-        -k|--keep-running)
+  logTask begin "Cloning main Zendro server"
 
-          # set flag
-          KEEP_RUNNING=true
-          # Msg
-          echo -e "@@ Keep containers running at end: $KEEP_RUNNING"
-          # Past argument
-          shift
-          let "NUM_ARGS--"
-        ;;
+  # Declare main server path
+  MAIN_SERVER="${TARGET_DIR}/graphql-server"
+
+  # Clone graphql-server and checkout the feature branch
+  git clone \
+    --branch $TARGET_BRANCH \
+    git@github.com:Zendro-dev/graphql-server.git \
+    $MAIN_SERVER
+
+  # Force "node-jq" to use the docke image "jq"
+  export NODE_JQ_SKIP_INSTALL_BINARY=true
+
+  # Install module dependencies
+  npm install --prefix $MAIN_SERVER
+
+  logTask end "Installed Zendro server"
+
+  # Copy graphql-server instances
+  logTask begin "Creating Zendro instances"
+
+  for instance in ${INSTANCE_DIRS[@]}; do
+
+    mkdir -p $TARGET_DIR/servers
+    cp -r $MAIN_SERVER ${TARGET_DIR}/${instance}
 
-        *)
-          # Msg
-          echo -e "@@ Discarting option: ${RED}$a${NC}"
-          # Past argument
-          shift
-          let "NUM_ARGS--"
-        ;;
-      esac
   done
+
+  logTask end "Zendro instances created"
+
 }
+
 #
-# Function: man()
+# Function: upContainers()
 #
-# Show man page of this script.
+# Up docker containers.
 #
-man() {
-  # Show
-  more ${MANPAGE}
+upContainers() {
+
+  logTask begin "Starting up containers"
+
+  # Up
+  docker-compose -f ./docker/docker-compose-test.yml up -d --no-recreate
+
+  # List
+  docker-compose -f ./docker/docker-compose-test.yml ps
+
+  logTask end "Containers up"
+
+}
+
+#
+# Function: waitForGql()
+#
+# Waits for GraphQL Server to start, for a maximum amount of SERVER_CHECK_WAIT_TIME seconds.
+#
+waitForGql() {
+
+  logTask begin "Waiting for GraphQL servers to start"
+
+  hosts=(3000 3030)
+  pids=( )
+
+  for h in ${hosts[@]}; do
+
+    checkGqlServer $h &
+    pids+="$! "
+
+  done
+
+  # Wait until Zendro GraphQL servers are up and running
+  for id in ${pids[@]}; do
+
+    wait $id || exit 0
+
+  done
+
+  logTask end "GraphQL servers are up!"
+
 }
 
 #
 # Main
 #
 if [ $# -gt 0 ]; then
-    #Processes comand line arguments.
+    # Process comand line arguments.
     while [[ $NUM_ARGS -gt 0 ]]
     do
         key="$1"
 
         case $key in
+            -b|--branch)
+
+              shift
+              let "NUM_ARGS--"
+
+              TARGET_BRANCH=$1
+
+              if [[ -z $TARGET_BRANCH || $TARGET_BRANCH =~ ^-|^-- ]]; then
+                logTask quit "-b requires a value: ... ${key} ${RED}<BRANCH>${NC} $@"
+                exit 0
+              fi
+
+              logTask msg "setting test environment branch to: $TARGET_BRANCH"
+
+              # Forcefully checkout instances to the specified branch
+              cd $TARGET_DIR
+              bash scripts/checkout-branch.sh $TARGET_BRANCH
+              cd - 1>/dev/null
+
+              shift
+              let "NUM_ARGS--"
+            ;;
+
             -k|--keep-running)
               # Set flag
               KEEP_RUNNING=true
               # Msg
-              echo -e "@@ keep containers running at end: $KEEP_RUNNING"
+              logTask msg "keep containers running at end: $KEEP_RUNNING"
 
               # Past argument
               shift
@@ -529,6 +623,15 @@ if [ $# -gt 0 ]; then
               exit 0
             ;;
 
+            -s|--setup)
+
+              # Setup testing environment
+              setupTestingEnvironment
+
+              # Done
+              exit 0
+            ;;
+
             -r|--restart-containers)
               # Restart containers
               restartContainers
@@ -538,22 +641,24 @@ if [ $# -gt 0 ]; then
             ;;
 
             -g|--generate-code)
-              # Light cleanup
-              softCleanup
-              # Generate code
+              # Check server instances
+              checkWorkspace
+              # Remove previously generated code
+              deleteGenCode
+              # Run code generator
               genCode
-              # Ups containers
-              upContainers
 
               # Done
               exit 0
             ;;
 
             -t|--run-tests-only)
-              # Check code
-              checkCode
+              # Check workspace folders
+              checkWorkspace
               # Restart containers
               upContainers
+              # Wait for graphql servers
+              waitForGql
               # Do the tests
               doTests
 
@@ -569,12 +674,15 @@ if [ $# -gt 0 ]; then
             ;;
 
             -T|--generate-code-and-run-tests)
-              # Light cleanup
-              softCleanup
-              # Generate code
+              # Reset containers and volumes
+              resetDockerSetup
+              # Re-generate code
+              deleteGenCode
               genCode
               # Up containers
               upContainers
+              # Wait for graphql servers
+              waitForGql
               # Do the tests
               doTests
 
@@ -590,16 +698,26 @@ if [ $# -gt 0 ]; then
             ;;
 
             -c|--cleanup)
-              # Cleanup
-              cleanup
+              # Docker cleanup
+              deleteDockerSetup
+              # Testing environment cleanup
+              deleteServerSetup
+              # Done
+              exit 0
+            ;;
 
+            -C|--soft-cleanup)
+              # Reset containers and volumes
+              resetDockerSetup
+              # Remove generated code
+              deleteGenCode
               # Done
               exit 0
             ;;
 
             *)
               # Msg
-              echo -e "@@ Bad option: ... ${RED}$key${NC} ... ${YEL}exit${NC}"
+              logTask quit "Bad option: ... ${RED}$key${NC} ... ${YEL}exit${NC}"
               exit 0
             ;;
         esac
@@ -610,15 +728,27 @@ fi
 # Default
 #
 if [ $DO_DEFAULT = true ]; then
-  # Default: no arguments
-    # Cleanup
-    cleanup
-    # Generate code
-    genCode
-    # Ups containers
-    upContainers
-    # Do the tests
-    doTests
+
+  # Default run: no arguments #
+
+  # Docker cleanup
+  deleteDockerSetup
+
+  # Reset testing environment
+  setupTestingEnvironment
+
+  # Generate code
+  genCode
+
+  # Ups containers
+  upContainers
+
+  # Wait for graphql servers
+  waitForGql
+
+  # Do the tests
+  doTests
+
 fi
 
 #
@@ -626,13 +756,19 @@ fi
 #
 if [ $KEEP_RUNNING = false ]; then
 
-  # Msg
-  echo -e "@@ Doing final cleanup..."
-  # Cleanup
-  cleanup
+  logTask msg "Doing final cleanup"
+
+  # Docker cleanup
+  deleteDockerSetup
+
+  # Testing environment cleanup
+  deleteServerSetup
+
 else
-  # Msg
-  echo -e "@@ Keeping containers running ... ${LGREEN}done${NC}"
-  # List
+
+  # List containers
   docker-compose -f ./docker/docker-compose-test.yml ps
+
+  logTask end "Keep containers running"
+
 fi
diff --git a/views/create-migrations.ejs b/views/create-migrations.ejs
index 5d8868e2..7134bf09 100644
--- a/views/create-migrations.ejs
+++ b/views/create-migrations.ejs
@@ -1,5 +1,5 @@
 'use strict';
-const dict = require('../utils/graphql-sequelize-types');
+const dict = require('../../utils/graphql-sequelize-types');
 
 /**
  * @module - Migrations to create and to undo a table correpondant to a sequelize model.
diff --git a/views/create-models.ejs b/views/create-models.ejs
index f3ef90b8..093f8fbb 100644
--- a/views/create-models.ejs
+++ b/views/create-models.ejs
@@ -325,7 +325,7 @@ module.exports = class <%- name -%> extends Sequelize.Model{
     //validate input
     await validatorUtil.validateData('validateForCreate', this, input);
     try{
-      const result = await sequelize.transaction( async(t) =>{
+      const result = await this.sequelize.transaction( async(t) =>{
         let item = await super.create(input, {transaction:t});
         return item;
       });
@@ -351,7 +351,7 @@ module.exports = class <%- name -%> extends Sequelize.Model{
     //validate input
     await validatorUtil.validateData('validateForUpdate', this, input);
     try{
-      let result = await sequelize.transaction( async (t) =>{
+      let result = await this.sequelize.transaction( async (t) =>{
         let updated = await super.update( input, { where:{ [this.idAttribute()] : input[this.idAttribute()] }, returning: true, transaction: t  } );
         return updated;
       });
diff --git a/views/create-sql-adapter.ejs b/views/create-sql-adapter.ejs
index 186f52a8..8033d565 100644
--- a/views/create-sql-adapter.ejs
+++ b/views/create-sql-adapter.ejs
@@ -261,7 +261,7 @@ module.exports = class <%- adapterName -%> extends Sequelize.Model{
   static async addOne(input){
 
     try{
-      const result = await sequelize.transaction( async(t) =>{
+      const result = await this.sequelize.transaction( async(t) =>{
         let item = await super.create(input, {transaction:t});
         return item;
       });
@@ -283,7 +283,7 @@ module.exports = class <%- adapterName -%> extends Sequelize.Model{
 
   static async updateOne(input){
     try{
-      let result = await sequelize.transaction( async (t) =>{
+      let result = await this.sequelize.transaction( async (t) =>{
         let updated = await super.update( input, { where:{ [this.idAttribute()] : input[this.idAttribute()] }, returning: true, transaction: t  } );
         return updated;
       });
diff --git a/views/includes/create-models-fieldMutations.ejs b/views/includes/create-models-fieldMutations.ejs
index 3f925231..1ab0168e 100644
--- a/views/includes/create-models-fieldMutations.ejs
+++ b/views/includes/create-models-fieldMutations.ejs
@@ -1,10 +1,10 @@
 <%for(let i=0; i < associationsArguments["to_one"].length; i++){-%>
   <% if (associationsArguments["to_one"][i].holdsForeignKey) { -%>
     /**
-    * <%- op %>_<%-associationsArguments["to_one"][i].targetKey-%> - field Mutation (model-layer) for to_one associationsArguments to <%- op %> 
+    * <%- op %>_<%-associationsArguments["to_one"][i].targetKey-%> - field Mutation (model-layer) for to_one associationsArguments to <%- op %>
     *
     * @param {Id}   <%- idAttribute-%>   IdAttribute of the root model to be updated
-    * @param {Id}   <%-associationsArguments["to_one"][i].targetKey-%> Foreign Key (stored in "Me") of the Association to be updated. 
+    * @param {Id}   <%-associationsArguments["to_one"][i].targetKey-%> Foreign Key (stored in "Me") of the Association to be updated.
     */
     static async <%- op -%>_<%-associationsArguments["to_one"][i].targetKey-%>(<%- idAttribute-%>, <%-associationsArguments["to_one"][i].targetKey-%>) {
       let updated = await <%- name -%> .update({ <%-associationsArguments["to_one"][i].targetKey-%>:  <% if (op == 'remove') { -%>null<% } else { %><%-associationsArguments["to_one"][i].targetKey-%><%}-%>},{where: {<%- idAttribute -%>: <%- idAttribute -%><% if (op == 'remove') { -%>,<%-associationsArguments["to_one"][i].targetKey-%>: <%-associationsArguments["to_one"][i].targetKey-%> <%}-%>}});
@@ -14,13 +14,13 @@
 <%}-%>
 <%for(let i=0; i < associationsArguments["to_many_through_sql_cross_table"].length; i++){-%>
   /**
-  * <%- op %>_<%-associationsArguments["to_many_through_sql_cross_table"][i].targetKey-%> - field Mutation (model-layer) for to_one associationsArguments to <%- op %> 
+  * <%- op %>_<%-associationsArguments["to_many_through_sql_cross_table"][i].targetKey-%> - field Mutation (model-layer) for to_one associationsArguments to <%- op %>
   *
   * @param {Id}   <%- idAttribute-%>   IdAttribute of the root model to be updated
-  * @param {Id}   <%-associationsArguments["to_many_through_sql_cross_table"][i].targetKey-%> Foreign Key (stored in "Me") of the Association to be updated. 
+  * @param {Id}   <%-associationsArguments["to_many_through_sql_cross_table"][i].targetKey-%> Foreign Key (stored in "Me") of the Association to be updated.
   */
   static async <%- op -%>_<%-associationsArguments["to_many_through_sql_cross_table"][i].targetKey-%>(record, <%- op -%><%-associationsArguments["to_many_through_sql_cross_table"][i].name_cp-%>){
-    const updated = await sequelize.transaction(async (transaction) => {
+    const updated = await this.sequelize.transaction(async (transaction) => {
     return await record.<%-op-%><%-associationsArguments["to_many_through_sql_cross_table"][i].name_cp-%>(<%- op -%><%-associationsArguments["to_many_through_sql_cross_table"][i].name_cp-%>, {transaction: transaction});
     });
     return updated;