docs updated

docs/installation.rst

@@ -44,7 +44,7 @@ Here, we create a virtual machine that runs docker.
 
   - Run docker engine::
 
-      docker run hello-world
+      $ docker run hello-world
 
 
     + You will see a message similar to the one below::
@@ -62,12 +62,12 @@ Here, we create a virtual machine that runs docker.
 
   - Run docker-compose::
 
-      docker-compose --version
+      $ docker-compose --version
 
     + The output will be ``docker-compose version x.x.x, build xxxxxxx``
     + For users with an older Mac, you will get ``Illegal instruction: 4``. This error can be fixed by upgrading docker-compose::
 
-        pip install --upgrade docker-compose
+        $ pip install --upgrade docker-compose
 
 
 .. _linux_req:
@@ -103,21 +103,21 @@ Installation
 
 3. Clone the ``docker-chiminey`` source code from http://github.com.au::
 
-     git clone https://github.com/chiminey/docker-chiminey.git
+     $ git clone https://github.com/chiminey/docker-chiminey.git
 
 
 4. Change your working directory::
 
-     cd docker-chiminey
+     $ cd docker-chiminey
 
 
 5. Setup a self-signed certificate. You will be prompted to enter country code, state, city, and etc::
 
-    sh makecert
+    $ sh makecert
 
 6. Deploy the Chiminey platform::
 
-    docker-compose up -d
+    $ docker-compose up -d
 
 
 7. Verify Chiminey was deployed successfully.
@@ -148,19 +148,19 @@ Here, we will configure the Chiminey deployment by creating a superuser, initial
 
 2. Change to ``docker-chiminey`` directory::
 
-    cd docker-chiminey
+    $ cd docker-chiminey
 
 3. Create a superuser::
 
-    ./createsuper
+    $ ./createsuper
 
 4. Initialise the database::
 
-    ./init
+    $ ./init
 
 5. Create a regular user::
 
-    ./createuser
+    $ ./createuser
 
 6. Verify the Chiminey platform is configured correctly.
 
@@ -178,11 +178,11 @@ When a Chiminey platform is deployed,  each `smart connector <smart_connector_de
 
 2. Change to ``docker-chiminey`` directory::
 
-    cd docker-chiminey
+    $ cd docker-chiminey
 
 3. List all available smart connectors::
 
-    ./listsc
+    $ ./listsc
 
     NAME:       DESCRIPTION
     hrmclite:   Hybrid Reverse Monte Carlo without PSD
@@ -192,7 +192,7 @@ When a Chiminey platform is deployed,  each `smart connector <smart_connector_de
 
 4. Activate a smart connector. The syntax to activate a smart connector is `./activatesc smart-connector-name`. Thus, activate `randnum` smart connector as follows::
 
-    ./activatesc randnum
+    $ ./activatesc randnum
 
 5. Verify the smart connector is successfully activated.
 
@@ -202,7 +202,7 @@ When a Chiminey platform is deployed,  each `smart connector <smart_connector_de
 
   - Click Create Job.  `randnum` will appear under the Smart Connectors list.
 
-  
+
 
 
 .. seealso::

docs/loginterm.rst

@@ -0,0 +1,6 @@
+**NB**: Login to the Chiminey docker container.
+
+    - For Mac OS X and Windows users, open `Docker Quickstart Terminal`. For linux-based OS users, login to your machine and open a terminal.
+
+    - Login to the chiminey docker container::
+        $ ./chimineyterm

docs/quick_example.rst

@@ -6,9 +6,8 @@ Quick Example: The Unix Random Number Smart Connector
 =====================================================
 
 In this example, we create a basic smart connector that generates two
-random numbers on a unix machine (or the Chiminey server machine,
-for simplicity), saves the numbers to a file, and then transfers the file
-to a provided output location. This smart connector will be known as the
+random numbers on a  unix machine, saves the numbers to a file, and then transfers the file
+to a provided output location.  The unix machine must have ssh service  enabled. This smart connector will be known as the
 *Unix Random Number Smart Connector*.
 
 - The **purpose** of this example is to create a basic smart connector that executes programs on a unix server. We also add an :ref:`external parameter sweep <external_parameter_sweep>` to this connector.
@@ -19,16 +18,10 @@ to a provided output location. This smart connector will be known as the
 Requirements
 ------------
 
-#. Installation and configuration of the Chiminey server on a virtual machine,
-   according to the :ref:`Installation Guide <installation_guide>`.
-#. Registration of a computation platform, which is where the core
-   functionality of a smart connector is executed within the Chiminey
-   UI. For this example, the platform could be any unix server,
-   including the Chiminey server itself (see registering :ref:`Cluster/Unix  Computation Platform <hpc_resource>`).
-#. Registration of a storage platform, which is the destination of the
-   smart connector output within the Chiminey UI. As for the computation
-   platform above, the platform could be any unix server, again
-   including the Chiminey server itself (see registering :ref:`Unix Storage Platform <remote_storage>`).
+#. :ref:`Install and configure <installation_guide>` the Chiminey platform.
+#. Register an :ref:`HPC compute resource <hpc_resource>`. For this example, the HPC resource could be any unix server where ssh service is enabled,
+   including the Chiminey deployment itself.
+#. Register a storage resource, specifically a :ref:`remote file system <remote_storage>`. Similar to the compute resource, the Chiminey deployment can be used a storage resource. 
 
 
 Creating the Unix Random Number Smart Connector

docs/sc_create.rst

@@ -6,16 +6,19 @@ Creating a smart connector
 
 Creating a smart connector involves completing three tasks:
 
-  #. providing the core functionality of the smart connector,
-  #. attaching resources and optional non-functional properties, and
-  #. registering the new smart connector with the Chiminey platform.
+  #. providing :ref:`the core functionality <sc_core_fcn>`` of the smart connector,
+  #. attaching :ref:`resources and optional non-functional properties <sc_attach_resources>``, and
+  #. :ref:`registering <sc_registration>` the new smart connector with the Chiminey platform.
 
 
-Let's create a new smart connector that generates a random number with a timestamp,  and then writes the output to a file.
+Each tasks are discussed below by  creating an example smart connector. This  smart connector  generates a random number with a timestamp,  and then writes the output to a file.
 
+.. include:: <loginterm.rst>
 
 
 
+.. _sc_core_fcn:
+
 The Core Function
 """"""""""""""""
 
@@ -41,6 +44,8 @@ Notice ``OUTPUT_DIR``. This is the path to the output directory, and thus Chimin
 The contents of ``OUTPUT_DIR`` will be transferred to the output location at the end of each computation.
 
 
+.. _sc_attach_resources:
+
 Attaching resources and non-functional properties
 """""""""""""""""""""""""""""""""""""""""""""""""""
 Resources and non-functional properties are attached to a smart connector by overriding ``get_ui_schema_namespace`` method of ``chiminey.initialisation.coreinitial.CoreInitial`` class.
@@ -58,6 +63,31 @@ Under chiminey/, we create a python package `randnum`, and add ``initialise.py``
     ] return schemas
     # ---EOF ---
 
+
+
+.. _sc_registration:
+
+Registration
+"""""""""""""""
+
+The final step is registering the smart connector  with the Chiminey platform. The details of this smart connector
+ will be added to the dictionary ``SMART CONNECTORS`` in ``chiminey/settings changeme.py``.
+  The details include a unique name (with no spaces), a python path to ``RandNumInitial`` class,
+   the description of the smart connector, and the absolute path to the payload.
+
+"randnum": {
+           "name": "randnum",
+           "init": "chiminey.randnum.initialise.RandNumInitial",
+           "description": "Randnum generator, with timestamp",
+           "payload": "/opt/chiminey/current/payload_randnum"
+},
+
+Finally, restart the Chiminey platform and then activate ``randnum`` smart connector. You need to exit the docker container and execute the following::
+
+  $ sh restart
+  $ ./activatesc randnum
+
+
 The list
     of available resources and non-functional properties is given by ``INPUT_FIELDS`` parameter in ``chiminey/settings_changeme.py``