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Posted to commits@airavata.apache.org by er...@apache.org on 2022/07/07 12:32:07 UTC
[airavata-admin-user-docs] branch main updated: Adding gateway admin documentation
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The following commit(s) were added to refs/heads/main by this push:
new 440c0c1 Adding gateway admin documentation
440c0c1 is described below
commit 440c0c1d4fe3a0ba060d873a4830fc884f8ce1b8
Author: eroma2014 <er...@gmail.com>
AuthorDate: Thu Jul 7 08:31:58 2022 -0400
Adding gateway admin documentation
---
docs/img/appdetails.png | Bin 0 -> 135563 bytes
docs/index.md | 36 ++-
.../{airavata-user-profiles.md => admin-groups.md} | 0
docs/user-documentation/admin-tutorials.md | 286 -----------------
docs/user-documentation/advance-inputs.md | 342 +++++++++++++++++++++
docs/user-documentation/application-catalog.md | 131 ++++++++
docs/user-documentation/cms-tutorials.md | 54 ----
docs/user-documentation/cred-store.md | 13 +
docs/user-documentation/develop-console.md | 1 +
docs/user-documentation/django-documenation.md | 0
docs/user-documentation/exp-statistics.md | 15 +
docs/user-documentation/group-resource-profile.md | 96 ++++++
docs/user-documentation/gtwy-resource-profile.md | 28 ++
docs/user-documentation/manage-notices.md | 12 +
.../{JSON-tutorials.md => manage-users.md} | 0
docs/user-documentation/quick-start.md | 21 ++
docs/user-documentation/supported-applications.md | 2 +-
docs/user-documentation/tutorials.md | 149 +++++++++
docs/user-documentation/user-tutorials.md | 3 -
mkdocs.yml | 45 +--
20 files changed, 844 insertions(+), 390 deletions(-)
diff --git a/docs/img/appdetails.png b/docs/img/appdetails.png
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diff --git a/docs/index.md b/docs/index.md
index 148cbb2..b695680 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -1,29 +1,35 @@
-# Apache Airavata
+# Django Portal Admin User Documentation
+###Airavata Middleware
- A distributed framework that supports execution and management of computational scientific applications and workflows in grid based systems, remote clusters and cloud based systems.
- Primarily focused on submitting and managing application executions and workflows in grid based systems.
-- Architecturally extensible to support other underlying resources.
-- Used by scientific gateway developers as their middleware layer. They can directly call Airavata API in order to communicate with grid based system.
+- Architecturally extensible to support other underlying resources.<!-- Used by scientific gateway developers as their middleware layer. They can directly call Airavata API in order to communicate with grid based system.-->
- Provides a desktop tools and browser-based web interface components for managing applications, workflows and generated data.
- Contains sophisticated server-side tools for registering and managing scientific applications on computational resources.
-- The Django portal provides tools and methods to easily integrate with post processing applications and application centric interfaces.
-For more information on Airavata visit; <a href="http://airavata.apache.org/" target="_blank">Apache Airavata</a>
+### Django Portal
+- The Django portal, the 'Science Gateway' provides tools and methods to easily integrate with post processing applications and application centric interfaces.
+- Django portal is the users interface to use services available through Apache Airavata Middleware.
+- Django portal mainly has 3 user groups; General User, Read-only- admin user and Admin user
+- This documentation provides step by step instructions on functionality available for general users.
+
+
+
+More information on <a href="https://airavata.apache.org/" target="_blank">Apache Airavata</a><br>
+More information on <a href="https://apache-airavata-django-portal.readthedocs.io/en/latest/" target="_blank">Django Portal</a>
<br>
<br>
-<button type="button" style="color:#f2f2f2;text-align:center;font-weight:lighter;background-color:#2481b9;width:220px;border: 2px solid #2481b9;border-radius:4px"><a style="color:white" href="user-documentation/Django-Instructions" target="_blank" ><b>Django Gateway</b><br/><br/>Django Gateway admin and general user instructions & tutorials!</br></br>Collection of tutorials and instructions for gateway set-up.</a></button>
-<button type="button" style="color:#f2f2f2;text-align:center;font-weight:lighter;background-color:#2481b9;width:220px;border: 2px solid #2481b9;border-radius:4px"><a style="color:white" href="user-documentation/Custos-Instructions" target="_blank" ><b>Data Portal</b><br/><br/>User docs for Data Portal admins and general users</br>Tutorials for gateway users. </br></br><br/>Assistance with job submission, management and sharing!.</a></button>
-<button type="button" style="color:#f2f2f2;text-align:center;font-weight:lighter;background-color:#2481b9;width:220px;border: 2px solid #2481b9;border-radius:4px"><a style="color:white" href="installation/EMC-Instructions" target="_blank"><b>Custos</b><br/><br/>Manage user access? </br></br>Configuration instructions for Custos users & Tutorial!<br/></br></a></button>
+<button type="button" style="color:#f2f2f2;text-align:center;font-weight:lighter;background-color:#2481b9;width:220px;border: 2px solid #2481b9;border-radius:4px"><a style="color:white" href="user-documentation/quick-start" target="_blank" ><br/><br/><b>Admin User Quick Start</b><br/></br></br></a></button>
+<button type="button" style="color:#f2f2f2;text-align:center;font-weight:lighter;background-color:#2481b9;width:220px;border: 2px solid #2481b9;border-radius:4px"><a style="color:white" href="user-documentation/application-catalog" target="_blank" ><br/><br/><b>Application Catalog</b><br/></br></br></a></button>
+<button type="button" style="color:#f2f2f2;text-align:center;font-weight:lighter;background-color:#2481b9;width:220px;border: 2px solid #2481b9;border-radius:4px"><a style="color:white" href="installation/manage-users" target="_blank"><br/><br/><b>Manage Users</b><br/></br><br/></a></button>
+<button type="button" style="color:#f2f2f2;text-align:center;font-weight:lighter;background-color:#2481b9;width:220px;border: 2px solid #2481b9;border-radius:4px"><a style="color:white" href="user-documentation/exp-statistics" target="_blank" ><br/><br/><b>Experiment Statistics</b><br/><br></br></a></button>
<!--<button type="button" style="color:#f2f2f2;text-align:center;font-weight:lighter;background-color:#2481b9;width:220px;border: 2px solid #2481b9;border-radius:4px"><a style="color:white" href="http://airavata.readthedocs.io/en/latest/ target="_blank"><b>User Guide</b></br><br>In-detail documentation on how to install, configure and do upgrades for gateway admins.</br>Step by step guide for gateway users as well.</br></a></button>-->
<br></br>
<!--The Installation section of the documentation applies to on-premise installation of Apache Airavata. -->
-/*
-<b>If you are interested in </b><br>
-1. Using an already hosted gateway<br>
-OR<br>
-2. Having your own gateway hosted<br>
-you can contact a downstream project <a href="http://scigap.org/" target="_blank">Science Gateways Platform as a Service (SciGaP)</a> and request your gateway.
-<br>SciGaP runs Apache Airavata as a platform service. */
+
+###Latest on Django Release !
+<b>July release user documentation </b><br>
+1. Coming Soon!
diff --git a/docs/user-documentation/airavata-user-profiles.md b/docs/user-documentation/admin-groups.md
similarity index 100%
rename from docs/user-documentation/airavata-user-profiles.md
rename to docs/user-documentation/admin-groups.md
diff --git a/docs/user-documentation/admin-tutorials.md b/docs/user-documentation/admin-tutorials.md
deleted file mode 100644
index eb5380a..0000000
--- a/docs/user-documentation/admin-tutorials.md
+++ /dev/null
@@ -1,286 +0,0 @@
-## Gateway Admin Tutorial
-
-###Quick Admin Instructions
-This documentation is a quick set-up instructions for gateway Settings configurations for Admins. For more details please refer to tutorials provide as well.
-<a href="https://cwiki.apache.org/confluence/display/AIRAVATA/Django+Portal+for+Airavata%3A+Gateway+Admin+Guide" target="_blank"> Django Portal Admin Instructions</a>
-
-## Gateway Admin Tutorials
-### Prior to starting your configurations
-1. You need to have admin access to the Django portal, Settings. You need to be a member of the Admin Group.
- - How to check?
- - Log in to the gateway portal
- - You would land on Dashboard with all the applications you have access to launch jobs.
- - Click 'Settings' from top right drop down menu.
- - Do you see icon 'Application Catalog' ? In it can you create applications using 'New Application +'?.
- - Then you are good !<br>
- - If not, contact your gateway admin OR SciGaP team
-<!--3. Credentials generated, assigned and added to authorized_keys files of compute resources -->
-<!--- To generate key refer [Credential Store](../configuration/pga-configuration.md#credential-store)-->
-<!-- - Token Assignment [Gateway Management](../configuration/pga-configuration.md#gateway-management-of-resources)-->
-<!-- - Copy the public key for the assigned token frm credential store and add it to authorized_keys file in both compute and storage resources.-->
-
-<!--NOTE: If you are using a hosted gateway the 2 and 4 would be taken cared by the SciGaP team. -->
-
-
-### Select Your Quick Start Tutorial
-1. <a href= "#Secure">Using Credential Store</a></br>
-2. <a href= "#Resources">Register your Compute & Storage Resources</a></br>
-3. <a href= "#GroupResourceProfile">Configure Group Resource Profile (GRP)</a></br>
-4. <a href="#GaussianJob">Register Gaussian Application</a></br>
-8. <a href= "#StorePreference">Gateway Resource Profile</a></br>
-9. <a href= "#GtwyAccess">Managing User Accounts & User Groups</a></br>
-10. <a href= "#Notices">Communication with Gateway Users</a></br>
-11. <a href= "#Traffic">Monitor Gateway Traffic</a></br>
-
-
-##### <h5 id="Secure">Using Credential Store</h5>
-1. Navigate to Settings → Credential Store.
-2. Click 'New SSH Credential +' and provide a key description.
-3. The new key will be generated and available to copy.
-4. Apart from using the key for SSH communications with compute resources and gateway storage resource, you can share the key with other gateway users and user groups.
-5. When sharing a key, there are 3 permission levels, READ, WRITE and MANAGE_SHARING.
-6. READ permission enables the users to use the key, WRITE permission enables using the key plus deleting the key. MANAGE_SHARING is use the key, delete it and also share with other users and user groups behalf of the owner of the key.
-7. NOTE: Make sure not to delete once assigned to a compute resource or the storage resource. </br>
-
-
-
-##### <h5 id="Resources">Register your Compute & Storage Resources</h5><br>
-
-<b class="lred"> NOTE:</b> Only SciGaP admins or gateway service provider can add compute resources and storage resources. <br> If the gateway and middleware is hsoted by you, You can add the Compute Resources and Storage Resource.
-<br></br><b>What is a compute resource? </b><br>A compute resource is an object that represents a host, host cluster, or pool in a virtualization platform, a virtual data center, or an Amazon region on which machines can be provisioned.
-<br>Compute resource could come as national resources, campus resources or even private cluster.
-<br>NOTE:For testing purposes users (mainly gateway developers) this could even be the local machine.
-<br></br><b>What is a storage resource?</b><br>A storage resource is the server that stores all user data files: application input files and output files.
-<br>Most of the time this is the same server that the gateway is deployed in. The storage resource can be either provided by the gateway provider or by you.
-<br>If the gateway service provider is providing the resource, then there will be file retention policies in place.
-
-###### <b><u>Compute Resource Information </u></b>
-Provide the information below to get your compute resource/HPC registered with Super admin portal, <a href="https://scigap.org/" target="_blank">SciGaP</a><br>
-1. HPC Name (This is the name used to SSH to the resource)<br>
-2. Queue details (Queue name, maximum limits of nodes, CPUs and Walltime.)<br>
-3. Resource manager type (SLURM, PBS)<br>
-4. Job command binary path <br>
-
-###### <b><u>Register a XSEDE Resource </u></b>
-NOTE: Please note this set of instructions are ONLY for gateways hosted by the user. If not SciGaP admins will do this configuration for you in <a href="https://scigap.org/" target="_blank">SciGaP Portal</a>. <br>
-1. Navigate to Admin Dashboard → Compute Resource → Register <br>
-2. Provide
- - Host Name: comet.sdsc.edu<br>
- - Host Aliases: <br>
- - IP Addresses:<br>
- - Resource Description: SDSC Comet Cluster ( Just a description)<br>
- - Create<br>
-3. In Queues tab<br>
- - Click 'Add a Queue'<br>
- - Queue 1
- - Queue Name: compute ( Per resource this is a unique value. Once created cannot edit the name. If need to change, delete and create again)<br>
- - Queue Description: Used for access to regular compute nodes<br>
- - Queue Max Run Time (In Minutes): 280 (Note required for the local resource)<br>
- - Queue Max Nodes: 72 (Note required for the local resource)<br>
- - Queue Max Processors: 1728 (Note required for the local resource)<br>
- - Max Jobs in Queue: 0 (Note required for the local resource)<br>
- - Max Memory For Queue( In MB ): (Note required for the local resource)<br>
- - Queue 2
- - Queue Name: shared ( Per resource this is a unique value. Once created cannot edit the name. If need to change, delete and create again)<br>
- - Queue Description: Single-node jobs using fewer than 24 cores<br>
- - Queue Max Run Time (In Minutes): 2880 (Note required for the local resource)<br>
- - Queue Max Nodes: 1 (Note required for the local resource)<br>
- - Queue Max Processors: 24 (Note required for the local resource)<br>
- - Max Jobs in Queue: 0 (Note required for the local resource)<br>
- - Max Memory For Queue( In MB ): (Note required for the local resource)<br>
-4. File System<br>
- - Nothing to add here, this is futuristic development.<br>
-5. Job Submission Interface<br>
- - Click on the tab<br>
- - Add a new Job Submission Interface<br>
- - Job Submission Protocol: SSH<br>
- - Select Security Protocol: SSH_KEYS
- - SSH Port: 22
- - Select resource manager type: SLURM<br>
- - Job Manager Bin Path: /usr/bin/
- - Job Commands (SUBMISSION): sbatch<br>
- - Job Commands (JOB_MONITORING): squeue<br>
- - Job Commands (DELETION): scancel<br>
- - Parallelism Prefixes (MPI): mpiexec <br>
- - Add Job Submission Protocol<br>
-6. Data Movement Interface<br>
- - Add a new Data Submission Interface<br>
- - Data Movement Protocol: SCP<br>
- - Select Security Protocol: SSH_KEYS <br>
- - SSH Port: 22 <br>
- - Add Data Movement Protocol<br>
-Now the Local resource is ready for job submissions.<br>
-Comet is ready for job submissions.
-
-###### <b><u>Register a Campus Resource </u></b>
-NOTE: Adding a campus resource is similar to adding a XSEDE resource. Same steps to follow with similar information.
-
-###### <h6 id="StoreR"><b><u>Register Storage Resource</u></b></h6>
-NOTE: Please note this set of instructions are ONLY for gateways hosted by the user. If not SciGaP admins will do this configuration for you in <a href="https://scigap.org/" target="_blank">SciGaP Portal</a>. <br>
-1. Navigate to Admin Dashboard → Storage Resource → Register <br>
-2. Provide <br>
- - Host Name: sg03.iu.xsede.org<br>
- - Storage Resource Description: Storage for airavata gateway<br>
- - Create<br>
-3. In Data Movement Interfaces tab<br>
- - Click 'Add a new Data Movement Interface'<br>
- - Select 'SCP' from the list<br>
- - Select Security Protocol: SSH_KEYS<br>
- - Alternate SSH Host Name: Leave empty<br>
- - SSH Port: 22<br>
- - Add Data Movement Interface<br>
-
-#####<h5 id="GroupResourceProfile">Add a Group Resource Profile for Comet (GRP)</h5>
-1. What is a group resource profile?
- - Group resource profile is a configuration which states how a particular HPC resource (campus, national, cloud) is available for users to use.
- - One or many HPCs can be added to a GRP and then it can be shared with the users and user groups to enable use.
- - A gateway can have multiple GRPs and a gateway user can be in one or many GRPs
- - At the time of experiment creation, user need to select which GRP to move forward to launch experiment jobs.
-2. To Create a GRP
- - Navigate to Settings → Group Resource Profile.
- - Click New Group Resource Profile +.
- - Add Name: Default Gateway Profile
- - Default SSH Credential: Select a key from the list or generate a new one.
- - Click New Compute Resource +.
- - Select the resource from the list provided.
- - In next page provide the details required for SSH communication
- - Login Username: This is the login name to use in SSH login
- - SSH Credential: Select from the list, or generate a new one
- - Allocation Project Number: this is applicable for resources which maintains an account for user allocation and usage.
- - Scratch Location: The location for users' computational working directories
- - Provide computational queue policies
- - This section will provide details of maximum node, walltime and CPUs per HPC resource that a gateway user could use in experiment creation.
- - If you don't specify these limits, then the maximum allowed from the HPC resource will be available for users.
- - NOTE: This feature is more popular with gateways which are used in educational purposes and also for gateways where the gateway admin provides XSEDE resoruces for free via community allocations.
- - Click Save
- - Next page, click Save
-
-
-#####<h5 id="GaussianJob">Register Gaussian Application</h5>
-End of this tutorial you will know how to register a new application to run on a a HPC resource through Django portal.
-
-1. Navigate to Settings → Application Catalog. Click New Application +
-2. In Details tab enter:
- - Enter Application Name: Gaussian16
- - Enter Application Version: Gaussian 16 (Not mandatory)
- - Enter Application Description: Gaussian provides capabilities for electronic structure modeling
- - Save
-
-3. In Interface tab:
- - Set 'Enable Archiving Working Directory' to True (Why? - This is set to true when you want to bring back all the files in working directory back to PGA. Caution: If there are very large files they may not be able to SCP)
- - Set 'Enable Optional File Inputs' to False (Why? - Set to false because there won't be any additional optional inputs for Gaussian)
- - Provide Input Fields
- - Click Add Application Input
- - Name: Input-File
- - Initial Value: gaussian.com
- - Type: URI (Why? - This is the type for file uploads)
- - Application Arguments:
- - Standard Input: False (Why? - Futuristic property and not in real use at the moment)
- - Read Only: False (Why? - this is only meaningful for String, Integer or Float inputs)
- - User Friendly Description: Gaussian input file specifying desired calculation type, model chemistry, molecular system and other parameters. (This is information to the user at creating job experiment. Not mandatory)
- - Data is Staged: False
- - Is the Input Required: True
- - Required in Commandline: True
- - Advanced Input Field Modification Metadata:
- - Provide application outputs</br>
- NOTE: 3 application outputs to define. </br>
- - 1st Output
- - Click Add Application Output
- - Name: Gaussian-Application-Output
- - Value: *.log
- - Type: URI
- - Application Argument:
- - Is the Output required?: True
- - Required on command line?: True
- - Metadata:
- - 2nd output
- - Click Add Application Output
- - Name: Gaussian_Checkpoint_File
- - Value: *.chk
- - Type: URI
- - Application Argument:
- - Data Movement: False
- - Is the Output required?: True
- - Required on command line?: True
- - Metadata
- - For applications, STDOUT and STDERR will be automatically added for you.
- - Search Query:</br>
-
-
-
-
-</br></br>
-3. In Deployment tab
- - Click 'New Deployment +'
- - Click Share and add groups and users you want to share this deployment and let run on the particular cluster.
- - Application Executable Path: /home/gridchem/bin/rung09_with_chk_recovery.sh
- - Application Parallelism Type: SERIAL </br>
- - Application Deployment Description: Gaussian16 Rev A.03 ( to avoid G4 output printing issues in Rev B.01)
- - Application Compute Host: Local (Local machine has to be added as a compute resource prior to this step)
- - Add Module load commands:
- - <pre><code>#SBATCH -N 1</code></pre>
- - export MODULEPATH=/share/apps/compute/modulefiles/applications:$MODULEPATH; module load gaussian/16.B.01
- - Pre Job Commands:
- - export AIRAVATA_USERNAME=$gatewayUserName
- - export AIRAVATA_INPUTS=$inputs
- - export AIRAVATA_ExptDataDir=$experimentDataDir;
- - Default Queue Name: shared
- - Default Node Count: 1
- - Default CPU Count: 4
- - Default Walltime: 30
-
-
-
-##### <h5 id="StorePreference">Gateway Resource Profile </h5>
-1. NOTE: This is the section to configure the storage resource for the gateway. Storage resource is the place to hold all gateway user data: inputs and outputs from computations.<br>
-2. Navigate to Settings → Gateway Resource Profile.
-3. Select a SSH key from the list or generate new one and assign it.
-4. Click: New Storage Preference +.
-5. Select Storage Resource: This is the storage resource for the user files and generally its the same server that holds the Django portal. If the gateway is deployed for you, this part would be taken cared by the SciGaP team. If the gateway is self-deployed select the host name of the server you deployed the gateway.
-6. Login Username: pga (This is the username which uses to ssh to the storage resource)
-7. File System Root Location: /var/www/portals/gateway-user-data/seagrid (The path which stores all user files, input files and output files)
-8. Resource Specific Credential Store Token: Select a token from the list. (Public key of this token need to be added to authorized_keys in your storage resource 'pga' login)
-9. Save.
-
-
-##### <h5 id="GtwyAccess">Managing User Accounts & User Groups</h5><br>
-1. Read: [User Groups](airavata-user-profiles.md)
-2. To manage gateway users access use, Groups from top right-hand dropdown.
-3. Click 'Edit' on the group you want to add users.
-4. Mostly the users are added to Gateway-user group by the gateway admins.
-4. Search for the user account using search text field.
-5. The name entered, will be searched across username, first name, last name and email.
-6. User with the matching search string will be listed in the dropdown.
-8. Select the user account, it will get added in to the list highlighted in green.
-9. By default users are added with Member role.
-10. Using the Groups interface, searching for already added users, deleting existing users and changing their roles are supported.
-
-
-##### <h5 id="Notices">Communication with Gateway Users</h5><br>
-1. Provides a method to notify the gateway user.
-2. When user logs in, a 'Bell' icon will be displayed with the number of unread messages next to Dashboard on top menu bar.
-3. Gateway admin can create these notices with an assigned priority.
-4. navigate to Settings → Manage Notices
-5. Click 'New Notice +'
-6. Provide:
- - Notice Title: Gordon cluster is retiring (A heading for the notice)
- - Notice Message: Gordon cluster is retiring from Dec 31st 2016. Preserve your files now.
- - Publish Date: Select from the provided calendar
- - Expiration Date: Mandatory.
- - Priority: LOW (Default is 'LOW'. Admin can change)
-
-
-
-##### <h5 id="Traffic">Monitor Gateway Traffic</h5><br>
-1. To monitor current gateway experiment and job statuses navigate to Settings → Experiment Statistics.
-2. Gateway admin can view and filter experiments of the gateway using this page.
-3. In experiment statistics page, by default gateway status for last 24 hours will be displayed.
-4. Two buttons, 'Past 24 Hours' and 'Past Week' will group and list the experiments for the selected time.
-5. In order to further filter the experiments use, Filters dropdown.
- - Username: AnneMarie (Gateway username need to be typed in)
- - Application Name: Gaussian (All the application in teh gateway will be listed)
- - Hostname: Comet.sdsc.edu (A drop down will provide all the compute resources to select from)
- - Click 'Get Statistics'
-6. Using the calendar, you can search experiments for a time duration you need.
-7. Once the experiments are filtered and grouped, click on the desired group (Existing experiments groups are 'Total','Created','Running', Completed','Cancelled' and 'Failed').
-8. When you list an experiment group you can select the experiment you want to view using 'View Details'. This will open the experiment Details Summary in a new tab.
diff --git a/docs/user-documentation/advance-inputs.md b/docs/user-documentation/advance-inputs.md
new file mode 100644
index 0000000..f517f99
--- /dev/null
+++ b/docs/user-documentation/advance-inputs.md
@@ -0,0 +1,342 @@
+# Advanced Applicaton Input Configuration
+
+The Airavata Django Portal supports customization of the user interface used to
+configure an application input. For example, instead of the default text input
+box for a string input, with customization the UI can be configured to be a drop
+down list of options.
+
+To configure application inputs one needs to provide JSON configuration in the
+**Advanced Input Field Modification Metadata** field of the application input.
+To get there:
+
+1. Select **Settings** from the drop down menu in the header.
+2. You should see the **Application Catalog**. If not, click the gears icon on
+ the left hand side.
+3. Select the application you want to configure by clicking on it.
+4. Select the _Interface_ tab.
+5. Scroll down to the _Input Field_ that you want to customize then scroll down
+ to the **Advanced Input Field Modification Metadata** text box. This is the
+ field where you will input your JSON configuration. This field will outline
+ in green when the JSON is valid and in red when invalid. See the following
+ screenshot.
+
+
+
+## Validation
+
+### Example
+
+```json
+{
+ "editor": {
+ "ui-component-id": "textarea-input-editor",
+ "config": {
+ "rows": 6
+ },
+ "validations": [
+ {
+ "type": "min-length",
+ "value": 10
+ },
+ {
+ "type": "max-length",
+ "value": 200
+ },
+ {
+ "type": "regex",
+ "value": "^[XYL\\s]+$",
+ "message": "Target sequence may only contain letters X, Y and L."
+ }
+ ]
+ }
+}
+```
+
+## Dependencies
+
+You can hide/show inputs based on the values of other inputs. For example, if
+the option selected in input A is 'list-of-urls' then you can have input B show
+a field to upload a file.
+
+### Example
+
+```json
+{
+ "editor": {
+ "dependencies": {
+ "show": {
+ "Select reading options": {
+ "comparison": "equals",
+ "value": "list-urls"
+ }
+ }
+ }
+ }
+}
+```
+
+## Alternate UI Components
+
+### Checkboxes
+
+#### Example
+
+```json
+{
+ "editor": {
+ "ui-component-id": "checkbox-input-editor",
+ "config": {
+ "options": [
+ {
+ "value": "a",
+ "text": "A label"
+ },
+ {
+ "value": "b",
+ "text": "B label"
+ },
+ {
+ "value": "c",
+ "text": "C label"
+ }
+ ]
+ }
+ }
+}
+```
+
+### Radio Buttons
+
+#### Example
+
+```json
+{
+ "editor": {
+ "ui-component-id": "radio-button-input-editor",
+ "config": {
+ "options": [
+ {
+ "value": "breakfast",
+ "text": "Breakfast"
+ },
+ {
+ "value": "lunch",
+ "text": "Lunch"
+ },
+ {
+ "value": "dinner",
+ "text": "Dinner"
+ }
+ ]
+ }
+ }
+}
+```
+
+### Selects
+
+#### Example
+
+```json
+{
+ "editor": {
+ "ui-component-id": "select-input-editor",
+ "config": {
+ "options": [
+ {
+ "value": "breakfast",
+ "text": "Breakfast"
+ },
+ {
+ "value": "lunch",
+ "text": "Lunch"
+ },
+ {
+ "value": "dinner",
+ "text": "Dinner"
+ }
+ ]
+ }
+ }
+}
+```
+
+### Slider
+
+Displays a slider for picking a value between some minimum and maximum value.
+
+#### Config options
+
+- _min_ - minimum value, defaults to 0.
+- _max_ - maximum value, defaults to 100.
+- _step_ - step between values. Default is 1. Can be less that one for decimal
+ values.
+- _valueFormat.percentage_ - whether to save the value with a trailing "%".
+ Defaults to false. Note, this is the value that will be placed in the job
+ script.
+- _displayFormat.percentage_ - whether to display the value to the user with a
+ trailing "%". Defaults to false.
+
+#### Example
+
+```json
+{
+ "editor": {
+ "ui-component-id": "slider-input-editor",
+ "config": {
+ "min": 32,
+ "max": 212,
+ "step": 0.1,
+ "valueFormat": {
+ "percentage": true
+ },
+ "displayFormat": {
+ "percentage": true
+ }
+ }
+ }
+}
+```
+
+### Range Slider
+
+Like the Slider component but there are two sliders, one for selecting the
+beginning and one for selecting the end of a range.
+
+#### Config options
+
+All of the options of the Slider component, plus:
+
+- _delimiter_ - the character to place between the values, for example, ",".
+ The default value is a hyphen, "-". This will be placed into the job script.
+
+```json
+{
+ "editor": {
+ "ui-component-id": "range-slider-input-editor",
+ "config": {
+ "min": 32,
+ "max": 212,
+ "step": 0.1,
+ "valueFormat": {
+ "percentage": true
+ },
+ "displayFormat": {
+ "percentage": true
+ },
+ "delimiter": ","
+ }
+ }
+}
+```
+
+### Autocomplete
+
+The Autocomplete UI component looks up matching entries for the given substring
+typed by the user. This one requires that a custom Django app be developed to
+implement the REST API for returning autocomplete suggestions.
+
+#### REST API contract
+
+- URL is called with query parameter search with value of whatever the user
+ has currently typed
+- URL should return a JSON response with a search key and the value of that
+ key used for the search and an results key with a list matching results,
+ limited to the top 10. Each result should have a text key with the text
+ displayed to the user and a value key which is the value applied to the
+ experiment input if selected. For example:
+
+```json
+{
+ "search": "mammal",
+ "results": [
+ {
+ "text": "Horse",
+ "value": "horse"
+ },
+ {
+ "text": "Mouse",
+ "value": "mouse"
+ }
+ ]
+}
+```
+
+- URL can also be called with query parameter exact with a value that was
+ previously returned. This call is made by the UI to retrieve the "text"
+ value to display to the user for this value. The JSON response should be
+ similar to the above except that it should only have one result:
+
+```json
+{
+ "search": "horse",
+ "results": [
+ {
+ "text": "Horse",
+ "value": "horse"
+ }
+ ]
+}
+```
+
+- If the exact query parameter is specified and there is no match for that
+ value, the JSON response should have HTTP status 404. The error reason can
+ be added to the "detail" key of the response body, for example:
+
+```json
+{
+ "detail": "No matching value was found."
+}
+```
+
+#### Example REST API implementation
+
+To create the REST API backend needed by the Autocomplete component, first you
+need a create a custom Django app. See
+[Custom Django Apps](../dev/custom_django_app) for more information.
+
+Here's a simple implementation of a view function that looks up words in the
+system dictionary file:
+
+```python
+def test_autocomplete_search(request):
+ """Find matching words for given search string."""
+ import re
+ if 'search' in request.GET:
+ query = request.GET['search']
+ pattern = re.compile(re.escape(query), re.IGNORECASE)
+ elif 'exact' in request.GET:
+ query = request.GET['exact']
+ pattern = re.compile(r"^" + re.escape(query) + r"$")
+ else:
+ return generic_json_exception_response(
+ "Missing required query parameter: one of 'search' or 'exact'", status=400)
+
+ matches = []
+ with open("/usr/share/dict/words", 'r') as f:
+ matches = [line.strip() for line in f if pattern.search(line)]
+ # TODO: if 'exact', make sure len(matches) == 1. if 0, then return 404
+ if 'exact' in request.GET and len(matches) == 0:
+ return generic_json_exception_response(f"No match for exact = {request.GET['exact']}", status=404)
+ return JsonResponse({
+ "search": query,
+ "results": [{"text": m, "value": m} for m in matches[:20]]
+ })
+```
+
+See also a real world example
+[miga-autocomplete](https://github.com/bio-miga/miga-autocomplete).
+
+#### Example Input Metadata Configuration
+
+```json
+{
+ "editor": {
+ "ui-component-id": "autocomplete-input-editor",
+ "config": {
+ "url": "/custom/search/"
+ }
+ }
+}
+```
+
diff --git a/docs/user-documentation/application-catalog.md b/docs/user-documentation/application-catalog.md
new file mode 100644
index 0000000..0ffc645
--- /dev/null
+++ b/docs/user-documentation/application-catalog.md
@@ -0,0 +1,131 @@
+#####<h5 id="GaussianJob">Register Gaussian Application</h5>
+End of this tutorial you will know how to register a new application to run on a a HPC resource through Django portal.
+
+1. Navigate to Settings → Application Catalog. Click New Application +
+2. In Details tab enter:
+ - Enter Application Name: Gaussian16
+ - Enter Application Version: Gaussian 16 (Not mandatory)
+ - Enter Application Description: Gaussian provides capabilities for electronic structure modeling
+ - Save
+
+3. In Interface tab:
+ - Set 'Enable Archiving Working Directory' to True (Why? - This is set to true when you want to bring back all the files in working directory back to PGA. Caution: If there are very large files they may not be able to SCP)
+ - Set 'Enable Optional File Inputs' to False (Why? - Set to false because there won't be any additional optional inputs for Gaussian)
+ - Provide Input Fields
+ - Click Add Application Input
+ - Name: Input-File
+ - Initial Value: gaussian.com
+ - Type: URI (Why? - This is the type for file uploads)
+ - Application Arguments:
+ - Standard Input: False (Why? - Futuristic property and not in real use at the moment)
+ - Read Only: False (Why? - this is only meaningful for String, Integer or Float inputs)
+ - User Friendly Description: Gaussian input file specifying desired calculation type, model chemistry, molecular system and other parameters. (This is information to the user at creating job experiment. Not mandatory)
+ - Data is Staged: False
+ - Is the Input Required: True
+ - Required in Commandline: True
+ - Advanced Input Field Modification Metadata:
+ - Provide application outputs</br>
+ NOTE: 3 application outputs to define. </br>
+ - 1st Output
+ - Click Add Application Output
+ - Name: Gaussian-Application-Output
+ - Value: *.log
+ - Type: URI
+ - Application Argument:
+ - Is the Output required?: True
+ - Required on command line?: True
+ - Metadata:
+ - 2nd output
+ - Click Add Application Output
+ - Name: Gaussian_Checkpoint_File
+ - Value: *.chk
+ - Type: URI
+ - Application Argument:
+ - Data Movement: False
+ - Is the Output required?: True
+ - Required on command line?: True
+ - Metadata
+ - For applications, STDOUT and STDERR will be automatically added for you.
+ - Search Query:</br>
+
+
+
+
+</br></br>
+3. In Deployment tab
+ - Click 'New Deployment +'
+ - Click Share and add groups and users you want to share this deployment and let run on the particular cluster.
+ - Application Executable Path: /home/gridchem/bin/rung09_with_chk_recovery.sh
+ - Application Parallelism Type: SERIAL </br>
+ - Application Deployment Description: Gaussian16 Rev A.03 ( to avoid G4 output printing issues in Rev B.01)
+ - Application Compute Host: Local (Local machine has to be added as a compute resource prior to this step)
+ - Add Module load commands:
+ - <pre><code>#SBATCH -N 1</code></pre>
+ - export MODULEPATH=/share/apps/compute/modulefiles/applications:$MODULEPATH; module load gaussian/16.B.01
+ - Pre Job Commands:
+ - export AIRAVATA_USERNAME=$gatewayUserName
+ - export AIRAVATA_INPUTS=$inputs
+ - export AIRAVATA_ExptDataDir=$experimentDataDir;
+ - Default Queue Name: shared
+ - Default Node Count: 1
+ - Default CPU Count: 4
+ - Default Walltime: 30
+
+
+
+
+
+## Django Gateway Theme Management
+In Django portal, the gateway branding or the theme is managed through a CMS. The Djangop portal uses WagTail CMS for the theme.<br>
+The CMS takes care fo the gateway home page, child pages content. <br>
+Gateways are initially deployed with a common base theme, but the gateway admins can re-brand according to their needs.<br>
+In order to change the theme user needs to be in the Admin group.<br>
+
+### Instructions on Gateway Theme
+NOTE: For details instructions please refer <a href="https://github.com/apache/airavata-django-portal/blob/master/docs/cms.md" target="_blank"> Github CMS Instructions</a>
+
+1. Login to your gateway portal.
+ <br></br>
+
+2. Once logged in navigate to Home page.
+<br></br>
+
+3. Click on the Wagtail icon → Go to Wagtail Admin
+<br></br>
+
+4. You are no in Wagtail CMS
+<br></br>
+
+5. To create a new child page or to edit the existing Home page, navigate to Pages, on left.
+<br></br>
+
+6. Keep using the arrow and navigating until the page you want to edit appears in the list. To edit the Home page, use the right arrow and then click on Home or the pen icon.
+<br></br>
+
+7. Once the changes are done, Save as a draft or Publish or Preview from options at the bottom.
+8. If you want to create a page as a child page of Home page, Click on the Pages link on the left side-bar.
+9. You will get a side pop-up which will contain "Welcome to your new Wagtail Site" and a "pencil" icon and a "right-arrow" icon.
+10. You will get "Home" Link. This is the default page. If you want to modify it you can click on "pencil" icon. if you already have any child pages to "Home", you will also be able to find a "right-arrow" icon
+11. To create a new page as a child of "Home". you need to click on "Home" Link.
+12. Then Click on "ADD CHILD PAGE" link.
+13. Choose a page template type. Currently, three of them are available.
+ - Blank Page -> (Build a page from scratch (Best Way))
+ - Cybergateway Home Page -> (Build an IU Themed Home Page)
+ - Home Page -> (Build a seagrid website based Home page)
+14. Each page has four tabs namely:
+ - CONTENT (On page load)
+ - CUSTOMIZATION
+ - PROMOTE
+ - SETTINGS
+15. Provide a title(required) for the page so that you can see it in the CMS.
+16. Head over to the PROMOTE Section.
+ - Provide a slug url ( which is the url extension at which the page will be available). for example if you are creating a documentation page. Provide a slug like documentation so that when you visit <--yourwebsite.com-->/documentation you will visit this page.
+ - Provide a Page Title. This will show up in the page title of each page.
+<br></br>
+
+17. Once the changes are done, you can preview, publish or save as a draft.
+
+
+
+
+
diff --git a/docs/user-documentation/cms-tutorials.md b/docs/user-documentation/cms-tutorials.md
deleted file mode 100644
index 486a78b..0000000
--- a/docs/user-documentation/cms-tutorials.md
+++ /dev/null
@@ -1,54 +0,0 @@
-## Django Gateway Theme Management
-In Django portal, the gateway branding or the theme is managed through a CMS. The Djangop portal uses WagTail CMS for the theme.<br>
-The CMS takes care fo the gateway home page, child pages content. <br>
-Gateways are initially deployed with a common base theme, but the gateway admins can re-brand according to their needs.<br>
-In order to change the theme user needs to be in the Admin group.<br>
-
-### Instructions on Gateway Theme
-NOTE: For details instructions please refer <a href="https://github.com/apache/airavata-django-portal/blob/master/docs/cms.md" target="_blank"> Github CMS Instructions</a>
-
-1. Login to your gateway portal.
- <br></br>
-
-2. Once logged in navigate to Home page.
-<br></br>
-
-3. Click on the Wagtail icon → Go to Wagtail Admin
-<br></br>
-
-4. You are no in Wagtail CMS
-<br></br>
-
-5. To create a new child page or to edit the existing Home page, navigate to Pages, on left.
-<br></br>
-
-6. Keep using the arrow and navigating until the page you want to edit appears in the list. To edit the Home page, use the right arrow and then click on Home or the pen icon.
-<br></br>
-
-7. Once the changes are done, Save as a draft or Publish or Preview from options at the bottom.
-8. If you want to create a page as a child page of Home page, Click on the Pages link on the left side-bar.
-9. You will get a side pop-up which will contain "Welcome to your new Wagtail Site" and a "pencil" icon and a "right-arrow" icon.
-10. You will get "Home" Link. This is the default page. If you want to modify it you can click on "pencil" icon. if you already have any child pages to "Home", you will also be able to find a "right-arrow" icon
-11. To create a new page as a child of "Home". you need to click on "Home" Link.
-12. Then Click on "ADD CHILD PAGE" link.
-13. Choose a page template type. Currently, three of them are available.
- - Blank Page -> (Build a page from scratch (Best Way))
- - Cybergateway Home Page -> (Build an IU Themed Home Page)
- - Home Page -> (Build a seagrid website based Home page)
-14. Each page has four tabs namely:
- - CONTENT (On page load)
- - CUSTOMIZATION
- - PROMOTE
- - SETTINGS
-15. Provide a title(required) for the page so that you can see it in the CMS.
-16. Head over to the PROMOTE Section.
- - Provide a slug url ( which is the url extension at which the page will be available). for example if you are creating a documentation page. Provide a slug like documentation so that when you visit <--yourwebsite.com-->/documentation you will visit this page.
- - Provide a Page Title. This will show up in the page title of each page.
-<br></br>
-
-17. Once the changes are done, you can preview, publish or save as a draft.
-
-
-
-
-
diff --git a/docs/user-documentation/cred-store.md b/docs/user-documentation/cred-store.md
new file mode 100644
index 0000000..13794b3
--- /dev/null
+++ b/docs/user-documentation/cred-store.md
@@ -0,0 +1,13 @@
+
+
+
+
+##### <h5 id="Secure">Using Credential Store</h5>
+1. Navigate to Settings → Credential Store.
+2. Click 'New SSH Credential +' and provide a key description.
+3. The new key will be generated and available to copy.
+4. Apart from using the key for SSH communications with compute resources and gateway storage resource, you can share the key with other gateway users and user groups.
+5. When sharing a key, there are 3 permission levels, READ, WRITE and MANAGE_SHARING.
+6. READ permission enables the users to use the key, WRITE permission enables using the key plus deleting the key. MANAGE_SHARING is use the key, delete it and also share with other users and user groups behalf of the owner of the key.
+7. NOTE: Make sure not to delete once assigned to a compute resource or the storage resource. </br>
+
\ No newline at end of file
diff --git a/docs/user-documentation/develop-console.md b/docs/user-documentation/develop-console.md
new file mode 100644
index 0000000..61955ac
--- /dev/null
+++ b/docs/user-documentation/develop-console.md
@@ -0,0 +1 @@
+Add developer console details
diff --git a/docs/user-documentation/django-documenation.md b/docs/user-documentation/django-documenation.md
deleted file mode 100644
index e69de29..0000000
diff --git a/docs/user-documentation/exp-statistics.md b/docs/user-documentation/exp-statistics.md
new file mode 100644
index 0000000..d303c7e
--- /dev/null
+++ b/docs/user-documentation/exp-statistics.md
@@ -0,0 +1,15 @@
+
+
+##### <h5 id="Traffic">Monitor Gateway Traffic</h5><br>
+1. To monitor current gateway experiment and job statuses navigate to Settings → Experiment Statistics.
+2. Gateway admin can view and filter experiments of the gateway using this page.
+3. In experiment statistics page, by default gateway status for last 24 hours will be displayed.
+4. Two buttons, 'Past 24 Hours' and 'Past Week' will group and list the experiments for the selected time.
+5. In order to further filter the experiments use, Filters dropdown.
+ - Username: AnneMarie (Gateway username need to be typed in)
+ - Application Name: Gaussian (All the application in teh gateway will be listed)
+ - Hostname: Comet.sdsc.edu (A drop down will provide all the compute resources to select from)
+ - Click 'Get Statistics'
+6. Using the calendar, you can search experiments for a time duration you need.
+7. Once the experiments are filtered and grouped, click on the desired group (Existing experiments groups are 'Total','Created','Running', Completed','Cancelled' and 'Failed').
+8. When you list an experiment group you can select the experiment you want to view using 'View Details'. This will open the experiment Details Summary in a new tab.
diff --git a/docs/user-documentation/group-resource-profile.md b/docs/user-documentation/group-resource-profile.md
new file mode 100644
index 0000000..2a2b5c9
--- /dev/null
+++ b/docs/user-documentation/group-resource-profile.md
@@ -0,0 +1,96 @@
+#####<h5 id="GroupResourceProfile">Add a Group Resource Profile for Comet (GRP)</h5>
+1. What is a group resource profile?
+ - Group resource profile is a configuration which states how a particular HPC resource (campus, national, cloud) is available for users to use.
+ - One or many HPCs can be added to a GRP and then it can be shared with the users and user groups to enable use.
+ - A gateway can have multiple GRPs and a gateway user can be in one or many GRPs
+ - At the time of experiment creation, user need to select which GRP to move forward to launch experiment jobs.
+2. To Create a GRP
+ - Navigate to Settings → Group Resource Profile.
+ - Click New Group Resource Profile +.
+ - Add Name: Default Gateway Profile
+ - Default SSH Credential: Select a key from the list or generate a new one.
+ - Click New Compute Resource +.
+ - Select the resource from the list provided.
+ - In next page provide the details required for SSH communication
+ - Login Username: This is the login name to use in SSH login
+ - SSH Credential: Select from the list, or generate a new one
+ - Allocation Project Number: this is applicable for resources which maintains an account for user allocation and usage.
+ - Scratch Location: The location for users' computational working directories
+ - Provide computational queue policies
+ - This section will provide details of maximum node, walltime and CPUs per HPC resource that a gateway user could use in experiment creation.
+ - If you don't specify these limits, then the maximum allowed from the HPC resource will be available for users.
+ - NOTE: This feature is more popular with gateways which are used in educational purposes and also for gateways where the gateway admin provides XSEDE resoruces for free via community allocations.
+ - Click Save
+ - Next page, click Save
+
+##### <h5 id="Resources">Register your Compute & Storage Resources</h5><br>
+
+<b class="lred"> NOTE:</b> Only SciGaP admins or gateway service provider can add compute resources and storage resources. <br> If the gateway and middleware is hsoted by you, You can add the Compute Resources and Storage Resource.
+<br></br><b>What is a compute resource? </b><br>A compute resource is an object that represents a host, host cluster, or pool in a virtualization platform, a virtual data center, or an Amazon region on which machines can be provisioned.
+<br>Compute resource could come as national resources, campus resources or even private cluster.
+<br>NOTE:For testing purposes users (mainly gateway developers) this could even be the local machine.
+<br></br><b>What is a storage resource?</b><br>A storage resource is the server that stores all user data files: application input files and output files.
+<br>Most of the time this is the same server that the gateway is deployed in. The storage resource can be either provided by the gateway provider or by you.
+<br>If the gateway service provider is providing the resource, then there will be file retention policies in place.
+
+###### <b><u>Compute Resource Information </u></b>
+Provide the information below to get your compute resource/HPC registered with Super admin portal, <a href="https://scigap.org/" target="_blank">SciGaP</a><br>
+1. HPC Name (This is the name used to SSH to the resource)<br>
+2. Queue details (Queue name, maximum limits of nodes, CPUs and Walltime.)<br>
+3. Resource manager type (SLURM, PBS)<br>
+4. Job command binary path <br>
+
+###### <b><u>Register a XSEDE Resource </u></b>
+NOTE: Please note this set of instructions are ONLY for gateways hosted by the user. If not SciGaP admins will do this configuration for you in <a href="https://scigap.org/" target="_blank">SciGaP Portal</a>. <br>
+1. Navigate to Admin Dashboard → Compute Resource → Register <br>
+2. Provide
+ - Host Name: comet.sdsc.edu<br>
+ - Host Aliases: <br>
+ - IP Addresses:<br>
+ - Resource Description: SDSC Comet Cluster ( Just a description)<br>
+ - Create<br>
+3. In Queues tab<br>
+ - Click 'Add a Queue'<br>
+ - Queue 1
+ - Queue Name: compute ( Per resource this is a unique value. Once created cannot edit the name. If need to change, delete and create again)<br>
+ - Queue Description: Used for access to regular compute nodes<br>
+ - Queue Max Run Time (In Minutes): 280 (Note required for the local resource)<br>
+ - Queue Max Nodes: 72 (Note required for the local resource)<br>
+ - Queue Max Processors: 1728 (Note required for the local resource)<br>
+ - Max Jobs in Queue: 0 (Note required for the local resource)<br>
+ - Max Memory For Queue( In MB ): (Note required for the local resource)<br>
+ - Queue 2
+ - Queue Name: shared ( Per resource this is a unique value. Once created cannot edit the name. If need to change, delete and create again)<br>
+ - Queue Description: Single-node jobs using fewer than 24 cores<br>
+ - Queue Max Run Time (In Minutes): 2880 (Note required for the local resource)<br>
+ - Queue Max Nodes: 1 (Note required for the local resource)<br>
+ - Queue Max Processors: 24 (Note required for the local resource)<br>
+ - Max Jobs in Queue: 0 (Note required for the local resource)<br>
+ - Max Memory For Queue( In MB ): (Note required for the local resource)<br>
+4. File System<br>
+ - Nothing to add here, this is futuristic development.<br>
+5. Job Submission Interface<br>
+ - Click on the tab<br>
+ - Add a new Job Submission Interface<br>
+ - Job Submission Protocol: SSH<br>
+ - Select Security Protocol: SSH_KEYS
+ - SSH Port: 22
+ - Select resource manager type: SLURM<br>
+ - Job Manager Bin Path: /usr/bin/
+ - Job Commands (SUBMISSION): sbatch<br>
+ - Job Commands (JOB_MONITORING): squeue<br>
+ - Job Commands (DELETION): scancel<br>
+ - Parallelism Prefixes (MPI): mpiexec <br>
+ - Add Job Submission Protocol<br>
+6. Data Movement Interface<br>
+ - Add a new Data Submission Interface<br>
+ - Data Movement Protocol: SCP<br>
+ - Select Security Protocol: SSH_KEYS <br>
+ - SSH Port: 22 <br>
+ - Add Data Movement Protocol<br>
+Now the Local resource is ready for job submissions.<br>
+Comet is ready for job submissions.
+
+###### <b><u>Register a Campus Resource </u></b>
+NOTE: Adding a campus resource is similar to adding a XSEDE resource. Same steps to follow with similar information.
+
diff --git a/docs/user-documentation/gtwy-resource-profile.md b/docs/user-documentation/gtwy-resource-profile.md
new file mode 100644
index 0000000..9fac472
--- /dev/null
+++ b/docs/user-documentation/gtwy-resource-profile.md
@@ -0,0 +1,28 @@
+###### <h6 id="StoreR"><b><u>Register Storage Resource</u></b></h6>
+NOTE: Please note this set of instructions are ONLY for gateways hosted by the user. If not SciGaP admins will do this configuration for you in <a href="https://scigap.org/" target="_blank">SciGaP Portal</a>. <br>
+1. Navigate to Admin Dashboard → Storage Resource → Register <br>
+2. Provide <br>
+ - Host Name: sg03.iu.xsede.org<br>
+ - Storage Resource Description: Storage for airavata gateway<br>
+ - Create<br>
+3. In Data Movement Interfaces tab<br>
+ - Click 'Add a new Data Movement Interface'<br>
+ - Select 'SCP' from the list<br>
+ - Select Security Protocol: SSH_KEYS<br>
+ - Alternate SSH Host Name: Leave empty<br>
+ - SSH Port: 22<br>
+ - Add Data Movement Interface<br>
+
+
+
+##### <h5 id="StorePreference">Gateway Resource Profile </h5>
+1. NOTE: This is the section to configure the storage resource for the gateway. Storage resource is the place to hold all gateway user data: inputs and outputs from computations.<br>
+2. Navigate to Settings → Gateway Resource Profile.
+3. Select a SSH key from the list or generate new one and assign it.
+4. Click: New Storage Preference +.
+5. Select Storage Resource: This is the storage resource for the user files and generally its the same server that holds the Django portal. If the gateway is deployed for you, this part would be taken cared by the SciGaP team. If the gateway is self-deployed select the host name of the server you deployed the gateway.
+6. Login Username: pga (This is the username which uses to ssh to the storage resource)
+7. File System Root Location: /var/www/portals/gateway-user-data/seagrid (The path which stores all user files, input files and output files)
+8. Resource Specific Credential Store Token: Select a token from the list. (Public key of this token need to be added to authorized_keys in your storage resource 'pga' login)
+9. Save.
+
diff --git a/docs/user-documentation/manage-notices.md b/docs/user-documentation/manage-notices.md
new file mode 100644
index 0000000..34d5acf
--- /dev/null
+++ b/docs/user-documentation/manage-notices.md
@@ -0,0 +1,12 @@
+##### <h5 id="Notices">Communication with Gateway Users</h5><br>
+1. Provides a method to notify the gateway user.
+2. When user logs in, a 'Bell' icon will be displayed with the number of unread messages next to Dashboard on top menu bar.
+3. Gateway admin can create these notices with an assigned priority.
+4. navigate to Settings → Manage Notices
+5. Click 'New Notice +'
+6. Provide:
+ - Notice Title: Gordon cluster is retiring (A heading for the notice)
+ - Notice Message: Gordon cluster is retiring from Dec 31st 2016. Preserve your files now.
+ - Publish Date: Select from the provided calendar
+ - Expiration Date: Mandatory.
+ - Priority: LOW (Default is 'LOW'. Admin can change)
\ No newline at end of file
diff --git a/docs/user-documentation/JSON-tutorials.md b/docs/user-documentation/manage-users.md
similarity index 100%
rename from docs/user-documentation/JSON-tutorials.md
rename to docs/user-documentation/manage-users.md
diff --git a/docs/user-documentation/quick-start.md b/docs/user-documentation/quick-start.md
new file mode 100644
index 0000000..c9555f3
--- /dev/null
+++ b/docs/user-documentation/quick-start.md
@@ -0,0 +1,21 @@
+## Quick Start Steps for Admins
+
+- Admin users or the main 'Admin' of the gateway portal will set up the gateway for its users.
+
+In-Progress
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff --git a/docs/user-documentation/supported-applications.md b/docs/user-documentation/supported-applications.md
index 2a7c22b..0450ec6 100644
--- a/docs/user-documentation/supported-applications.md
+++ b/docs/user-documentation/supported-applications.md
@@ -40,4 +40,4 @@ Inputs for all applications currently available in Airavata can be found <a href
### Application Configuration
-For sample configurations please refer [Admin Tutorials](admin-tutorials.md)
\ No newline at end of file
+For sample configurations please refer [Admin Tutorials](quick-start.md)
\ No newline at end of file
diff --git a/docs/user-documentation/tutorials.md b/docs/user-documentation/tutorials.md
new file mode 100644
index 0000000..a2f96f1
--- /dev/null
+++ b/docs/user-documentation/tutorials.md
@@ -0,0 +1,149 @@
+## Admin Tutorial Hands on: Create an Application with Advance Input Components
+
+1. Log into <a href="https://testdrive.airavata.org/" target="_blank">TestDrive Portal</a>
+<br></br>
+2. First, you'll need a user account. <a href="https://testdrive.airavata.org/auth/login" target="_blank">Create an account</a> using your existing institutional login through CILogon.
+<br></br>
+3. After you've logged in, an administrator can grant you access to run the Gaussian16 application.
+<br></br>
+4. During the tutorial we'll grant you access right away and let you know.
+<br></br>
+5. When you log in for the first time you will be in the 'Workspace'. Switch to 'Settings'
+<br></br>
+6. 'Settings' is the admin space of the gateway. Here the first is "Application Catalog"
+<br></br>
+
+NOTE: the purpose of this hands on is to demonstrate some of the advance application input options available in the gateway.
+
+#####Create New Application "Detect Covid"
+1. Application Catalog is where all the available applications are listed as well as the option to create new.
+<br></br>
+2. Use "New Application" to create new application.
+<br></br>
+3. In the 'Details' tab provide the name, version and description.
+<br></br>
+4. For _Application Name_ provide `DetectCovid-<your username>`. Appending your
+ username will allow you to distinguish your version of _DetectCovid_ from other
+ users.
+<br></br>
+
+Image: Application Details Tab
+<br></br>
+4. Upon saving the 'Details' users can add 'Interface' and 'Deployment' of the application in respective tabs.
+
+#####Application Interface
+
+1. Click on the **Interface** tab.
+<br></br>
+2. Add the first Application Input
+ - _Name_: Vaccinated?
+ - _Type_: String
+ - _Initial Value_: Yes
+ - _Application Argument_: `-v`
+ - _User Friendly Description_: `Add your Vaccintion Status`
+ - _Required_: `True`
+ - _Required on Command Line_: `True`
+
+3. Add the second Application Input
+ - _Name_: Symptoms Exists?
+ - _Type_: String
+ - _Initial Value_: a
+ - _Application Argument_: `-s`
+ - _User Friendly Description_: `Select all your symptoms`
+ - _Required_: `True`
+ - _Required on Command Line_: `True`
+ - _metadata_:
+<div id="target_id">
+```json
+{
+ "editor": {
+ "ui-component-id": "checkbox-input-editor",
+ "config": {
+ "options": [
+ {
+ "value": "a",
+ "text": "Cough"
+ },
+ {
+ "value": "b",
+ "text": "Fever"
+ },
+ {
+ "value": "c",
+ "text": "Shortness of Breath"
+ },
+ {
+ "value": "d",
+ "text": "loss of smell"
+ }
+ ]
+ }
+ }
+}
+```
+</div>
+
+4. Add the third Application Input
+ - _Name_: Last Location
+ - _Type_: String
+ - _Initial Value_: main
+ - _Application Argument_: `-l`
+ - _User Friendly Description_: `Select your last location`
+ - _Required_: `True`
+ - _Required on Command Line_: `True`
+ - _Metadata_
+<div id="target_id">
+```json
+{
+ "editor": {
+ "ui-component-id": "radio-button-input-editor",
+ "config": {
+ "options": [
+ {
+ "value": "lobby",
+ "text": "Lobby"
+ },
+ {
+ "value": "loft",
+ "text": "Loft"
+ },
+ {
+ "value": "main",
+ "text": "Main"
+ }
+ ]
+ }
+ }
+}
+```
+</div>
+
+5. Add the last Application Input
+ - _Name_: Crowd Size
+ - _Type_: String
+ - _Initial Value_: 50
+ - _Application Argument_: `-cd`
+ - _User Friendly Description_: `Select the crowd size of the location`
+ - _Required_: `True`
+ - _Required on Command Line_: `True`
+ - _Metadata_
+<div id="target_id">
+```json
+{
+ "editor": {
+ "ui-component-id": "slider-input-editor",
+ "config": {
+ "min": 0,
+ "max": 200,
+ "step": 10,
+ "valueFormat": {
+ "percentage": false
+ },
+ "displayFormat": {
+ "percentage": false
+ }
+ }
+ }
+}
+```
+</div>
\ No newline at end of file
diff --git a/docs/user-documentation/user-tutorials.md b/docs/user-documentation/user-tutorials.md
deleted file mode 100644
index eae3c20..0000000
--- a/docs/user-documentation/user-tutorials.md
+++ /dev/null
@@ -1,3 +0,0 @@
-
-###Basic tutorials for gateway end users and admin users.
-1. <a href="https://cwiki.apache.org/confluence/display/AIRAVATA/Django+Portal+for+Airavata+-+End-User+Guide" target="_blank">Django Portal End User Tutorial</a> <br>
\ No newline at end of file
diff --git a/mkdocs.yml b/mkdocs.yml
index 7b0e96d..09843b7 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -1,4 +1,4 @@
-site_name: Apache Airavata User Docs
+site_name: Apache Airavata Admin User Docs
site_url: https://airavata.apache.org/
site_description: Apache Airavata Documentation
@@ -8,36 +8,19 @@ docs_dir: docs
nav:
- Home: 'index.md'
-- User Documentation:
- - Gateway User Tutorials: 'user-documentation/user-tutorials.md'
- - Gateway Admin Tutorials: 'user-documentation/admin-tutorials.md'
- - Gateway Theme Implemenetation: 'user-documentation/cms-tutorials.md'
- - Advance Application Configuration: 'user-documentation/JSON-tutorials.md'
- - Apache Airavata User Groups: 'user-documentation/airavata-user-profiles.md'
-# - Application Support: 'user-documentation/supported-applications.md'
-#- System Configuration:
-# - Keycloak Configuration: 'configuration/keycloak-configuration.md'
-# - Django Configuration: 'configuration/pga-configuration.md'
-# - Django FAQ: 'maintenance/pga-maintenance.md'
-#- Installation:
-# - Apache Airavata Installation: 'installation/airavata-installation.md'
-# - Django Installation: 'installation/pga-installation.md'
-# - Apache Airavata Server Properties: 'installation/airavata-server-properties.md'
-# - Code Update:
-# - Code Update:
-# - Apache Airavata Update: 'maintenance/code-update/airavata-update.md'
-# - PGA Update: 'maintenance/code-update/pga-update.md'
-#- Technical Documentation:
-# - Apache Airavata API: 'technical-documentation/airavata-api.md'
-# - Helix Job Management: 'technical-documentation/helix-job-management.md'
-# - Django Portal: 'technical-documentation/django-portal.md'
-# - Sharing Documentation:
-# - Introduction: 'technical-documentation/sharing-documentation/introduction.md'
-# - API Overview: 'technical-documentation/sharing-documentation/api-overview.md'
-# - Sharing CPI: 'technical-documentation/sharing-documentation/sharing-cpi.md'
-# - Sharing Models: 'technical-documentation/sharing-documentation/sharing-models.md'
-#- FAQ: 'faq.md'
-#- Previous Releses: 'previous-releases.md'
+- Admin User Documentation:
+ - Quick Start: 'user-documentation/quick-start.md'
+ - Tutorial: 'user-documentation/tutorials.md'
+ - Application Catalog: 'user-documentation/application-catalog.md'
+ - Advance Application Inputs: 'user-documentation/advance-inputs.md'
+ - Experiment Statistis: 'user-documentation/exp-statistics.md'
+ - Manage Users: 'user-documentation/manage-users.md'
+ - Admin User Groups: 'user-documentation/admin-groups.md'
+ - Credential Store: 'user-documentation/cred-store.md'
+ - Group Resource Profile: 'user-documentation/group-resource-profile.md'
+ - Gateway Resource Profile: 'user-documentation/gtwy-resource-profile.md'
+ - Manage Notices: 'user-documentation/manage-notices.md'
+ - Developer Console: 'user-documentation/develop-console.md'
- Contact Us: 'contact-us.md'
theme: readthedocs