Provides an admin layer and forms for users to submit organisms and analysis into Chado
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tripal_chado_datasets.module

README.md

Build Status

Try Out Tripal HQ Instead

This module is largely redundant with the functionality provided by Tripal HeadQuarters. Try that out instead!

Tripal Chado Datasets

The Tripal Chado Datasets module allows users to propose new Chado organisms and analyses to a site's database. This module provides:

  • Forms for users to request content creation
  • Administrative area for approving or rejecting requests
  • Creation of content after requests are approved (organism only)
  • Emails confirming submissions, notifying admins, and notifying users of administrative decisions.

To see this module in action, pleas visit https://i5k.nal.usda.gov/datasets/submit-a-dataset

Set up

Module installation

Prior to installation, make sure Tripal is installed and up to date. This module currently supports both Tripal 2 and Tripal 3.

We suggest installing Tripal Chado Datasets via git:

## Navigate to your site's custom modules directory
cd /var/www/html/sites/all/modules/custom  
git clone https://github.com/NAL-i5K/tripal_chado_datasets.git
drush pm-enable tripal_chado_datasets

Dependencies

the below modules will be installed when enabling Tripal Chado Datasets:

  1. Date
  2. Honeypot
  3. File Resumable Uploads
  4. Captcha

Configure your site

Make sure that the site name and email variables are set for your site, as these will be used in the email messages sent to admins and users. You can check your configuration at /admin/config/system/site-information

Module usage

Account creation

Coming soon.

Organism request (Project request)

Users should be directed to /datasets/request-project. This form will provide fields for your users to fill out to request a new Organism.

request project form When the request is submitted, an email goes to the site administrator, summarizing the submission, and to the user, notifying them the request was received. The administrator checks if the organism should be approved or rejected. Requests are listed at admin/structure/datasets and individual requests are approved by clicking Edit and and then Reject/Approve.

organism request table

An email is sent to the user when the request is approved (but not if it is rejected). Approved organisms are inserted into the chado database.

Note: if running a Tripal 3 site, organism records will be inserted into Chado after approving a request at admin/structure/datasets in the "Request Project List" tab. They will not be available to users until they are published. Visit admin -> Content Types -> Tripal Content types -> Publish after approving an organism to publish it.

Analysis requests (datasets)

Users request the creation of an analysis at datasets/submit-a-dataset. They will select their previously submitted organism from the dropdown box, and fill out requested information which will be stored in Chado in the analysis table.

analysis request table

After the user presses submit, email notifications will go out to users and admins as before.

User requests can be viewed by the admin at /admin/structure/datasets/report. Clicking "Edit" on a given dataset will let you view the details of the proposed record.

Note: Currently there is no way to automatically create the requested analysis. This feature is coming soon.

Module customization

We recommend using hook_form_alter and hook_mail_alter to customize the forms and emails sent to users.