This repository holds a fork of the "Materials Data Curation System (MDCS)" that has been customized for use as part of the NexusLIMS laboratory information management system (see the published manuscript for more details about NexusLIMS). This repository contains the "front-end" system that gives users access to experimental XML records built by the NexusLIMS backend.
The software was developed by the National Institute of Standards and Technology (NIST), and the standard NIST license
and disclaimer apply (see the LICENSE.txt file for details).
In general, the NexusLIMS developers strive to keep this code up-to-date with the "upstream" version of MDCS, although it may lag behind by a version or two at times due to the development effort required to integrate upstream changes.
It is recommended to deploy this application as described in the NexusLIMS Docker Deployment repository. For further details and suggestions for deployment, please see that repository.
A few values in this code have placeholders in order to make it less-specific to the NIST deployment environment. As a result, there are a couple places where values should be changed (either by the Docker deployment scripts, or manually) in order to get a working installation. The following table (potentially non-exhaustive) contains values you should or might want to change in order to customize the application to your specific needs:
| File | Value to Change | Notes |
|---|---|---|
xslt/detail_stylesheet.xsl |
datasetBaseUrl |
This <xsl:variable> value (and the others below) are
used to control the target of certain links on the HTML
conversion of the XML (which uses one of the XSLT files).
datasetBaseUrl should be a web-accessible path to the
root of the file structure (i.e. all location nodes
within a record's XML will be appended to
datasetBaseUrl to generate download links for the
individual files). |
xslt/detail_stylesheet.xsl |
previewBaseUrl |
Like above, but used with preview nodes to locate the
preview images that will be shown on the "detail view"
page. This could be the same as datasetBaseUrl if
the files are all in the same location, but is separated
out to provide flexibility. |
xslt/detail_stylesheet.xsl |
sharepointBaseUrl |
Mostly deprecated, but if using the older-style
SharePoint harvester, the web-accessible path to the
Lists page of the Sharepoint site should be given
in this variable value. Can be safely left blank if not
using the SharePoint harvester (which no one should be,
at this point). |
xslt/detail_stylesheet.xsl |
instr-color-
dictionary |
This portion of the XSLT should be customized with your
own instruments' PID values, and whatever colors you
would like to be used for the display badges when that
instrument is found. These PIDs correspond to the pid
attribute in the summary/instrument node of the
built XML records. |
xslt/detail_stylesheet.xsl |
sharepoint-
instrument-dictionary |
This is a deprecated holdover from the formerly used SharePoint calendar harvester, but it allows you to map instrument "display names" to specific calendar pages on the SharePoint site. Since most people will not be using SharePoint for calendaring, these values most likely can be safely deleted. |
xslt/list_stylesheet.xsl |
datasetBaseUrl |
Same as for in xslt/detail_stylesheet.xsl |
xslt/list_stylesheet.xsl |
previewBaseUrl |
Same as for in xslt/detail_stylesheet.xsl |
mdcs/settings.py |
DOCUMENTATION_LINK |
Set this value to a web-accessible documentation location. The link will be used to add a menu item to the navigation bar to allow easy access to the documentation pages. |
mdcs_home/menus.py |
Various
Menu.add_item(...)
lines |
In menus.py, there are multiple Menu.add_item()
calls that should be customized to reflect whatever
links and icons you would like to show up in the top
navigation bar. In the NIST deployment, these lines
provide links to the NEMO reservation system and the
EM Nexus shared file system, but they can be customized
as dictated by the specific deployment's needs. Note,
after changing any of these, you'll need to also update
static/js/menu-custom.js if you want the tutorial
to work properly by updating link IDs and the tutorial
text. |
static/js/menu-custom.js |
Tutorial steps defined
in create_tour()
function |
This javascript file defines the "steps" of a guided tutorial. Since some of those steps are specific to the NIST deployment, this tutorial should be reconfigured for your own environment if you desire. |
templates/theme/menu.html |
#cdcs-menu-title |
If you want to change the logo in the top menu bar, this is where you would do so |
templates/core_main_app/
user/homepage.html |
All the text | This template page controls the text on the NexusLIMS CDCS homepage, and so it should be customized to meet your deployment's specific needs. Likewise, you could change the NexusLIMS logo here to something more appropriate for your deployment. |