Linking community and technology to enable FAIR data

Tools Confluence
DISQOVER
DMPMaastricht
Maastricht Data Repository

Page tree

Linking community and technology to enable FAIR data

Skip to end of metadata
Go to start of metadata

 User manual


Introduction

This user manual will guide you through the process of uploading data to the Maastricht Data Repository (MDR) via the drop zones method. 

Before you start!

Prerequisites and general conditions for uploading new data are: 

  1. You have been assigned a project from the DataHub intake interview. If not, please refer to this page: Starting a new project
  2. You are connected to the UM- or MUMC-network. Either physically or via VPN
  3. You are using a compatible web browser (Chrome or Firefox recommended)
  4. You have an UM- or MUMC-account
  5. You have the drop zones network drive mounted:

    Windows users 

    1. The network drive W:\ should be visible from Windows Explorer - My Computer.
    2. In case you don't see the W:\ drive, you can copy-paste this URL in the address bar of Windows Explorer \\ca-um-nas201.unimaas.nl\RIT-iRODS-ingestzones\prod

    Mac and Linux users

    1. Make sure to mount the SMB/CIFS network location ca-um-nas201.unimaas.nl/RIT-iRODS-ingestzones/prod

    Windows users 

    1. Copy-paste this URL in the address bar of Windows Explorer \\researchitrc04.prd.corp\resitcachprod

    Mac and Linux users

    1. Make sure to mount the SMB/CIFS network location researchitrc04.prd.corp/resitcachprod



The end result will be a data set that is:

  • annotated with ontology-enriched metadata;
  • safely stored in the iRODS storage environment;
  • findable (on metadata) for all MUMC+ users;
  • accessible by the members of your project.



Instructions

If you meet the requirements listed above, you can begin uploading a new data set (also called Collection) to the Maastricht Data Repository.

Click on the screenshots to enlarge them!

Step 1 - Open MDR

Point your browser to https://mdr.datahubmaastricht.nl/
Use the menu on the left side to login with your UM- or MUMC+ credentials.


Step 2 - Listing drop zones

Click the Preserve data item to expand the menu at the left side and click Drop zones.




This will display the list of active drop zones for your account. 
If no active drop zones can be found, for instance because this is your first time visiting MDR, only the "Create new drop zone" button is shown. 



There are 2 active drop zones for this account

This user does not have any drop zones yet.



Step 3 - Create a new drop zone and enter metadata

Click on Create new drop zone. This opens the create drop zone configuration form, requiring you to choose a project and metadata schema. Submitting the configuration opens a new metadata entry form based on the schema you selected

  • Try to fill in as much info as possible.

The new customizable metadata feature allows to update metadata, even after the drop zone is ingested into a collection. 

  • Some fields are required, marked with an asterisk
  • More information about fields that are not self-explanatory can be found by clicking the blue i icon

After entering the metadata, press Submit to store the metadata information and return to the drop zones listing.












Step 4 - Access the new drop zone

By pressing Submit in step 3, you return to the listing of drop zones and will see a new card containing the information of your drop zone and most important, the internal name that this drop zone has been assigned (eg. hungry-hazel).

The metadata that you've just entered has been saved in an XML file and the new drop zone is also created on your network drive W:


Open your file browser (i.e. Windows Explorer) and navigate to the W:\ network drive. You will see that the drop zone folder with the generated name (eg. hungry-hazel) appears in the listing.

If you don't have a W:\ network disk, you can use these direct links to access the drop zones:

Windows users 

  1. Copy-paste this URL in the address bar of Windows Explorer \\ca-um-nas201.unimaas.nl\RIT-iRODS-ingestzones\prod

Mac and Linux users

  1. Make sure to mount the SMB/CIFS network location ca-um-nas201.unimaas.nl/RIT-iRODS-ingestzones/prod

Windows users 

  1. Copy-paste this URL in the address bar of Windows Explorer \\researchitrc04.prd.corp\resitcachprod

Mac and Linux users

  1. Make sure to mount the SMB/CIFS network location researchitrc04.prd.corp/resitcachprod









UM drop zones


MUMC drop zones


Step 5 - Copy data to the drop zone

Add the actual data files of this data set to the newly created dropzone folder. Data files can consist of raw data, derived data, protocols etc. Any file format is allowed. It is also possible to upload subfolders.

Just copy-and-paste or drag-and-drop the data from your local hard drive (or USB-drive) to this dropzone folder.



Step 6 - Ingest the data

When the data transfer into the drop zone has finished, you can ingest the data into Maastricht Data Repository for persistent storage. 
To do so, choose the appropriate drop zone card (here: silly-toad) and click the blue pencil icon to continue.







Optional: if you just want to save the changed metadata and not start the ingest operation yet, click Save drop zone.

Please make sure that all the metadata is still correct and click Ingest at the very end of the form.

A message pops up asking for confirmation. Click Start ingest.



What happens now is that your data set is moved from the temporary drop zone to a permanent location in the Maastricht Data Repository.
Your will also see that the status of your data set changes sequentially to:

  • in queue for validation
  • validating
  • in queue for ingestion
  • ingesting
  • ingested

  

24 hours after a successful ingest, the drop zone card will disappear from the list and the drop zone will be deleted from the network drive. 




Step 7 - Retrieve the data

To browse and download the data, please follow the User manual: Methods for retrieving data guide.