Batch Submitting Multiple Media

Owned by Julie Winchester
Last updated: Aug 07, 2024
4 min read

Before continuing, please be sure you are familiar with the concepts and workflows described in How to Create and Edit Media, because almost all of the concepts discussed there apply for batch submitting multiple media as well. 

After you are granted access to batch submission features, you can begin batch submitting multiple media. This process involves two phases: uploading media files to your personal file deposit folder in the MorphoSource Globus share, and then providing a media metadata manifest to initiate a batch submission ingest. Important: Each ingest is limited to media files representing specimens from one organization (museum collection, laboratory, etc.) and imaged by one imaging device. You will need to create multiple ingests for each combination of organizations and devices your media are associated with.

Uploading media files to Globus

In order for media files to be available for batch submission ingestion, they must be uploaded to your personal deposit folder within the MorphoSource Batch Submission Deposits Globus share. This folder will be created for you when you are granted access to batch submission. In many ways, uploading files to Globus is easier than uploading files through the MorphoSource web interface, as you can initiate the upload of multiple files, leave them uploading unattended or overnight, and restart downloads automatically if they are interrupted. 

Please see the following tutorials for instructions on adding files to your Globus folder.

Initiate a batch submission ingest

  1. Log in to MorphoSource and visit your Dashboard. 

  2. In the left sidebar, under Repository Contents you will find Batch Submission. Click this link. On the batch submission dashboard page, you can either view the status of your currently in-progress batch submissions or create a new batch submission ingest. Click Create a new batch upload submission. 

  3. You must provide the metadata relating to each individual media file using an Excel-format media metadata manifest file. Click Download blank submission manifest Excel file (XLSX) to download the blank initial version of the manifest file. 

  4. Fill out the manifest file, using one row for each individual media file. Please note: this is slightly different from the previous MorphoSource 1 batch upload manifest file. For MorphoSource 1, related CT image stacks and meshes were listed in the same row together. In this new format, the CT stack would be listed on its own row, and the mesh file would be listed in a separate row of its own as well. The mesh would be associated with the CT stack using the parent media referencing columns. 

  5. After the manifest file is completely filled out, return to the batch submission ingest form. Provide the basic details and the ownership and permission details that relate to your entire batch submission. Important: If these media are covered by a fund code that supports the cost of storage for these media, be sure to select it at this step!

  6. When you are finished filling out the web form, upload the manifest Excel file, then click Submit. 

  7. The system will validate your manifest Excel file. It may find issues with how you have described the media in the file. If this is the case, it will show you which rows and specific cells caused issues. If any exist, fix them in the manifest file, and then go back and resubmit the form. If no issues were found, you can then choose to proceed to creating the batch submission ingest. 

  8. Batch submission ingests can take some time to complete, especially if many other users are using MorphoSource at the same time. You can return to the batch submission dashboard page to track the progress of your batch submission job. Additionally, when the batch submission completes, you will receive an email and a site notification informing you of this. If your batch submission fails for any reason, please let us know and allow us to investigate the situation before submitting a new batch submission ingest. 

Video Tutorial