Skip to content

Including EMBER related instructions #4

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Draft
wants to merge 1 commit into
base: master
Choose a base branch
from
Draft

Including EMBER related instructions #4

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
16 changes: 8 additions & 8 deletions docs/13_upload.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# Creating Dandisets and Uploading Data
# Creating Dandisets and Uploading Data to EMBER-DANDI

This page provides instructions for creating a new Dandiset and uploading data to DANDI.

Expand All @@ -14,7 +14,7 @@ This page provides instructions for creating a new Dandiset and uploading data t
Feel free to [reach out to us for help](https://github.com/dandi/helpdesk/discussions).

2. **Choose a server.**
- **Production server**: https://dandiarchive.org. This is the main server for DANDI and should be used for sharing neuroscience data.
- **Production server**: https://dandi.emberarchive.org. This is the main server for EMBER-DANDI and should be used for sharing neuroscience data.
When you create a Dandiset, a permanent ID is automatically assigned to it.
This Dandiset can be fully public or embargoed according to NIH policy.
All data are uploaded as draft and can be adjusted before publishing on the production server.
Expand All @@ -24,11 +24,11 @@ This page provides instructions for creating a new Dandiset and uploading data t

The below instructions will alert you to where the commands for interacting with these two different servers differ slightly.

3. **Register for DANDI and copy the API key.** To create a new Dandiset and upload your data, you need to have a DANDI account.
* If you do not already have an account, see [Create a DANDI Account](./16_account.md) page for instructions.
3. **Register for EMBER-DANDI and copy the API key.** To create a new Dandiset and upload your data, you need to have an EMBER-DANDI account.
* If you do not already have an account, see [Create an EMBER-DANDI Account](./16_account.md) page for instructions.
* Once you are logged in, copy your API key.
Click on your user initials in the top-right corner after logging in.
Production (https://dandiarchive.org) and staging (https://gui-staging.dandiarchive.org) servers have different API keys and different logins.
Production (https://dandi.emberarchive.org) and staging (https://dandi.emberarchive.org) servers have different API keys and different logins.
* Store your API key somewhere that the CLI can find it; see ["Storing Access Credentials"](#storing-access-credentials) below.

## Data upload/management workflow
Expand Down Expand Up @@ -57,7 +57,7 @@ The CLI approach may be more suitable for users who are comfortable with the com
nwbinspector --help

Thoroughly read the NWBInspector report and try to address as many issues as possible.
**DANDI will prevent validation and upload of any issues labeled as level 'CRITICAL' or above when using the `--config dandi` option.**
**EMBER-DANDI will prevent validation and upload of any issues labeled as level 'CRITICAL' or above when using the `--config dandi` option.**
See ["Validation Levels for NWB Files"](./135_validation.md) for more information about validation criteria for
uploading NWB files and which are deemed critical. We recommend regularly running the inspector early in the process to generate the best NWB files possible. Note that some auto-detected violations, such as `check_data_orientation`, may be safely ignored in the event
that the data is confirmed to be in the correct form. See [the NWBInspector CLI documentation](https://nwbinspector.readthedocs.io/en/dev/user_guide/using_the_command_line_interface.html) for more information.
Expand All @@ -74,7 +74,7 @@ The CLI approach may be more suitable for users who are comfortable with the com

1. **Upload the data to DANDI.** This can either be done through the NWB GUIDE, or programmatically:

dandi download https://dandiarchive.org/dandiset/<dataset_id>/draft
dandi download https://dandi.emberarchive.org/<dataset_id>/draft
Copy link
Member

@NEStock NEStock Mar 10, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

should this be

        dandi download https://dandi.emberarchive.org/dandiset/<dataset_id>/draft

or

        dandi download https://dandi.emberarchive.org/<dataset_id>/draft

cd <dataset_id>
dandi organize <source_folder> -f dry
dandi organize <source_folder>
Expand All @@ -87,7 +87,7 @@ The CLI approach may be more suitable for users who are comfortable with the com
If you have an issue using the DANDI Client, see the [DANDI Debugging section](./15_debugging.md).

1. **Add metadata to the Dandiset.** Visit your Dandiset landing page:
`https://dandiarchive.org/dandiset/<dataset_id>/draft` and click on the `METADATA` link.
`https://dandi.emberarchive.org/dandiset/<dataset_id>/draft` and click on the `METADATA` link.


## Storing Access Credentials
Expand Down
16 changes: 8 additions & 8 deletions docs/16_account.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,17 +1,17 @@
# Create a DANDI Account

A DANDI account enhances your capabilities within the DANDI Archive.
A EMBER-DANDI account enhances your capabilities within the EMBER-DANDI Archive.
Without an account, users can freely search, view, and download available datasets.
With an account, users can create and edit Dandisets, and use the DANDI Hub to analyze data.
With an account, users can create and edit Dandisets, and use the EMBER-DANDI Hub to analyze data.

DANDI provides two servers:
EMBER-DANDI provides two servers:

- **Main server**: [https://dandiarchive.org/](https://dandiarchive.org/) - This is the primary platform for most users.
- **Staging server**: [https://gui-staging.dandiarchive.org/](https://gui-staging.dandiarchive.org/) - Ideal for training and testing purposes.
- **Main server**: [https://dandi.emberarchive.org](https://dandi.emberarchive.org) - This is the primary platform for most users using EMBER-DANDI.
- **Staging server**: [https://dandi.emberarchive.org](https://dandi.emberarchive.org) - Ideal for training and testing purposes.
Copy link
Member

@NEStock NEStock Mar 10, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Suggested change
- **Staging server**: [https://dandi.emberarchive.org](https://dandi.emberarchive.org) - Ideal for training and testing purposes.
- **Staging server**: [https://sandbox--ember-dandi-archive.netlify.app](https://sandbox--ember-dandi-archive.netlify.app/) - Ideal for training and testing purposes.

Copy link
Member

@NEStock NEStock Mar 10, 2025

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Actually, @laurendiaz @sandyhider -- do we even want to advertise the sandbox? Maybe no?

Copy link

@sandyhider sandyhider Mar 10, 2025 •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I think Nicole Stock is right. The sandbox is really for us to test with. We don't want other people uploading to it, unless we specifically ask them to, for a specific test case.


Accounts are independently managed on each server, allowing users to register on one or both, depending on their testing and deployment needs.

DANDI is freely accessible to the neuroscience research community.
EMBER-DANDI is freely accessible to the neuroscience research community.
Membership is usually granted automatically to GitHub accounts with a `.edu` or similar academic email.
If your registration is denied:

Expand All @@ -21,9 +21,9 @@ If your registration is denied:
## How to Register for a DANDI Account

1. **Create a GitHub Account**: If not already a GitHub user, [sign up here](https://github.com/).
2. **Register on DANDI**: Navigate to the [DANDI homepage](https://dandiarchive.org) and click the `LOG IN WITH GITHUB` button to register using your GitHub account.
2. **Register on EMBER-DANDI**: Navigate to the [EMBER-DANDI homepage](https://dandi.emberarchive.org) and click the `LOG IN WITH GITHUB` button to register using your GitHub account.
3. **Confirmation of Review**: Post-registration, you will receive an email confirming that your account is under review. Your request will be reviewed within 24 hours.
- **Note**: Reviews may extend beyond 24 hours for new GitHub accounts or non-.edu email addresses, particularly if the registration does not describe immediate plans to contribute data.
4. **Accessing DANDI**: Upon approval, access DANDI by logging in through the `LOG IN WITH GITHUB` button.
4. **Accessing DANDI**: Upon approval, access EMBER-DANDI by logging in through the `LOG IN WITH GITHUB` button.

For support or further inquiries, reach out to [help@dandiarchive.org](mailto:help@dandiarchive.org).