From 2a711dc28139e29e3067f8e04077031b3c31040d Mon Sep 17 00:00:00 2001 From: Nicole Tregoning Date: Thu, 9 Apr 2026 17:07:50 -0400 Subject: [PATCH 1/2] add upload data instructions --- docs/user-guide/uploading-data.md | 89 +++++++++++++++++++++++++++++++ mkdocs.yml | 6 ++- pyproject.toml | 1 + uv.lock | 2 + 4 files changed, 97 insertions(+), 1 deletion(-) diff --git a/docs/user-guide/uploading-data.md b/docs/user-guide/uploading-data.md index e69de29..aa67295 100644 --- a/docs/user-guide/uploading-data.md +++ b/docs/user-guide/uploading-data.md @@ -0,0 +1,89 @@ +# Upload Data + +These instructions will guide you on how to upload data to EMBER-DANDI. + +Please follow the instructions for the option that best fits your needs: + +**My files are all in NWB and BIDS:** + +Below, we have provided one set of instructions for users that new to EMBER-DANDI, and one set for experienced users. + +1. [I've used DANDI or CLI tools before](#instructions-for-experienced-users) +2. [I'm new to Python, CLI, and/or DANDI](#instructions-for-new-users) + - Learn how to set up Python, install the DANDI CLI, and use NWB + +**My files are in a mix of standards or I have not used standards:** + +Please contact the EMBER team at [help@emberarchive.org](mailto:help@emberarchive.org) to facilitate data ingestion into EMBER-DANDI. We are also happy to add you to our Slack workspace. + + +## Instructions for Experienced Users + +The following is a quick reference of the steps for uploading data using the DANDI CLI: +``` +dandi download https://dandi.emberarchive.org/dandiset//draft +cd +dandi organize -f dry +dandi organize +dandi validate . +dandi upload -i ember-dandi +``` + +## Instructions for New Users + +### Install Python + +If you're new to Python, it may be useful to start by checking out (Python's Getting Started page)[https://www.python.org/about/gettingstarted/]. There are many ways to install and use Python, so we've highlighted a few common ways to get started below. +- [Install Anaconda](https://www.anaconda.com/docs/getting-started/getting-started) +- [Install uv](https://docs.astral.sh/uv/#installation) + +### Install the [DANDI Client](https://pypi.org/project/dandi/) + +Once you've gotten up and running with Python, the following command will install the DANDI CLI: +```bash +pip install -U dandi +``` + +### Register for an EMBER-DANDI Account + +The steps for registering for an EMBER-DANDI account can found on our [Getting Started](../getting-started/index.md#account-creation) page. + +### Getting Started with NWB + +For the latest information on NWB (Neurodata Without Borders), we recommend referring to their documentation at [nwb.org](https://nwb.org)! + +Below, you will find a brief set of steps to help you quickly get started with NWB. + +1. We recommended installing the [NWB Guide](https://nwb-guide.readthedocs.io/en/stable/installation.html), a desktop application that converts common neuroscience data formats into NWB to enable uploading to EMBER-DANDI. +2. Complete key tutorials for NWB GUIDE: + - [Generate a dataset](https://nwb-guide.readthedocs.io/en/stable/tutorials/dataset.html) + - Convert a [single session of data](https://nwb-guide.readthedocs.io/en/stable/tutorials/single_session.html) + - Convert a [multi-session of data](https://nwb-guide.readthedocs.io/en/stable/tutorials/multiple_sessions.html) +3. Repeat steps with your own your data + - Important Note: All data formats are not currently supported! Ensure your data is supported by checking the [ecosystem compatibility](https://nwb-guide.readthedocs.io/en/stable/format_support.html) + +### Create an EMBER-DANDI dandiset + +1. Log in to EMBER-DANDI with your approved GitHub account +2. Select the "New Dandiset" button in the top right corner +3. Fill out basic metadata and hit "Register Dandiset" + +### Upload data to your dandiset + +1. Validate your converted files, replacing `` with the path to your .nwb files: + + ```bash + dandi validate --ignore DANDI.NO_DANDISET_FOUND + ``` + +2. Navigate to your dataset in the EMBER-DANDI archive and copy the dandiset ID number +3. Upload your validated .nwb files using the following commands, replacing `` and `` with your specific information: + + ```bash + dandi download https://dandi.emberarchive.org/dandiset//draft + cd + dandi organize -f dry + dandi organize + dandi validate . + dandi upload -i ember-dandi + ``` \ No newline at end of file diff --git a/mkdocs.yml b/mkdocs.yml index 0de4310..3583d65 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -27,11 +27,15 @@ theme: extra_css: - stylesheets/extra.css +markdown_extensions: + - pymdownx.superfences + - pymdownx.highlight + nav: - Home: index.md - Getting Started: - Overview: getting-started/index.md - User Guide: - Overview: user-guide/index.md - # - user-guide/uploading-data.md + - user-guide/uploading-data.md # - user-guide/downloading-data.md diff --git a/pyproject.toml b/pyproject.toml index 1d944cc..ff6dcb1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -7,4 +7,5 @@ requires-python = ">=3.12" dependencies = [ "mkdocs>=1.6.1", "mkdocs-material>=9.7.0", + "pymdown-extensions>=10.17.1", ] diff --git a/uv.lock b/uv.lock index 4b732e3..fde7b11 100644 --- a/uv.lock +++ b/uv.lock @@ -32,12 +32,14 @@ source = { virtual = "." } dependencies = [ { name = "mkdocs" }, { name = "mkdocs-material" }, + { name = "pymdown-extensions" }, ] [package.metadata] requires-dist = [ { name = "mkdocs", specifier = ">=1.6.1" }, { name = "mkdocs-material", specifier = ">=9.7.0" }, + { name = "pymdown-extensions", specifier = ">=10.17.1" }, ] [[package]] From 7695ee9a0e3e5ce7dc8a70fb285a3f7e3ec4d898 Mon Sep 17 00:00:00 2001 From: Nicole Tregoning Date: Thu, 9 Apr 2026 17:12:09 -0400 Subject: [PATCH 2/2] rename upload -> uploading for consistency --- docs/user-guide/uploading-data.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/user-guide/uploading-data.md b/docs/user-guide/uploading-data.md index aa67295..bbfed51 100644 --- a/docs/user-guide/uploading-data.md +++ b/docs/user-guide/uploading-data.md @@ -1,4 +1,4 @@ -# Upload Data +# Uploading Data These instructions will guide you on how to upload data to EMBER-DANDI.