From c2c71a981c01c29a48433971c9f66e2e7a43b3e6 Mon Sep 17 00:00:00 2001
From: Tyler <tsingerclark@ucdavis.edu>
Date: Sun, 6 Jul 2025 12:29:53 -0700
Subject: [PATCH] Added a script to auto-download the data from Dryad

---
 README.md        |   2 +-
 download_data.py | 111 +++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 112 insertions(+), 1 deletion(-)
 create mode 100644 download_data.py

diff --git a/README.md b/README.md
index ea78782..5109f61 100644
--- a/README.md
+++ b/README.md
@@ -25,7 +25,7 @@ The code is organized into five main directories: `utils`, `analyses`, `data`, `
 
 ## Data
 ### Data Overview
-The data used in this repository (which can be downloaded from [Dryad](https://datadryad.org/stash/dataset/doi:10.5061/dryad.dncjsxm85)) consists of various datasets for recreating figures and training/evaluating the brain-to-text model:
+The data used in this repository (which can be downloaded from [Dryad](https://datadryad.org/stash/dataset/doi:10.5061/dryad.dncjsxm85), either manually from the website, or using `download_data.py`) consists of various datasets for recreating figures and training/evaluating the brain-to-text model:
 - `t15_copyTask.pkl`: This file contains the online Copy Task results required for generating Figure 2.
 - `t15_personalUse.pkl`: This file contains the Conversation Mode data required for generating Figure 4.
 - `t15_copyTask_neuralData.zip`: This dataset contains the neural data for the Copy Task.
diff --git a/download_data.py b/download_data.py
new file mode 100644
index 0000000..9b37b2b
--- /dev/null
+++ b/download_data.py
@@ -0,0 +1,111 @@
+"""
+Run this file to download data from Dryad and unzip the zip files. Downloaded files end
+up in this repostitory's data/ directory.
+
+First create the b2txt25 conda environment. Then in a Terminal, at this repository's
+top-level directory (nejm-brain-to-text/), run:
+
+conda activate b2txt25
+python download_data.py
+"""
+
+import sys
+import os
+import urllib.request
+import json
+import zipfile
+
+
+########################################################################################
+#
+# Helpers.
+#
+########################################################################################
+
+
+def display_progress_bar(block_num, block_size, total_size, message=""):
+    """"""
+    bytes_downloaded_so_far = block_num * block_size
+    MB_downloaded_so_far = bytes_downloaded_so_far / 1e6
+    MB_total = total_size / 1e6
+    sys.stdout.write(
+        f"\r{message}\t\t{MB_downloaded_so_far:.1f} MB / {MB_total:.1f} MB"
+    )
+    sys.stdout.flush()
+
+
+########################################################################################
+#
+# Main function.
+#
+########################################################################################
+
+
+def main():
+    """"""
+    DRYAD_DOI = "10.5061/dryad.dncjsxm85"
+
+    ## Make sure the command is being run from the right place and we can see the data/
+    ## directory.
+
+    DATA_DIR = "data/"
+    data_dirpath = os.path.abspath(DATA_DIR)
+    assert os.getcwd().endswith(
+        "nejm-brain-to-text"
+    ), f"Please run the download command from the nejm-brain-to-text directory (instead of {os.getcwd()})"
+    assert os.path.exists(
+        data_dirpath
+    ), "Cannot find the data directory to download into."
+
+    ## Get the list of files from the latest version on Dryad.
+
+    DRYAD_ROOT = "https://datadryad.org"
+    urlified_doi = DRYAD_DOI.replace("/", "%2F")
+
+    versions_url = f"{DRYAD_ROOT}/api/v2/datasets/doi:{urlified_doi}/versions"
+    with urllib.request.urlopen(versions_url) as response:
+        versions_info = json.loads(response.read().decode())
+
+    files_url_path = versions_info["_embedded"]["stash:versions"][-1]["_links"][
+        "stash:files"
+    ]["href"]
+    files_url = f"{DRYAD_ROOT}{files_url_path}"
+    with urllib.request.urlopen(files_url) as response:
+        files_info = json.loads(response.read().decode())
+
+    file_infos = files_info["_embedded"]["stash:files"]
+
+    ## Download each file into the data directory (and unzip for certain files).
+
+    for file_info in file_infos:
+        filename = file_info["path"]
+
+        if filename == "README.md":
+            continue
+
+        download_path = file_info["_links"]["stash:download"]["href"]
+        download_url = f"{DRYAD_ROOT}{download_path}"
+
+        download_to_filepath = os.path.join(data_dirpath, filename)
+
+        urllib.request.urlretrieve(
+            download_url,
+            download_to_filepath,
+            reporthook=lambda *args: display_progress_bar(
+                *args, message=f"Downloading {filename}"
+            ),
+        )
+        sys.stdout.write("\n")
+
+        # If this file is a zip file, unzip it into the data directory.
+
+        if file_info["mimeType"] == "application/zip":
+            print(f"Extracting files from {filename} ...")
+            with zipfile.ZipFile(download_to_filepath, "r") as zf:
+                zf.extractall(data_dirpath)
+
+    print(f"Download complete. See data files in {data_dirpath}\n")
+
+
+if __name__ == "__main__":
+    main()