From 50df1cf7f2057f396fa0616418f2d877f428d90f Mon Sep 17 00:00:00 2001
From: sneakers-the-rat <JLSaunders987@gmail.com>
Date: Mon, 23 Oct 2023 23:57:44 -0700
Subject: [PATCH] initial and probably only

---
 poetry.lock              | 2341 ++++++++++++++++++++++++++++++++++++++
 pyproject.toml           |   21 +
 scrape_dandi/__init__.py |   58 +
 3 files changed, 2420 insertions(+)
 create mode 100644 poetry.lock
 create mode 100644 pyproject.toml
 create mode 100644 scrape_dandi/__init__.py

diff --git a/poetry.lock b/poetry.lock
new file mode 100644
index 0000000..ee488e3
--- /dev/null
+++ b/poetry.lock
@@ -0,0 +1,2341 @@
+# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand.
+
+[[package]]
+name = "aiohttp"
+version = "3.8.6"
+description = "Async http client/server framework (asyncio)"
+optional = false
+python-versions = ">=3.6"
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+
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+multidict = ">=4.0"
+
+[[package]]
+name = "zarr"
+version = "2.16.1"
+description = "An implementation of chunked, compressed, N-dimensional arrays for Python"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "zarr-2.16.1-py3-none-any.whl", hash = "sha256:de4882433ccb5b42cc1ec9872b95e64ca3a13581424666b28ed265ad76c7056f"},
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+
+[package.dependencies]
+asciitree = "*"
+fasteners = "*"
+numcodecs = ">=0.10.0"
+numpy = ">=1.20,<1.21.0 || >1.21.0"
+
+[package.extras]
+docs = ["numcodecs[msgpack]", "numpydoc", "pydata-sphinx-theme", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx-issues", "sphinx-rtd-theme"]
+jupyter = ["ipytree (>=0.2.2)", "ipywidgets (>=8.0.0)", "notebook"]
+
+[[package]]
+name = "zarr-checksum"
+version = "0.2.9"
+description = "Checksum support for zarrs stored in various backends"
+optional = false
+python-versions = ">=3.7,<4.0"
+files = [
+    {file = "zarr_checksum-0.2.9-py3-none-any.whl", hash = "sha256:a218f53a6a1ae4ba57b52306a4ec16de6b8aec14e7a7059c4a01b2ac1eed9209"},
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+]
+
+[package.dependencies]
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+click = ">=8.1.3,<9.0.0"
+pydantic = ">=1.10.2,<2.0.0"
+tqdm = ">=4.64.1,<5.0.0"
+zarr = ">=2.12,<3.0"
+
+[package.extras]
+dev = ["black (>=22.12.0,<23.0.0)", "boto3-stubs[s3] (>=1.24,<2.0)", "flake8 (>=5.0.4,<6.0.0)", "flake8-black (>=0.3.6,<0.4.0)", "flake8-bugbear (>=23.1.20,<24.0.0)", "flake8-docstrings (>=1.7.0,<2.0.0)", "flake8-isort (>=6.0.0,<7.0.0)", "flake8-quotes (>=3.3.2,<4.0.0)", "isort (>=5.11.4,<6.0.0)", "pep8-naming (>=0.13.3,<0.14.0)"]
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+test = ["pytest (>=7.2.1,<8.0.0)"]
+
+[[package]]
+name = "zipp"
+version = "3.17.0"
+description = "Backport of pathlib-compatible object wrapper for zip files"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "zipp-3.17.0-py3-none-any.whl", hash = "sha256:0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31"},
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+]
+
+[package.extras]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (<7.2.5)", "sphinx (>=3.5)", "sphinx-lint"]
+testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-black (>=0.3.7)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy (>=0.9.1)", "pytest-ruff"]
+
+[metadata]
+lock-version = "2.0"
+python-versions = "^3.11"
+content-hash = "255b26438bcdaa14b4614da06a257e5d344691e5248c07e90e1fa4032045a5c4"
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..1bd0615
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,21 @@
+[tool.poetry]
+name = "scrape-dandi"
+version = "0.1.0"
+description = "scraping dandi"
+authors = ["sneakers-the-rat <JLSaunders987@gmail.com>"]
+readme = "README.md"
+packages = [
+	{ include = "scrape_dandi" }
+]
+
+[tool.poetry.scripts]
+scrape-dandi = "scrape_dandi:main"
+
+[tool.poetry.dependencies]
+python = "^3.11"
+dandi = "^0.56.2"
+
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
diff --git a/scrape_dandi/__init__.py b/scrape_dandi/__init__.py
new file mode 100644
index 0000000..9a57816
--- /dev/null
+++ b/scrape_dandi/__init__.py
@@ -0,0 +1,58 @@
+from pathlib import Path
+from tqdm import trange
+from datetime import datetime
+
+from dandi.consts import ZARR_EXTENSIONS, metadata_all_fields
+from dandi.dandiarchive import DandisetURL, _dandi_url_parser, parse_dandi_url
+from dandi.cli.cmd_download import download
+
+
+#OUT_DIR = Path('/mnt/seedbank/p2p/dandi/')
+OUT_DIR = '.'
+LOG_TXT = 'log.txt'
+SKIP_DANDISETS = [
+    '000108' # humongous 372 human light sheet imaging
+]
+DANDI_ID = 'DANDI:{:06d}'
+MAX_DANDISET = 683
+
+
+
+def check_nwb(dandiset:int) -> bool:
+    if dandiset == 108:
+        return False
+
+    id = DANDI_ID.format(dandiset)
+    try:
+        url = parse_dandi_url(id)
+        with url.navigate(strict=True) as (c, dandiset,assets):
+            is_nwb = any([a.path.endswith('nwb') for a in assets])
+            is_not_draft = dandiset.version.identifier != 'draft'
+            return is_nwb and is_not_draft
+    except:
+        return False
+
+
+def main():
+
+    for i in trange(MAX_DANDISET):
+
+        if not check_nwb(i):
+            with open(LOG_TXT, 'a') as lfile:
+                lfile.write(f"{datetime.now().isoformat()} - {i:03d} - SKIP\n")
+            continue
+        id = DANDI_ID.format(i)
+        download(
+            [
+                id,
+                '-o', str(OUT_DIR),
+                '--existing', 'refresh',
+                '--jobs', '24'
+             ]
+        )
+        with open(LOG_TXT, 'a') as lfile:
+            lfile.write(f"{datetime.now().isoformat()} - {i:03d} - GET\n")
+
+
+
+