From 77447038552601822b9d79ceca26d762094d0fb6 Mon Sep 17 00:00:00 2001
From: bjhardcastle <ben.hardcastle@alleninstitute.org>
Date: Fri, 20 Sep 2024 17:09:36 -0700
Subject: [PATCH] Use aind-session to get latest ks2.5 sorted asset

---
 pdm.lock                 | 353 ++++++++++++++++++++++++++++++++++++++-
 pyproject.toml           |   6 +
 src/npc_lims/paths/s3.py |  11 +-
 3 files changed, 359 insertions(+), 11 deletions(-)

diff --git a/pdm.lock b/pdm.lock
index 2e693d9..1999d4d 100644
--- a/pdm.lock
+++ b/pdm.lock
@@ -5,11 +5,75 @@
 groups = ["default", "dev", "docs"]
 strategy = []
 lock_version = "4.5.0"
-content_hash = "sha256:49d94109960cae3b577c4e2aef167a9be67457065ebda98d75d419faefa63b6b"
+content_hash = "sha256:7b3ff55e5bc2413064ce3fdac40ecdedaba3aafe98e7875fc52dd4172e569f80"
 
 [[metadata.targets]]
 requires_python = ">=3.9"
 
+[[package]]
+name = "aind-codeocean-api"
+version = "0.5.0"
+requires_python = ">=3.7"
+summary = "CodeOcean API manager in Python"
+dependencies = [
+    "boto3",
+    "pydantic-settings>=2.0",
+    "pydantic>=2.0",
+    "requests",
+]
+files = [
+    {file = "aind_codeocean_api-0.5.0-py3-none-any.whl", hash = "sha256:0ab46cd51553c7b7dc51dd9ff961863ff58231dab102bdaa59571432a110e66d"},
+    {file = "aind_codeocean_api-0.5.0.tar.gz", hash = "sha256:02425b1f49c588467050b007f45c727ea6f0fcc30b09a30d231e9b85b7bac5c0"},
+]
+
+[[package]]
+name = "aind-data-access-api"
+version = "0.15.0"
+requires_python = ">=3.8"
+summary = "API to interact with a few AIND databases"
+dependencies = [
+    "aind-codeocean-api>=0.4.0",
+    "pydantic-settings>=2.0",
+    "pydantic>=2.0",
+    "requests",
+]
+files = [
+    {file = "aind_data_access_api-0.15.0-py3-none-any.whl", hash = "sha256:bf9c0ba72ac77da4731d57ab77b400420a2bd4c0ed7251aea05f9a274ada0ead"},
+    {file = "aind_data_access_api-0.15.0.tar.gz", hash = "sha256:bc9135bac043f9d7edc86b5eb7a5439d5d6ef23327746672e6b79b9330a58330"},
+]
+
+[[package]]
+name = "aind-data-access-api"
+version = "0.15.0"
+extras = ["docdb"]
+requires_python = ">=3.8"
+summary = "API to interact with a few AIND databases"
+dependencies = [
+    "aind-data-access-api==0.15.0",
+    "pymongo==4.3.3",
+    "sshtunnel",
+]
+files = [
+    {file = "aind_data_access_api-0.15.0-py3-none-any.whl", hash = "sha256:bf9c0ba72ac77da4731d57ab77b400420a2bd4c0ed7251aea05f9a274ada0ead"},
+    {file = "aind_data_access_api-0.15.0.tar.gz", hash = "sha256:bc9135bac043f9d7edc86b5eb7a5439d5d6ef23327746672e6b79b9330a58330"},
+]
+
+[[package]]
+name = "aind-session"
+version = "0.2.5"
+requires_python = ">=3.9"
+summary = "User-friendly tools for accessing paths, metadata and assets related to AIND sessions."
+dependencies = [
+    "aind-data-access-api[docdb]>=0.14.0",
+    "codeocean>=0.1.5",
+    "npc-io>=0.1.30",
+    "npc-session>=0.1.39",
+]
+files = [
+    {file = "aind_session-0.2.5-py3-none-any.whl", hash = "sha256:b29d0428b19b49d84d76a8433621e7d06f669833a5d2a62e6a70e1859d4aae96"},
+    {file = "aind_session-0.2.5.tar.gz", hash = "sha256:7635d95fc496201e89ecef75bba658d14145eb345b541e2fd5319e60b7d29314"},
+]
+
 [[package]]
 name = "aiobotocore"
 version = "2.7.0"
@@ -140,6 +204,19 @@ files = [
     {file = "aiosignal-1.3.1.tar.gz", hash = "sha256:54cd96e15e1649b75d6c87526a6ff0b6c1b0dd3459f43d9ca11d48c339b68cfc"},
 ]
 
+[[package]]
+name = "annotated-types"
+version = "0.7.0"
+requires_python = ">=3.8"
+summary = "Reusable constraint types to use with typing.Annotated"
+dependencies = [
+    "typing-extensions>=4.0.0; python_version < \"3.9\"",
+]
+files = [
+    {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"},
+    {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"},
+]
+
 [[package]]
 name = "appdirs"
 version = "1.4.4"
@@ -207,6 +284,41 @@ files = [
     {file = "backports_strenum-1.3.1.tar.gz", hash = "sha256:77c52407342898497714f0596e86188bb7084f89063226f4ba66863482f42414"},
 ]
 
+[[package]]
+name = "bcrypt"
+version = "4.2.0"
+requires_python = ">=3.7"
+summary = "Modern password hashing for your software and your servers"
+files = [
+    {file = "bcrypt-4.2.0-cp37-abi3-macosx_10_12_universal2.whl", hash = "sha256:096a15d26ed6ce37a14c1ac1e48119660f21b24cba457f160a4b830f3fe6b5cb"},
+    {file = "bcrypt-4.2.0-cp37-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:c02d944ca89d9b1922ceb8a46460dd17df1ba37ab66feac4870f6862a1533c00"},
+    {file = "bcrypt-4.2.0-cp37-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:1d84cf6d877918620b687b8fd1bf7781d11e8a0998f576c7aa939776b512b98d"},
+    {file = "bcrypt-4.2.0-cp37-abi3-manylinux_2_28_aarch64.whl", hash = "sha256:1bb429fedbe0249465cdd85a58e8376f31bb315e484f16e68ca4c786dcc04291"},
+    {file = "bcrypt-4.2.0-cp37-abi3-manylinux_2_28_x86_64.whl", hash = "sha256:655ea221910bcac76ea08aaa76df427ef8625f92e55a8ee44fbf7753dbabb328"},
+    {file = "bcrypt-4.2.0-cp37-abi3-musllinux_1_1_aarch64.whl", hash = "sha256:1ee38e858bf5d0287c39b7a1fc59eec64bbf880c7d504d3a06a96c16e14058e7"},
+    {file = "bcrypt-4.2.0-cp37-abi3-musllinux_1_1_x86_64.whl", hash = "sha256:0da52759f7f30e83f1e30a888d9163a81353ef224d82dc58eb5bb52efcabc399"},
+    {file = "bcrypt-4.2.0-cp37-abi3-musllinux_1_2_aarch64.whl", hash = "sha256:3698393a1b1f1fd5714524193849d0c6d524d33523acca37cd28f02899285060"},
+    {file = "bcrypt-4.2.0-cp37-abi3-musllinux_1_2_x86_64.whl", hash = "sha256:762a2c5fb35f89606a9fde5e51392dad0cd1ab7ae64149a8b935fe8d79dd5ed7"},
+    {file = "bcrypt-4.2.0-cp37-abi3-win32.whl", hash = "sha256:5a1e8aa9b28ae28020a3ac4b053117fb51c57a010b9f969603ed885f23841458"},
+    {file = "bcrypt-4.2.0-cp37-abi3-win_amd64.whl", hash = "sha256:8f6ede91359e5df88d1f5c1ef47428a4420136f3ce97763e31b86dd8280fbdf5"},
+    {file = "bcrypt-4.2.0-cp39-abi3-macosx_10_12_universal2.whl", hash = "sha256:c52aac18ea1f4a4f65963ea4f9530c306b56ccd0c6f8c8da0c06976e34a6e841"},
+    {file = "bcrypt-4.2.0-cp39-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:3bbbfb2734f0e4f37c5136130405332640a1e46e6b23e000eeff2ba8d005da68"},
+    {file = "bcrypt-4.2.0-cp39-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:3413bd60460f76097ee2e0a493ccebe4a7601918219c02f503984f0a7ee0aebe"},
+    {file = "bcrypt-4.2.0-cp39-abi3-manylinux_2_28_aarch64.whl", hash = "sha256:8d7bb9c42801035e61c109c345a28ed7e84426ae4865511eb82e913df18f58c2"},
+    {file = "bcrypt-4.2.0-cp39-abi3-manylinux_2_28_x86_64.whl", hash = "sha256:3d3a6d28cb2305b43feac298774b997e372e56c7c7afd90a12b3dc49b189151c"},
+    {file = "bcrypt-4.2.0-cp39-abi3-musllinux_1_1_aarch64.whl", hash = "sha256:9c1c4ad86351339c5f320ca372dfba6cb6beb25e8efc659bedd918d921956bae"},
+    {file = "bcrypt-4.2.0-cp39-abi3-musllinux_1_1_x86_64.whl", hash = "sha256:27fe0f57bb5573104b5a6de5e4153c60814c711b29364c10a75a54bb6d7ff48d"},
+    {file = "bcrypt-4.2.0-cp39-abi3-musllinux_1_2_aarch64.whl", hash = "sha256:8ac68872c82f1add6a20bd489870c71b00ebacd2e9134a8aa3f98a0052ab4b0e"},
+    {file = "bcrypt-4.2.0-cp39-abi3-musllinux_1_2_x86_64.whl", hash = "sha256:cb2a8ec2bc07d3553ccebf0746bbf3d19426d1c6d1adbd4fa48925f66af7b9e8"},
+    {file = "bcrypt-4.2.0-cp39-abi3-win32.whl", hash = "sha256:77800b7147c9dc905db1cba26abe31e504d8247ac73580b4aa179f98e6608f34"},
+    {file = "bcrypt-4.2.0-cp39-abi3-win_amd64.whl", hash = "sha256:61ed14326ee023917ecd093ee6ef422a72f3aec6f07e21ea5f10622b735538a9"},
+    {file = "bcrypt-4.2.0-pp310-pypy310_pp73-manylinux_2_28_aarch64.whl", hash = "sha256:39e1d30c7233cfc54f5c3f2c825156fe044efdd3e0b9d309512cc514a263ec2a"},
+    {file = "bcrypt-4.2.0-pp310-pypy310_pp73-manylinux_2_28_x86_64.whl", hash = "sha256:f4f4acf526fcd1c34e7ce851147deedd4e26e6402369304220250598b26448db"},
+    {file = "bcrypt-4.2.0-pp39-pypy39_pp73-manylinux_2_28_aarch64.whl", hash = "sha256:1ff39b78a52cf03fdf902635e4c81e544714861ba3f0efc56558979dd4f09170"},
+    {file = "bcrypt-4.2.0-pp39-pypy39_pp73-manylinux_2_28_x86_64.whl", hash = "sha256:373db9abe198e8e2c70d12b479464e0d5092cc122b20ec504097b5f2297ed184"},
+    {file = "bcrypt-4.2.0.tar.gz", hash = "sha256:cf69eaf5185fd58f268f805b505ce31f9b9fc2d64b376642164e9244540c1221"},
+]
+
 [[package]]
 name = "black"
 version = "24.8.0"
@@ -752,6 +864,16 @@ files = [
     {file = "dataclasses_json-0.6.7.tar.gz", hash = "sha256:b6b3e528266ea45b9535223bc53ca645f5208833c29229e847b3f26a1cc55fc0"},
 ]
 
+[[package]]
+name = "dnspython"
+version = "2.6.1"
+requires_python = ">=3.8"
+summary = "DNS toolkit"
+files = [
+    {file = "dnspython-2.6.1-py3-none-any.whl", hash = "sha256:5ef3b9680161f6fa89daf8ad451b5f1a33b18ae8a1c6778cdf4b43f08c0a6e50"},
+    {file = "dnspython-2.6.1.tar.gz", hash = "sha256:e8f0f9c23a7b7cb99ded64e6c3a6f3e701d78f50c55e002b839dea7225cff7cc"},
+]
+
 [[package]]
 name = "et-xmlfile"
 version = "1.1.0"
@@ -1416,7 +1538,7 @@ files = [
 
 [[package]]
 name = "npc-io"
-version = "0.1.25"
+version = "0.1.30"
 requires_python = ">=3.9"
 summary = "File IO tools for MindScope Neuropixels projects in the cloud."
 dependencies = [
@@ -1428,21 +1550,21 @@ dependencies = [
     "universal-pathlib<0.2.0",
 ]
 files = [
-    {file = "npc-io-0.1.25.tar.gz", hash = "sha256:70d9811b2bb449087add82f6ed2b9889b757f5d06f4a3bc52cf9c8b4138bfee5"},
-    {file = "npc_io-0.1.25-py3-none-any.whl", hash = "sha256:dfed5b9cc33353fae12366a142c3c02bbd84ae96b2dadf3738d1d900bd033621"},
+    {file = "npc_io-0.1.30-py3-none-any.whl", hash = "sha256:4b37bcc9f61d8165190c3a2c2368ff3791569502a677f0ab8d2f99ed8941d859"},
+    {file = "npc_io-0.1.30.tar.gz", hash = "sha256:cef561d0a62815af394f397de40023cd8065a4006d1bcbb12558b83a97d7f0b8"},
 ]
 
 [[package]]
 name = "npc-session"
-version = "0.1.36"
+version = "0.1.39"
 requires_python = ">=3.9"
 summary = "Basic tools for parsing subject, session, date and time associated with data from the Mindscope Neuropixels team, in the cloud."
 dependencies = [
     "typing-extensions>=4.7.1",
 ]
 files = [
-    {file = "npc_session-0.1.36-py3-none-any.whl", hash = "sha256:9897c155b19550171804eafb7158eee6cb2466249c33ec3577ea5ede33dacb2f"},
-    {file = "npc_session-0.1.36.tar.gz", hash = "sha256:039da368643abb99a94d2acf1c991948fe72e0151025ac368520dc6db9221771"},
+    {file = "npc_session-0.1.39-py3-none-any.whl", hash = "sha256:b369ff7c71d9c2119fb18a4aa0f2a8bbab01c7a73ec3e67a0a0f94e594e5cbc3"},
+    {file = "npc_session-0.1.39.tar.gz", hash = "sha256:b32243cb6beb58802bae63208937bca6795726c483bef3354465c06f2ee11526"},
 ]
 
 [[package]]
@@ -1476,6 +1598,21 @@ files = [
     {file = "paginate-0.5.6.tar.gz", hash = "sha256:5e6007b6a9398177a7e1648d04fdd9f8c9766a1a945bceac82f1929e8c78af2d"},
 ]
 
+[[package]]
+name = "paramiko"
+version = "3.5.0"
+requires_python = ">=3.6"
+summary = "SSH2 protocol library"
+dependencies = [
+    "bcrypt>=3.2",
+    "cryptography>=3.3",
+    "pynacl>=1.5",
+]
+files = [
+    {file = "paramiko-3.5.0-py3-none-any.whl", hash = "sha256:1fedf06b085359051cd7d0d270cebe19e755a8a921cc2ddbfa647fb0cd7d68f9"},
+    {file = "paramiko-3.5.0.tar.gz", hash = "sha256:ad11e540da4f55cedda52931f1a3f812a8238a7af7f62a60de538cd80bb28124"},
+]
+
 [[package]]
 name = "parver"
 version = "0.5"
@@ -1531,6 +1668,124 @@ files = [
     {file = "pycparser-2.22.tar.gz", hash = "sha256:491c8be9c040f5390f5bf44a5b07752bd07f56edf992381b05c701439eec10f6"},
 ]
 
+[[package]]
+name = "pydantic"
+version = "2.9.2"
+requires_python = ">=3.8"
+summary = "Data validation using Python type hints"
+dependencies = [
+    "annotated-types>=0.6.0",
+    "pydantic-core==2.23.4",
+    "typing-extensions>=4.12.2; python_version >= \"3.13\"",
+    "typing-extensions>=4.6.1; python_version < \"3.13\"",
+]
+files = [
+    {file = "pydantic-2.9.2-py3-none-any.whl", hash = "sha256:f048cec7b26778210e28a0459867920654d48e5e62db0958433636cde4254f12"},
+    {file = "pydantic-2.9.2.tar.gz", hash = "sha256:d155cef71265d1e9807ed1c32b4c8deec042a44a50a4188b25ac67ecd81a9c0f"},
+]
+
+[[package]]
+name = "pydantic-core"
+version = "2.23.4"
+requires_python = ">=3.8"
+summary = "Core functionality for Pydantic validation and serialization"
+dependencies = [
+    "typing-extensions!=4.7.0,>=4.6.0",
+]
+files = [
+    {file = "pydantic_core-2.23.4-cp310-cp310-macosx_10_12_x86_64.whl", hash = "sha256:b10bd51f823d891193d4717448fab065733958bdb6a6b351967bd349d48d5c9b"},
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+    {file = "pymongo-4.3.3-cp39-cp39-manylinux_2_5_x86_64.manylinux1_x86_64.whl", hash = "sha256:fd7bb378d82b88387dc10227cfd964f6273eb083e05299e9b97cbe075da12d11"},
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+    {file = "pymongo-4.3.3.tar.gz", hash = "sha256:34e95ffb0a68bffbc3b437f2d1f25fc916fef3df5cdeed0992da5f42fae9b807"},
+]
+
+[[package]]
+name = "pynacl"
+version = "1.5.0"
+requires_python = ">=3.6"
+summary = "Python binding to the Networking and Cryptography (NaCl) library"
+dependencies = [
+    "cffi>=1.4.1",
+]
+files = [
+    {file = "PyNaCl-1.5.0-cp36-abi3-macosx_10_10_universal2.whl", hash = "sha256:401002a4aaa07c9414132aaed7f6836ff98f59277a234704ff66878c2ee4a0d1"},
+    {file = "PyNaCl-1.5.0-cp36-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.manylinux_2_24_aarch64.whl", hash = "sha256:52cb72a79269189d4e0dc537556f4740f7f0a9ec41c1322598799b0bdad4ef92"},
+    {file = "PyNaCl-1.5.0-cp36-abi3-manylinux_2_17_aarch64.manylinux2014_aarch64.whl", hash = "sha256:a36d4a9dda1f19ce6e03c9a784a2921a4b726b02e1c736600ca9c22029474394"},
+    {file = "PyNaCl-1.5.0-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.manylinux_2_24_x86_64.whl", hash = "sha256:0c84947a22519e013607c9be43706dd42513f9e6ae5d39d3613ca1e142fba44d"},
+    {file = "PyNaCl-1.5.0-cp36-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:06b8f6fa7f5de8d5d2f7573fe8c863c051225a27b61e6860fd047b1775807858"},
+    {file = "PyNaCl-1.5.0-cp36-abi3-musllinux_1_1_aarch64.whl", hash = "sha256:a422368fc821589c228f4c49438a368831cb5bbc0eab5ebe1d7fac9dded6567b"},
+    {file = "PyNaCl-1.5.0-cp36-abi3-musllinux_1_1_x86_64.whl", hash = "sha256:61f642bf2378713e2c2e1de73444a3778e5f0a38be6fee0fe532fe30060282ff"},
+    {file = "PyNaCl-1.5.0-cp36-abi3-win32.whl", hash = "sha256:e46dae94e34b085175f8abb3b0aaa7da40767865ac82c928eeb9e57e1ea8a543"},
+    {file = "PyNaCl-1.5.0-cp36-abi3-win_amd64.whl", hash = "sha256:20f42270d27e1b6a29f54032090b972d97f0a1b0948cc52392041ef7831fee93"},
+    {file = "PyNaCl-1.5.0.tar.gz", hash = "sha256:8ac7448f09ab85811607bdd21ec2464495ac8b7c66d146bf545b0f08fb9220ba"},
+]
+
 [[package]]
 name = "pyopenssl"
 version = "24.2.1"
@@ -1909,6 +2236,18 @@ files = [
     {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"},
 ]
 
+[[package]]
+name = "sshtunnel"
+version = "0.4.0"
+summary = "Pure python SSH tunnels"
+dependencies = [
+    "paramiko>=2.7.2",
+]
+files = [
+    {file = "sshtunnel-0.4.0-py2.py3-none-any.whl", hash = "sha256:98e54c26f726ab8bd42b47a3a21fca5c3e60f58956f0f70de2fb8ab0046d0606"},
+    {file = "sshtunnel-0.4.0.tar.gz", hash = "sha256:e7cb0ea774db81bf91844db22de72a40aae8f7b0f9bb9ba0f666d474ef6bf9fc"},
+]
+
 [[package]]
 name = "tomli"
 version = "2.0.1"
diff --git a/pyproject.toml b/pyproject.toml
index 4e260a1..4856a05 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -18,6 +18,7 @@ dependencies = [
     "types-requests>=2.31.0.6",
     "npc-io>=0.1.24",
     "codeocean>=0.1.5",
+    "aind-session>=0.2.5",
 ]
 requires-python = ">=3.9"
 readme = "README.md"
@@ -49,6 +50,11 @@ plugins = [
     "pdm-bump",
 ]
 
+[project.optional-dependencies]
+polars = [
+    "polars>=0.12.0",
+]
+
 [tool.pdm.dev-dependencies]
 dev = [
     "pytest>=7.4.0",
diff --git a/src/npc_lims/paths/s3.py b/src/npc_lims/paths/s3.py
index c96e6e3..ab901a5 100644
--- a/src/npc_lims/paths/s3.py
+++ b/src/npc_lims/paths/s3.py
@@ -7,6 +7,7 @@
 from collections.abc import Iterator
 
 import npc_session
+import aind_session
 import upath
 from codeocean.data_asset import DataAsset
 
@@ -108,12 +109,14 @@ def get_sorted_data_paths_from_s3(
         >>> assert len(sorted_data_s3_paths) > 0
     """
     if sorted_data_asset_id is not None:
-        sorted_data_asset = codeocean_utils.get_data_asset(sorted_data_asset_id)
+        np_session = npc_session.SessionRecord(session)
+        aind_session_ = aind_session.get_sessions(np_session.subject, np_session.date)[0]
+        sorted_data_asset = aind_session_.ecephys.latest_ks25_sorted_data_asset
     elif session is not None:
         sorted_data_asset = codeocean_utils.get_session_sorted_data_asset(session)
     else:
         raise ValueError("Must provide either session or sorted_data_asset_id")
-    return tuple(get_data_asset_s3_path(sorted_data_asset).iterdir())
+    return tuple(aind_session.get_data_asset_source_dir(sorted_data_asset).iterdir())
 
 
 @functools.cache
@@ -368,9 +371,9 @@ def get_LFP_subsampling_paths_from_s3(
     session: str | npc_session.SessionRecord,
 ) -> tuple[upath.UPath, ...]:
     """
-    >>> LFP_subsampled_s3_paths = get_LFP_subsampling_paths_from_s3('674562_2023-10-05')
+    >>> LFP_subsampled_s3_paths = get_LFP_subsampling_paths_from_s3('674562_2023-10-03')
     >>> len(LFP_subsampled_s3_paths)
-    8
+    7
     """
     session = npc_session.SessionRecord(session)
     session_LFP_asset = codeocean_utils.get_session_capsule_pipeline_data_asset(