diff --git a/apps/iatlas/data/.dockerignore b/apps/iatlas/data/.dockerignore
deleted file mode 100644
index d9a6724a1e..0000000000
--- a/apps/iatlas/data/.dockerignore
+++ /dev/null
@@ -1,6 +0,0 @@
-**/*.md
-.gitignore
-.git/
-Dockerfile
-no_commit/
-scripts/
\ No newline at end of file
diff --git a/apps/iatlas/data/.flake8 b/apps/iatlas/data/.flake8
new file mode 100644
index 0000000000..3da962c38e
--- /dev/null
+++ b/apps/iatlas/data/.flake8
@@ -0,0 +1,11 @@
+[flake8]
+exclude =
+	.git,
+	__pycache__,
+	build,
+	dist,
+	.tox,
+	venv,
+	.venv,
+	.pytest_cache
+max-line-length = 120
diff --git a/apps/iatlas/data/.python-version b/apps/iatlas/data/.python-version
index 2419ad5b0a..3e72aa6986 100644
--- a/apps/iatlas/data/.python-version
+++ b/apps/iatlas/data/.python-version
@@ -1 +1 @@
-3.11.9
+3.11.10
diff --git a/apps/iatlas/data/Dockerfile b/apps/iatlas/data/Dockerfile
index 986824a4c7..1ae8ccdd35 100644
--- a/apps/iatlas/data/Dockerfile
+++ b/apps/iatlas/data/Dockerfile
@@ -1,4 +1,4 @@
-FROM python:3.11.9
+FROM python:3.11.10
 
 SHELL ["/bin/bash", "-o", "pipefail", "-c"]
 
diff --git a/apps/iatlas/data/README.md b/apps/iatlas/data/README.md
index 2036b6ed45..b633670792 100644
--- a/apps/iatlas/data/README.md
+++ b/apps/iatlas/data/README.md
@@ -4,3 +4,9 @@
 
 Creates a Docker container that download iAtlas data and data schema from Synapse before seeding the
 iAtlas DB.
+
+## Prepare the project
+
+```console
+nx prepare iatlas-data
+```
diff --git a/apps/iatlas/data/prepare-python.sh b/apps/iatlas/data/install.sh
similarity index 71%
rename from apps/iatlas/data/prepare-python.sh
rename to apps/iatlas/data/install.sh
index 5b4cd66b6d..5275fc3dfc 100755
--- a/apps/iatlas/data/prepare-python.sh
+++ b/apps/iatlas/data/install.sh
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-PYTHON_VERSION="3.11.9"
+PYTHON_VERSION="3.11.10"
 
 pyenv install --skip-existing $PYTHON_VERSION
 
@@ -9,6 +9,5 @@ pyenv install --skip-existing $PYTHON_VERSION
 eval "$(pyenv init -)"
 
 pyenv local $PYTHON_VERSION
-poetry env use $PYTHON_VERSION
-poetry install
-# poetry install --with prod,dev
\ No newline at end of file
+poetry env use $(pyenv which python)
+poetry install --with dev
\ No newline at end of file
diff --git a/apps/iatlas/data/poetry.lock b/apps/iatlas/data/poetry.lock
index 94229e9565..aea27ec2c9 100644
--- a/apps/iatlas/data/poetry.lock
+++ b/apps/iatlas/data/poetry.lock
@@ -56,114 +56,143 @@ files = [
 [package.extras]
 test = ["pytest", "uvloop"]
 
+[[package]]
+name = "autopep8"
+version = "2.0.2"
+description = "A tool that automatically formats Python code to conform to the PEP 8 style guide"
+optional = false
+python-versions = ">=3.6"
+files = [
+    {file = "autopep8-2.0.2-py2.py3-none-any.whl", hash = "sha256:86e9303b5e5c8160872b2f5ef611161b2893e9bfe8ccc7e2f76385947d57a2f1"},
+    {file = "autopep8-2.0.2.tar.gz", hash = "sha256:f9849cdd62108cb739dbcdbfb7fdcc9a30d1b63c4cc3e1c1f893b5360941b61c"},
+]
+
+[package.dependencies]
+pycodestyle = ">=2.10.0"
+
 [[package]]
 name = "certifi"
-version = "2023.11.17"
+version = "2024.8.30"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 files = [
-    {file = "certifi-2023.11.17-py3-none-any.whl", hash = "sha256:e036ab49d5b79556f99cfc2d9320b34cfbe5be05c5871b51de9329f0603b0474"},
-    {file = "certifi-2023.11.17.tar.gz", hash = "sha256:9b469f3a900bf28dc19b8cfbf8019bf47f7fdd1a65a1d4ffb98fc14166beb4d1"},
+    {file = "certifi-2024.8.30-py3-none-any.whl", hash = "sha256:922820b53db7a7257ffbda3f597266d435245903d80737e34f8a45ff3e3230d8"},
+    {file = "certifi-2024.8.30.tar.gz", hash = "sha256:bec941d2aa8195e248a60b31ff9f0558284cf01a52591ceda73ea9afffd69fd9"},
 ]
 
 [[package]]
 name = "charset-normalizer"
-version = "3.3.2"
+version = "3.4.0"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 optional = false
 python-versions = ">=3.7.0"
 files = [
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+
 [[package]]
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 version = "1.2.14"
@@ -208,91 +311,123 @@ files = [
 [package.dependencies]
 packaging = "*"
 
+[[package]]
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+
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 ]
 
 [package.extras]
-docs = ["Sphinx"]
+docs = ["Sphinx", "furo"]
 test = ["objgraph", "psutil"]
 
 [[package]]
@@ -354,33 +489,58 @@ zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "idna"
-version = "3.6"
+version = "3.10"
 description = "Internationalized Domain Names in Applications (IDNA)"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.6"
 files = [
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 ]
 
+[package.extras]
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+
 [[package]]
 name = "importlib-metadata"
-version = "6.8.0"
+version = "8.4.0"
 description = "Read metadata from Python packages"
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 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
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 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
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 perf = ["ipython"]
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+test = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-perf (>=0.9.2)", "pytest-ruff (>=0.2.1)"]
+
+[[package]]
+name = "iniconfig"
+version = "2.0.0"
+description = "brain-dead simple config-ini parsing"
+optional = false
+python-versions = ">=3.7"
+files = [
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+]
+
+[[package]]
+name = "mccabe"
+version = "0.7.0"
+description = "McCabe checker, plugin for flake8"
+optional = false
+python-versions = ">=3.6"
+files = [
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+]
 
 [[package]]
 name = "nest-asyncio"
@@ -414,47 +574,64 @@ test = ["pytest (>=7.2)", "pytest-cov (>=4.0)"]
 
 [[package]]
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-version = "1.26.2"
+version = "2.1.2"
 description = "Fundamental package for array computing in Python"
 optional = false
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-
-[package.extras]
-email = ["email-validator (>=2.0.0)"]
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 name = "pydantic"
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 email = ["email-validator (>=2.0.0)"]
 timezone = ["tzdata"]
 
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 [package.dependencies]
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 [package.dependencies]
-greenlet = {version = "!=0.4.17", markers = "platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\""}
-typing-extensions = ">=4.2.0"
+greenlet = {version = "!=0.4.17", markers = "python_version < \"3.13\" and (platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\")"}
+typing-extensions = ">=4.6.0"
 
 [package.extras]
 aiomysql = ["aiomysql (>=0.2.0)", "greenlet (!=0.4.17)"]
 aioodbc = ["aioodbc", "greenlet (!=0.4.17)"]
-aiosqlite = ["aiosqlite", "greenlet (!=0.4.17)", "typing-extensions (!=3.10.0.1)"]
+aiosqlite = ["aiosqlite", "greenlet (!=0.4.17)", "typing_extensions (!=3.10.0.1)"]
 asyncio = ["greenlet (!=0.4.17)"]
 asyncmy = ["asyncmy (>=0.2.3,!=0.2.4,!=0.2.6)", "greenlet (!=0.4.17)"]
-mariadb-connector = ["mariadb (>=1.0.1,!=1.1.2,!=1.1.5)"]
+mariadb-connector = ["mariadb (>=1.0.1,!=1.1.2,!=1.1.5,!=1.1.10)"]
 mssql = ["pyodbc"]
 mssql-pymssql = ["pymssql"]
 mssql-pyodbc = ["pyodbc"]
 mypy = ["mypy (>=0.910)"]
 mysql = ["mysqlclient (>=1.4.0)"]
 mysql-connector = ["mysql-connector-python"]
-oracle = ["cx-oracle (>=8)"]
+oracle = ["cx_oracle (>=8)"]
 oracle-oracledb = ["oracledb (>=1.0.1)"]
 postgresql = ["psycopg2 (>=2.7)"]
 postgresql-asyncpg = ["asyncpg", "greenlet (!=0.4.17)"]
@@ -1353,17 +1578,17 @@ postgresql-psycopg2binary = ["psycopg2-binary"]
 postgresql-psycopg2cffi = ["psycopg2cffi"]
 postgresql-psycopgbinary = ["psycopg[binary] (>=3.0.7)"]
 pymysql = ["pymysql"]
-sqlcipher = ["sqlcipher3-binary"]
+sqlcipher = ["sqlcipher3_binary"]
 
 [[package]]
 name = "sqlalchemy-utils"
-version = "0.41.1"
+version = "0.41.2"
 description = "Various utility functions for SQLAlchemy."
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
@@ -1378,20 +1603,20 @@ intervals = ["intervals (>=0.7.1)"]
 password = ["passlib (>=1.6,<2.0)"]
 pendulum = ["pendulum (>=2.0.5)"]
 phone = ["phonenumbers (>=5.9.2)"]
-test = ["Jinja2 (>=2.3)", "Pygments (>=1.2)", "backports.zoneinfo", "docutils (>=0.10)", "flake8 (>=2.4.0)", "flexmock (>=0.9.7)", "isort (>=4.2.2)", "pg8000 (>=1.12.4)", "psycopg (>=3.1.8)", "psycopg2 (>=2.5.1)", "psycopg2cffi (>=2.8.1)", "pymysql", "pyodbc", "pytest (>=2.7.1)", "python-dateutil (>=2.6)", "pytz (>=2014.2)"]
-test-all = ["Babel (>=1.3)", "Jinja2 (>=2.3)", "Pygments (>=1.2)", "arrow (>=0.3.4)", "backports.zoneinfo", "colour (>=0.0.4)", "cryptography (>=0.6)", "docutils (>=0.10)", "flake8 (>=2.4.0)", "flexmock (>=0.9.7)", "furl (>=0.4.1)", "intervals (>=0.7.1)", "isort (>=4.2.2)", "passlib (>=1.6,<2.0)", "pendulum (>=2.0.5)", "pg8000 (>=1.12.4)", "phonenumbers (>=5.9.2)", "psycopg (>=3.1.8)", "psycopg2 (>=2.5.1)", "psycopg2cffi (>=2.8.1)", "pymysql", "pyodbc", "pytest (>=2.7.1)", "python-dateutil", "python-dateutil (>=2.6)", "pytz (>=2014.2)"]
+test = ["Jinja2 (>=2.3)", "Pygments (>=1.2)", "backports.zoneinfo", "docutils (>=0.10)", "flake8 (>=2.4.0)", "flexmock (>=0.9.7)", "isort (>=4.2.2)", "pg8000 (>=1.12.4)", "psycopg (>=3.1.8)", "psycopg2 (>=2.5.1)", "psycopg2cffi (>=2.8.1)", "pymysql", "pyodbc", "pytest (==7.4.4)", "python-dateutil (>=2.6)", "pytz (>=2014.2)"]
+test-all = ["Babel (>=1.3)", "Jinja2 (>=2.3)", "Pygments (>=1.2)", "arrow (>=0.3.4)", "backports.zoneinfo", "colour (>=0.0.4)", "cryptography (>=0.6)", "docutils (>=0.10)", "flake8 (>=2.4.0)", "flexmock (>=0.9.7)", "furl (>=0.4.1)", "intervals (>=0.7.1)", "isort (>=4.2.2)", "passlib (>=1.6,<2.0)", "pendulum (>=2.0.5)", "pg8000 (>=1.12.4)", "phonenumbers (>=5.9.2)", "psycopg (>=3.1.8)", "psycopg2 (>=2.5.1)", "psycopg2cffi (>=2.8.1)", "pymysql", "pyodbc", "pytest (==7.4.4)", "python-dateutil", "python-dateutil (>=2.6)", "pytz (>=2014.2)"]
 timezone = ["python-dateutil"]
 url = ["furl (>=0.4.1)"]
 
 [[package]]
 name = "synapseclient"
-version = "4.5.1"
+version = "4.6.0"
 description = "A client for Synapse, a collaborative, open-source research platform that allows teams to share data, track analyses, and collaborate."
 optional = false
-python-versions = ">=3.8"
+python-versions = "<3.13,>=3.9"
 files = [
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+    {file = "synapseclient-4.6.0-py3-none-any.whl", hash = "sha256:2da021585a6aa237a00fcca5992bc263523388c519d0b7e82525ba818bb5bd1b"},
+    {file = "synapseclient-4.6.0.tar.gz", hash = "sha256:0d6561b399b9ecec71f319c3c512c845e152179237816212cc42f928d67166b8"},
 ]
 
 [package.dependencies]
@@ -1416,7 +1641,7 @@ urllib3 = ">=1.26.18,<2"
 boto3 = ["boto3 (>=1.7.0,<2.0)"]
 dev = ["black", "flake8 (>=3.7.0,<4.0)", "func-timeout (>=4.3,<5.0)", "pandas (>=1.5,<3.0)", "pre-commit", "pytest (>=7.0.0,<8.0)", "pytest-asyncio (>=0.23.6,<1.0)", "pytest-cov (>=4.1.0,<4.2.0)", "pytest-mock (>=3.0,<4.0)", "pytest-rerunfailures (>=12.0,<13.0)", "pytest-socket (>=0.6.0,<0.7.0)", "pytest-xdist[psutil] (>=2.2,<3.0.0)"]
 docs = ["markdown-include (>=0.8.1,<0.9.0)", "mkdocs (>=1.5.3)", "mkdocs-material (>=9.4.14)", "mkdocs-open-in-new-tab (>=1.0.3,<1.1.0)", "mkdocstrings (>=0.24.0)", "mkdocstrings-python (>=1.7.5)", "termynal (>=0.11.1)"]
-pandas = ["numpy (<2.0.0)", "pandas (>=1.5,<3.0)"]
+pandas = ["pandas (>=1.5,<3.0)"]
 pysftp = ["pysftp (>=0.2.8,<0.3)"]
 tests = ["flake8 (>=3.7.0,<4.0)", "func-timeout (>=4.3,<5.0)", "pandas (>=1.5,<3.0)", "pytest (>=7.0.0,<8.0)", "pytest-asyncio (>=0.23.6,<1.0)", "pytest-cov (>=4.1.0,<4.2.0)", "pytest-mock (>=3.0,<4.0)", "pytest-rerunfailures (>=12.0,<13.0)", "pytest-socket (>=0.6.0,<0.7.0)", "pytest-xdist[psutil] (>=2.2,<3.0.0)"]
 
@@ -1435,6 +1660,20 @@ files = [
 doc = ["reno", "sphinx"]
 test = ["pytest", "tornado (>=4.5)", "typeguard"]
 
+[[package]]
+name = "termcolor"
+version = "2.5.0"
+description = "ANSI color formatting for output in terminal"
+optional = false
+python-versions = ">=3.9"
+files = [
+    {file = "termcolor-2.5.0-py3-none-any.whl", hash = "sha256:37b17b5fc1e604945c2642c872a3764b5d547a48009871aea3edd3afa180afb8"},
+    {file = "termcolor-2.5.0.tar.gz", hash = "sha256:998d8d27da6d48442e8e1f016119076b690d962507531df4890fcd2db2ef8a6f"},
+]
+
+[package.extras]
+tests = ["pytest", "pytest-cov"]
+
 [[package]]
 name = "tqdm"
 version = "4.66.6"
@@ -1457,35 +1696,35 @@ telegram = ["requests"]
 
 [[package]]
 name = "typing-extensions"
-version = "4.8.0"
+version = "4.12.2"
 description = "Backported and Experimental Type Hints for Python 3.8+"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "typing_extensions-4.12.2-py3-none-any.whl", hash = "sha256:04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d"},
+    {file = "typing_extensions-4.12.2.tar.gz", hash = "sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8"},
 ]
 
 [[package]]
 name = "tzdata"
-version = "2023.3"
+version = "2024.2"
 description = "Provider of IANA time zone data"
 optional = false
 python-versions = ">=2"
 files = [
-    {file = "tzdata-2023.3-py2.py3-none-any.whl", hash = "sha256:7e65763eef3120314099b6939b5546db7adce1e7d6f2e179e3df563c70511eda"},
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+    {file = "tzdata-2024.2.tar.gz", hash = "sha256:7d85cc416e9382e69095b7bdf4afd9e3880418a2413feec7069d533d6b4e31cc"},
 ]
 
 [[package]]
 name = "urllib3"
-version = "1.26.18"
+version = "1.26.20"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,>=2.7"
 files = [
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-    {file = "urllib3-1.26.18.tar.gz", hash = "sha256:f8ecc1bba5667413457c529ab955bf8c67b45db799d159066261719e328580a0"},
+    {file = "urllib3-1.26.20-py2.py3-none-any.whl", hash = "sha256:0ed14ccfbf1c30a9072c7ca157e4319b70d65f623e91e7b32fadb2853431016e"},
+    {file = "urllib3-1.26.20.tar.gz", hash = "sha256:40c2dc0c681e47eb8f90e7e27bf6ff7df2e677421fd46756da1161c39ca70d32"},
 ]
 
 [package.extras]
@@ -1588,20 +1827,24 @@ files = [
 
 [[package]]
 name = "zipp"
-version = "3.17.0"
+version = "3.20.2"
 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"},
-    {file = "zipp-3.17.0.tar.gz", hash = "sha256:84e64a1c28cf7e91ed2078bb8cc8c259cb19b76942096c8d7b84947690cabaf0"},
+    {file = "zipp-3.20.2-py3-none-any.whl", hash = "sha256:a817ac80d6cf4b23bf7f2828b7cabf326f15a001bea8b1f9b49631780ba28350"},
+    {file = "zipp-3.20.2.tar.gz", hash = "sha256:bc9eb26f4506fda01b81bcde0ca78103b6e62f991b381fec825435c836edbc29"},
 ]
 
 [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"]
+check = ["pytest-checkdocs (>=2.4)", "pytest-ruff (>=0.2.1)"]
+cover = ["pytest-cov"]
+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+enabler = ["pytest-enabler (>=2.2)"]
+test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"]
+type = ["pytest-mypy"]
 
 [metadata]
 lock-version = "2.0"
-python-versions = "^3.11"
-content-hash = "0e0165d1ad1715d7affe7033acad5116a866dc3529713e3d4d671bf793b46583"
+python-versions = "3.11.10"
+content-hash = "2cd9d41e161963e76259b68a4a6fe421c53c0523897c5af5975235ab0ea0de5f"
diff --git a/apps/iatlas/data/poetry.toml b/apps/iatlas/data/poetry.toml
index 62e2dff2a2..ab1033bd37 100644
--- a/apps/iatlas/data/poetry.toml
+++ b/apps/iatlas/data/poetry.toml
@@ -1,3 +1,2 @@
 [virtualenvs]
 in-project = true
-create = true
diff --git a/apps/iatlas/data/project.json b/apps/iatlas/data/project.json
index c965e63cf9..a633ee8f0a 100644
--- a/apps/iatlas/data/project.json
+++ b/apps/iatlas/data/project.json
@@ -1,68 +1,52 @@
 {
   "name": "iatlas-data",
   "$schema": "../../../node_modules/nx/schemas/project-schema.json",
-  "sourceRoot": "apps/iatlas/data/scripts",
   "projectType": "application",
+  "sourceRoot": "apps/iatlas/data/src",
   "targets": {
-    "create-config": {
+    "lock": {
       "executor": "nx:run-commands",
       "options": {
-        "command": "cp -n .env.example .env",
+        "command": "poetry lock --no-update",
         "cwd": "{projectRoot}"
       }
     },
-    "prepare": {
-      "executor": "nx:run-commands",
+    "build": {
+      "executor": "@nxlv/python:build",
+      "outputs": ["{projectRoot}/dist"],
       "options": {
-        "command": "./prepare-python.sh",
-        "cwd": "{projectRoot}"
+        "outputPath": "{projectRoot}/dist",
+        "publish": false,
+        "lockedVersions": true,
+        "bundleLocalDependencies": true
       }
     },
-    "serve": {
-      "executor": "nx:run-commands",
-      "options": {
-        "command": "docker compose up",
-        "cwd": "apps/iatlas/data"
-      },
-      "dependsOn": []
-    },
-    "serve-detach": {
+    "prepare": {
       "executor": "nx:run-commands",
       "options": {
-        "command": "docker/iatlas/serve-detach.sh {projectName}"
+        "command": "./install.sh",
+        "cwd": "{projectRoot}"
       }
     },
-    "build-image": {
-      "executor": "@nx-tools/nx-container:build",
+    "update": {
+      "executor": "nx:run-commands",
       "options": {
-        "context": "apps/iatlas/data",
-        "metadata": {
-          "images": ["ghcr.io/sage-bionetworks/{projectName}"],
-          "tags": ["type=edge,branch=main", "type=raw,value=local", "type=sha"]
-        },
-        "push": false
+        "command": "poetry update",
+        "cwd": "{projectRoot}"
       }
     },
-    "publish-image": {
-      "executor": "@nx-tools/nx-container:build",
+    "lint": {
+      "executor": "@nxlv/python:flake8",
+      "outputs": ["{workspaceRoot}/reports/{projectRoot}/pylint.txt"],
       "options": {
-        "context": "apps/iatlas/data",
-        "metadata": {
-          "images": ["ghcr.io/sage-bionetworks/{projectName}"],
-          "tags": ["type=edge,branch=main", "type=sha"]
-        },
-        "push": true
-      },
-      "dependsOn": ["build-image"]
-    },
-    "scan-image": {
-      "executor": "nx:run-commands",
-      "options": {
-        "command": "trivy image ghcr.io/sage-bionetworks/{projectName}:local --quiet",
-        "color": true
+        "outputFile": "reports/{projectRoot}/pylint.txt"
       }
     }
   },
-  "tags": ["type:db", "scope:backend", "language:python"],
-  "implicitDependencies": []
+  "tags": ["language:python", "package-manager:poetry"],
+  "release": {
+    "version": {
+      "generator": "@nxlv/python:release-version"
+    }
+  }
 }
diff --git a/apps/iatlas/data/pyproject.toml b/apps/iatlas/data/pyproject.toml
index 33ab742113..92f06f57ae 100644
--- a/apps/iatlas/data/pyproject.toml
+++ b/apps/iatlas/data/pyproject.toml
@@ -1,15 +1,37 @@
+[tool.coverage.run]
+branch = true
+source = [ "src" ]
+
+[tool.coverage.report]
+exclude_lines = [ "if TYPE_CHECKING:" ]
+show_missing = true
+
+[tool.pytest.ini_options]
+addopts = "--cov --cov-report html:'../../../coverage/apps/iatlas/data/html' --cov-report xml:'../../../coverage/apps/iatlas/data/coverage.xml' --html='../../../reports/apps/iatlas/data/unittests/html/index.html' --junitxml='../../../reports/apps/iatlas/data/unittests/junit.xml'"
+
 [tool.poetry]
 name = "iatlas-data"
-version = "0.1.0"
-description = ""
-authors = ["andrewelamb <andrewelamb@gmail.com>"]
+version = "1.0.0"
+description = "Automatically generated by Nx."
+authors = [ ]
+license = "Proprietary"
 readme = "README.md"
 
-[tool.poetry.dependencies]
-python = "^3.11"
-schematic-db = {version = "0.1.5", extras = ["postgres", "synapse"]}
+  [[tool.poetry.packages]]
+  include = "src"
+
+  [tool.poetry.dependencies]
+  python = "3.11.10"
+  schematic-db = {version = "0.1.6", extras = ["postgres", "synapse"]}
 
+[tool.poetry.group.dev.dependencies]
+autopep8 = "2.0.2"
+flake8 = "6.0.0"
+pytest = "7.3.1"
+pytest-sugar = "0.9.7"
+pytest-cov = "4.1.0"
+pytest-html = "3.2.0"
 
 [build-system]
-requires = ["poetry-core"]
+requires = [ "poetry-core" ]
 build-backend = "poetry.core.masonry.api"
diff --git a/apps/iatlas/data/pyrightconfig.json b/apps/iatlas/data/pyrightconfig.json
new file mode 100644
index 0000000000..7cba39a667
--- /dev/null
+++ b/apps/iatlas/data/pyrightconfig.json
@@ -0,0 +1,7 @@
+{
+  "include": ["src"],
+  "exclude": ["tests"],
+  "venvPath": ".",
+  "venv": ".venv",
+  "pythonVersion": "3.11"
+}
diff --git a/apps/iatlas/data/requirements.txt b/apps/iatlas/data/requirements.txt
index 819e157284..f65aabfcc3 100644
--- a/apps/iatlas/data/requirements.txt
+++ b/apps/iatlas/data/requirements.txt
@@ -1,47 +1,51 @@
-attrs==23.2.0 ; python_version >= "3.9" and python_version < "4.0"
-backoff==2.2.1 ; python_version >= "3.9" and python_version < "4.0"
-certifi==2024.2.2 ; python_version >= "3.9" and python_version < "4.0"
-charset-normalizer==3.3.2 ; python_version >= "3.9" and python_version < "4.0"
-click==8.1.7 ; python_version >= "3.9" and python_version < "4.0"
-colorama==0.4.6 ; python_version >= "3.9" and python_version < "4.0"
-decorator==5.1.1 ; python_version >= "3.9" and python_version < "4.0"
-deprecated==1.2.14 ; python_version >= "3.9" and python_version < "4.0"
-deprecation==2.1.0 ; python_version >= "3.9" and python_version < "4.0"
-googleapis-common-protos==1.62.0 ; python_version >= "3.9" and python_version < "4.0"
-greenlet==3.0.3 ; python_version >= "3.9" and python_version < "4.0" and (platform_machine == "aarch64" or platform_machine == "ppc64le" or platform_machine == "x86_64" or platform_machine == "amd64" or platform_machine == "AMD64" or platform_machine == "win32" or platform_machine == "WIN32")
-idna==3.6 ; python_version >= "3.9" and python_version < "4.0"
-importlib-metadata==6.11.0 ; python_version >= "3.9" and python_version < "4.0"
-interrogate==1.5.0 ; python_version >= "3.9" and python_version < "4.0"
-nest-asyncio==1.6.0 ; python_version >= "3.9" and python_version < "4.0"
-networkx==2.8.8 ; python_version >= "3.9" and python_version < "4.0"
-numpy==1.26.4 ; python_version >= "3.9" and python_version <= "3.11" or python_version >= "3.12" and python_version < "4.0"
-opentelemetry-api==1.21.0 ; python_version >= "3.9" and python_version < "4.0"
-opentelemetry-exporter-otlp-proto-common==1.21.0 ; python_version >= "3.9" and python_version < "4.0"
-opentelemetry-exporter-otlp-proto-http==1.21.0 ; python_version >= "3.9" and python_version < "4.0"
-opentelemetry-proto==1.21.0 ; python_version >= "3.9" and python_version < "4.0"
-opentelemetry-sdk==1.21.0 ; python_version >= "3.9" and python_version < "4.0"
-opentelemetry-semantic-conventions==0.42b0 ; python_version >= "3.9" and python_version < "4.0"
-packaging==23.2 ; python_version >= "3.9" and python_version < "4.0"
-pandas==2.2.1 ; python_version >= "3.9" and python_version < "4.0"
-protobuf==4.25.3 ; python_version >= "3.9" and python_version < "4.0"
-psycopg2-binary==2.9.9 ; python_version >= "3.9" and python_version < "4.0"
-py==1.11.0 ; python_version >= "3.9" and python_version < "4.0"
-pydantic==1.10.14 ; python_version >= "3.9" and python_version < "4.0"
-python-dateutil==2.8.2 ; python_version >= "3.9" and python_version < "4.0"
-pytz==2024.1 ; python_version >= "3.9" and python_version < "4.0"
-pyyaml==6.0.1 ; python_version >= "3.9" and python_version < "4.0"
-requests==2.31.0 ; python_version >= "3.9" and python_version < "4.0"
-schematic-db[postgres,synapse]==0.0.41 ; python_version >= "3.9" and python_version < "4.0"
-six==1.16.0 ; python_version >= "3.9" and python_version < "4.0"
-sqlalchemy-utils==0.41.1 ; python_version >= "3.9" and python_version < "4.0"
-sqlalchemy==2.0.27 ; python_version >= "3.9" and python_version < "4.0"
-synapseclient==4.1.1 ; python_version >= "3.9" and python_version < "4.0"
-tabulate==0.9.0 ; python_version >= "3.9" and python_version < "4.0"
-tenacity==8.2.3 ; python_version >= "3.9" and python_version < "4.0"
-toml==0.10.2 ; python_version >= "3.9" and python_version < "4.0"
-typing-extensions==4.10.0 ; python_version >= "3.9" and python_version < "4.0"
-tzdata==2024.1 ; python_version >= "3.9" and python_version < "4.0"
-urllib3==1.26.18 ; python_version >= "3.9" and python_version < "4.0"
-validators==0.20.0 ; python_version >= "3.9" and python_version < "4.0"
-wrapt==1.16.0 ; python_version >= "3.9" and python_version < "4.0"
-zipp==3.17.0 ; python_version >= "3.9" and python_version < "4.0"
+annotated-types==0.7.0 ; python_version >= "3.11" and python_version < "4.0"
+anyio==4.4.0 ; python_version >= "3.11" and python_version < "4.0"
+async-lru==2.0.4 ; python_version >= "3.11" and python_version < "4.0"
+asyncio-atexit==1.0.1 ; python_version >= "3.11" and python_version < "4.0"
+backoff==2.2.1 ; python_version >= "3.11" and python_version < "4.0"
+certifi==2024.7.4 ; python_version >= "3.11" and python_version < "4.0"
+charset-normalizer==3.3.2 ; python_version >= "3.11" and python_version < "4.0"
+colorama==0.4.6 ; python_version >= "3.11" and python_version < "4.0" and platform_system == "Windows"
+deprecated==1.2.14 ; python_version >= "3.11" and python_version < "4.0"
+deprecation==2.1.0 ; python_version >= "3.11" and python_version < "4.0"
+googleapis-common-protos==1.63.2 ; python_version >= "3.11" and python_version < "4.0"
+greenlet==3.0.3 ; python_version < "3.13" and (platform_machine == "aarch64" or platform_machine == "ppc64le" or platform_machine == "x86_64" or platform_machine == "amd64" or platform_machine == "AMD64" or platform_machine == "win32" or platform_machine == "WIN32") and python_version >= "3.11"
+h11==0.14.0 ; python_version >= "3.11" and python_version < "4.0"
+httpcore==1.0.5 ; python_version >= "3.11" and python_version < "4.0"
+httpx==0.27.0 ; python_version >= "3.11" and python_version < "4.0"
+idna==3.7 ; python_version >= "3.11" and python_version < "4.0"
+importlib-metadata==6.11.0 ; python_version >= "3.11" and python_version < "4.0"
+nest-asyncio==1.6.0 ; python_version >= "3.11" and python_version < "4.0"
+networkx==3.3 ; python_version >= "3.11" and python_version < "4.0"
+numpy==2.0.1 ; python_version >= "3.12" and python_version < "4.0" or python_version == "3.11"
+opentelemetry-api==1.21.0 ; python_version >= "3.11" and python_version < "4.0"
+opentelemetry-exporter-otlp-proto-common==1.21.0 ; python_version >= "3.11" and python_version < "4.0"
+opentelemetry-exporter-otlp-proto-http==1.21.0 ; python_version >= "3.11" and python_version < "4.0"
+opentelemetry-proto==1.21.0 ; python_version >= "3.11" and python_version < "4.0"
+opentelemetry-sdk==1.21.0 ; python_version >= "3.11" and python_version < "4.0"
+opentelemetry-semantic-conventions==0.42b0 ; python_version >= "3.11" and python_version < "4.0"
+packaging==24.1 ; python_version >= "3.11" and python_version < "4.0"
+pandas==2.2.2 ; python_version >= "3.11" and python_version < "4.0"
+protobuf==4.25.4 ; python_version >= "3.11" and python_version < "4.0"
+psutil==5.9.8 ; python_version >= "3.11" and python_version < "4.0"
+psycopg2-binary==2.9.9 ; python_version >= "3.11" and python_version < "4.0"
+pydantic-core==2.20.1 ; python_version >= "3.11" and python_version < "4.0"
+pydantic==2.8.2 ; python_version >= "3.11" and python_version < "4.0"
+python-dateutil==2.9.0.post0 ; python_version >= "3.11" and python_version < "4.0"
+pytz==2024.1 ; python_version >= "3.11" and python_version < "4.0"
+pyyaml==6.0.1 ; python_version >= "3.11" and python_version < "4.0"
+requests==2.32.3 ; python_version >= "3.11" and python_version < "4.0"
+schematic-db[postgres,synapse]==0.1.5 ; python_version >= "3.11" and python_version < "4.0"
+six==1.16.0 ; python_version >= "3.11" and python_version < "4.0"
+sniffio==1.3.1 ; python_version >= "3.11" and python_version < "4.0"
+sqlalchemy-utils==0.41.2 ; python_version >= "3.11" and python_version < "4.0"
+sqlalchemy==2.0.31 ; python_version >= "3.11" and python_version < "4.0"
+synapseclient==4.4.0 ; python_version >= "3.11" and python_version < "4.0"
+tenacity==9.0.0 ; python_version >= "3.11" and python_version < "4.0"
+tqdm==4.66.4 ; python_version >= "3.11" and python_version < "4.0"
+typing-extensions==4.12.2 ; python_version >= "3.11" and python_version < "4.0"
+tzdata==2024.1 ; python_version >= "3.11" and python_version < "4.0"
+urllib3==1.26.19 ; python_version >= "3.11" and python_version < "4.0"
+validators==0.29.0 ; python_version >= "3.11" and python_version < "4.0"
+wrapt==1.16.0 ; python_version >= "3.11" and python_version < "4.0"
+zipp==3.19.2 ; python_version >= "3.11" and python_version < "4.0"
diff --git a/apps/iatlas/data/src/build_database.py b/apps/iatlas/data/src/build_database.py
index 6cb7a7bfca..704b374c14 100755
--- a/apps/iatlas/data/src/build_database.py
+++ b/apps/iatlas/data/src/build_database.py
@@ -1851,19 +1851,28 @@
     },
 ]
 
-db = PostgresDatabase(
-    SQLConfig(
+if getenv("DB_PORT"):
+    sql_config = SQLConfig(
         username=getenv("DB_USER"),
         password=getenv("DB_PW"),
         host=getenv("DB_HOST"),
         name=getenv("DB_NAME"),
+        port=getenv("DB_PORT"),
     )
-)
+else:
+    sql_config = SQLConfig(
+        username=getenv("DB_USER"),
+        password=getenv("DB_PW"),
+        host=getenv("DB_HOST"),
+        name=getenv("DB_NAME"),
+    )
+
+
+db = PostgresDatabase(sql_config)
 
 schema = Schema(
-    SchemaConfig(schema_url=getenv("SCHEMA_URL")),
+    SchemaConfig(schema_url=getenv("SCHEMA_URL"), display_label_type="display_label"),
     DatabaseConfig(iatlas_config),
-    display_label_type="display_label",
 )
 
 
@@ -1878,108 +1887,124 @@
         synapse_auth_token=getenv("SCHEMA_AUTH_TOKEN"),
     ),
     display_label_type="display_label",
+    purge_synapse_cache=True,
 )
 
-# updater = RDBUpdater(db, ms)
-# updater.update_database(method="insert")
+updater = RDBUpdater(db, ms)
+updater.update_database(method="insert", chunk_size=100000)
 
 
-# def insert_as_chunk(df, db, table_name, chunk_size=20000):
-#     num_chunks = ((len(df) - 1) // chunk_size) + 1
-
-#     for i in range(num_chunks):
-#         # Getting chunk boundaries
-#         start_index = i * chunk_size
-#         end_index = (i + 1) * chunk_size
-
-#         # Selecting rows for the current chunk
-#         chunk = df[start_index:end_index]
-
-#         # Inserting rows into the table
-#         db.insert_table_rows(table_name, chunk)
-
-
-# cohorts_to_samples1 = db.execute_sql_query(
-#     (
-#         "SELECT DISTINCT c.id AS cohort_id, t.id AS cohorts_to_samples_tag_id, stt.sample_id "
-#         "FROM samples s "
-#         "INNER JOIN samples_to_tags stt ON s.id = stt.sample_id "
-#         "INNER JOIN tags t ON stt.tag_id = t.id "
-#         "INNER JOIN tags_to_tags ttt ON t.id = ttt.tag_id "
-#         "INNER JOIN tags t2 ON ttt.related_tag_id = t2.id "
-#         "INNER JOIN datasets_to_samples dts on s.id = dts.sample_id "
-#         "INNER JOIN cohorts c on t2.id = c.cohort_tag_id AND dts.dataset_id = c.dataset_id "
-#         "WHERE t.tag_type = 'group'"
-#     )
-# )
-# cohorts_to_samples1["id"] = [
-#     uuid.uuid1() for _ in range(len(cohorts_to_samples1.index))
-# ]
-# insert_as_chunk(cohorts_to_samples1, db, "cohorts_to_samples")
-# # db.insert_table_rows("cohorts_to_samples", cohorts_to_samples1)
+cohorts_to_samples1 = db.execute_sql_query(
+    (
+        "SELECT DISTINCT c.id AS cohort_id, t.id AS cohorts_to_samples_tag_id, stt.sample_id "
+        "FROM samples s "
+        "INNER JOIN samples_to_tags stt ON s.id = stt.sample_id "
+        "INNER JOIN tags t ON stt.tag_id = t.id "
+        "INNER JOIN tags_to_tags ttt ON t.id = ttt.tag_id "
+        "INNER JOIN tags t2 ON ttt.related_tag_id = t2.id "
+        "INNER JOIN datasets_to_samples dts on s.id = dts.sample_id "
+        "INNER JOIN cohorts c on t2.id = c.cohort_tag_id AND dts.dataset_id = c.dataset_id "
+        "WHERE t.tag_type = 'group'"
+    )
+)
+cohorts_to_samples1["id"] = [
+    uuid.uuid1() for _ in range(len(cohorts_to_samples1.index))
+]
+updater._update_table_with_manifest(
+    table=cohorts_to_samples1,
+    table_name="cohorts_to_samples",
+    manifest_id="None",
+    method="insert",
+    chunk_size=100000,
+)
 
 
-# cohorts_to_samples2 = db.execute_sql_query(
-#     (
-#         "SELECT DISTINCT c.id AS cohort_id, dts.sample_id "
-#         "FROM cohorts c "
-#         "INNER JOIN datasets_to_samples dts ON c.dataset_id = dts.dataset_id "
-#         "WHERE c.cohort_tag_id is NULL"
-#     )
-# )
-# cohorts_to_samples2["id"] = [
-#     uuid.uuid1() for _ in range(len(cohorts_to_samples2.index))
-# ]
-# insert_as_chunk(cohorts_to_samples2, db, "cohorts_to_samples")
-# # db.insert_table_rows("cohorts_to_samples", cohorts_to_samples2)
+cohorts_to_samples2 = db.execute_sql_query(
+    (
+        "SELECT DISTINCT c.id AS cohort_id, dts.sample_id "
+        "FROM cohorts c "
+        "INNER JOIN datasets_to_samples dts ON c.dataset_id = dts.dataset_id "
+        "WHERE c.cohort_tag_id is NULL"
+    )
+)
+cohorts_to_samples2["id"] = [
+    uuid.uuid1() for _ in range(len(cohorts_to_samples2.index))
+]
+updater._update_table_with_manifest(
+    table=cohorts_to_samples2,
+    table_name="cohorts_to_samples",
+    manifest_id="None",
+    method="insert",
+    chunk_size=100000,
+)
 
 
-# cohorts_to_features = db.execute_sql_query(
-#     (
-#         "SELECT DISTINCT cohort_id, feature_id "
-#         "FROM cohorts_to_samples cts "
-#         "INNER JOIN features_to_samples fts USING(sample_id)"
-#     )
-# )
-# cohorts_to_features["id"] = [
-#     uuid.uuid1() for _ in range(len(cohorts_to_features.index))
-# ]
-# insert_as_chunk(cohorts_to_features, db, "cohorts_to_features")
-# # db.insert_table_rows("cohorts_to_features", cohorts_to_features)
+cohorts_to_features = db.execute_sql_query(
+    (
+        "SELECT DISTINCT cohort_id, feature_id "
+        "FROM cohorts_to_samples cts "
+        "INNER JOIN features_to_samples fts USING(sample_id)"
+    )
+)
+cohorts_to_features["id"] = [
+    uuid.uuid1() for _ in range(len(cohorts_to_features.index))
+]
+updater._update_table_with_manifest(
+    table=cohorts_to_features,
+    table_name="cohorts_to_features",
+    manifest_id="None",
+    method="insert",
+    chunk_size=100000,
+)
 
 
-# cohorts_to_genes = db.execute_sql_query(
-#     (
-#         "SELECT DISTINCT cohort_id, gene_id "
-#         "FROM cohorts_to_samples cts "
-#         "INNER JOIN genes_to_samples gts USING(sample_id)"
-#     )
-# )
-# cohorts_to_genes["id"] = [uuid.uuid1() for _ in range(len(cohorts_to_genes.index))]
-# insert_as_chunk(cohorts_to_genes, db, "cohorts_to_genes")
-# # db.insert_table_rows("cohorts_to_genes", cohorts_to_genes)
+cohorts_to_genes = db.execute_sql_query(
+    (
+        "SELECT DISTINCT cohort_id, gene_id "
+        "FROM cohorts_to_samples cts "
+        "INNER JOIN genes_to_samples gts USING(sample_id)"
+    )
+)
+cohorts_to_genes["id"] = [uuid.uuid1() for _ in range(len(cohorts_to_genes.index))]
+updater._update_table_with_manifest(
+    table=cohorts_to_genes,
+    table_name="cohorts_to_genes",
+    manifest_id="None",
+    method="insert",
+    chunk_size=100000,
+)
 
 
-# cohorts_to_mutations = db.execute_sql_query(
-#     (
-#         "SELECT DISTINCT cohort_id, mutation_id "
-#         "FROM cohorts_to_samples cts "
-#         "INNER JOIN samples_to_mutations stm USING(sample_id)"
-#     )
-# )
-# cohorts_to_mutations["id"] = [
-#     uuid.uuid1() for _ in range(len(cohorts_to_mutations.index))
-# ]
-# insert_as_chunk(cohorts_to_mutations, db, "cohorts_to_mutations")
-# # db.insert_table_rows("cohorts_to_mutations", cohorts_to_mutations)
+cohorts_to_mutations = db.execute_sql_query(
+    (
+        "SELECT DISTINCT cohort_id, mutation_id "
+        "FROM cohorts_to_samples cts "
+        "INNER JOIN samples_to_mutations stm USING(sample_id)"
+    )
+)
+cohorts_to_mutations["id"] = [
+    uuid.uuid1() for _ in range(len(cohorts_to_mutations.index))
+]
+updater._update_table_with_manifest(
+    table=cohorts_to_mutations,
+    table_name="cohorts_to_mutations",
+    manifest_id="None",
+    method="insert",
+    chunk_size=100000,
+)
 
-# cohorts_to_tags = db.execute_sql_query(
-#     (
-#         "SELECT DISTINCT cohort_id, tag_id "
-#         "FROM cohorts_to_samples cts "
-#         "INNER JOIN samples_to_tags sts USING(sample_id)"
-#     )
-# )
-# cohorts_to_tags["id"] = [uuid.uuid1() for _ in range(len(cohorts_to_tags.index))]
-# insert_as_chunk(cohorts_to_tags, db, "cohorts_to_tags")
-# # db.insert_table_rows("cohorts_to_tags", cohorts_to_tags)
+cohorts_to_tags = db.execute_sql_query(
+    (
+        "SELECT DISTINCT cohort_id, tag_id "
+        "FROM cohorts_to_samples cts "
+        "INNER JOIN samples_to_tags sts USING(sample_id)"
+    )
+)
+cohorts_to_tags["id"] = [uuid.uuid1() for _ in range(len(cohorts_to_tags.index))]
+updater._update_table_with_manifest(
+    table=cohorts_to_tags,
+    table_name="cohorts_to_tags",
+    manifest_id="None",
+    method="insert",
+    chunk_size=100000,
+)