From 8c0cd7f3492d8ec1edbdc0ff3bca122625785cd0 Mon Sep 17 00:00:00 2001
From: Jesudas Joseph <jess.joseph@consbio.org>
Date: Thu, 23 Jul 2026 12:58:33 -0700
Subject: [PATCH 1/5] Add port as an option to the database config

---
 tablo/utils.py | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/tablo/utils.py b/tablo/utils.py
index 6ba1581..675d2a2 100644
--- a/tablo/utils.py
+++ b/tablo/utils.py
@@ -20,7 +20,12 @@ def get_sqlalchemy_engine():
         db_auth = ''
     db_host = settings['HOST']
     db_name = settings['NAME']
-    return create_engine('postgresql://{auth}{host}/{name}'.format(auth=db_auth, host=db_host, name=db_name))
+    db_port = settings.get("PORT", "5432")
+    return create_engine(
+        "postgresql://{auth}{host}:{port}/{name}".format(
+            auth=db_auth, host=db_host, name=db_name, port=db_port
+        )
+    )
 
 
 def dictfetchall(cursor):

From 244b795c66fcd13098824db57c17f0ff732fd24f Mon Sep 17 00:00:00 2001
From: Jesudas Joseph <jess.joseph@consbio.org>
Date: Thu, 23 Jul 2026 12:59:07 -0700
Subject: [PATCH 2/5] Fix pandas datetime conversion without precision

---
 tablo/csv_utils.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tablo/csv_utils.py b/tablo/csv_utils.py
index 693fbd4..7bbe83c 100644
--- a/tablo/csv_utils.py
+++ b/tablo/csv_utils.py
@@ -85,7 +85,7 @@ def prepare_csv_rows(csv_file, csv_info=None):
     if csv_info:
         date_fields = get_date_fields(csv_info)
         for field in date_fields:
-            row_set[field] = row_set[field].astype('datetime64')
+            row_set[field] = row_set[field].astype('datetime64[ns]')
 
     row_set.index += 1
     data_types = infer_data_types(row_set)

From d3abfed9485de8d3e2052ea109883339cc18db16 Mon Sep 17 00:00:00 2001
From: Jesudas Joseph <jess.joseph@consbio.org>
Date: Thu, 23 Jul 2026 12:59:32 -0700
Subject: [PATCH 3/5] Remove poetry.lock & travis.yml. No longer used

---
 .travis.yml |  32 --
 poetry.lock | 874 ----------------------------------------------------
 2 files changed, 906 deletions(-)
 delete mode 100644 .travis.yml
 delete mode 100644 poetry.lock

diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index 2e4d78b..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1,32 +0,0 @@
-dist: xenial
-group: edge
-
-language: python
-python:
-  - "3.8"
-  - "3.7"
-  - "3.6"
-env:
-  - TOXENV=django22
-  - TOXENV=coverage
-
-sudo: true  # Allow the sudo command
-
-before_install:
-  - sudo apt-get update
-  - sudo apt-get --yes remove postgresql\*
-  - sudo apt-get install -y postgresql-12 postgresql-client-12 postgresql-12-postgis-2.5 postgresql-12-postgis-2.5-scripts
-  - sudo sed -i 's/port = 5433/port = 5432/' /etc/postgresql/12/main/postgresql.conf
-  - sudo cp /etc/postgresql/{9.6,12}/main/pg_hba.conf
-  - sudo cp /etc/postgresql/{10,12}/main/pg_hba.conf
-  - sudo service postgresql restart 12
-install:
-  - pip install tox
-
-before_script:
-  - psql -c 'CREATE ROLE travis SUPERUSER LOGIN CREATEDB;' -U postgres
-  - psql -c 'CREATE DATABASE tablo;' -U postgres
-  - psql -c 'CREATE EXTENSION postgis;' -U postgres -d tablo
-  - psql -c 'CREATE EXTENSION postgis_topology;' -U postgres -d tablo
-script:
-  - tox
\ No newline at end of file
diff --git a/poetry.lock b/poetry.lock
deleted file mode 100644
index 15a18ae..0000000
--- a/poetry.lock
+++ /dev/null
@@ -1,874 +0,0 @@
-# This file is automatically @generated by Poetry 2.3.2 and should not be changed by hand.
-
-[[package]]
-name = "asgiref"
-version = "3.11.1"
-description = "ASGI specs, helper code, and adapters"
-optional = false
-python-versions = ">=3.9"
-groups = ["main"]
-files = [
-    {file = "asgiref-3.11.1-py3-none-any.whl", hash = "sha256:e8667a091e69529631969fd45dc268fa79b99c92c5fcdda727757e52146ec133"},
-    {file = "asgiref-3.11.1.tar.gz", hash = "sha256:5f184dc43b7e763efe848065441eac62229c9f7b0475f41f80e207a114eda4ce"},
-]
-
-[package.extras]
-tests = ["mypy (>=1.14.0)", "pytest", "pytest-asyncio"]
-
-[[package]]
-name = "boto3"
-version = "1.14.63"
-description = "The AWS SDK for Python"
-optional = false
-python-versions = "*"
-groups = ["main"]
-files = [
-    {file = "boto3-1.14.63-py2.py3-none-any.whl", hash = "sha256:37158c37a151eab5b9080968305621a40168171fda9584d50a309ceb4e5e6964"},
-    {file = "boto3-1.14.63.tar.gz", hash = "sha256:25c716b7c01d4664027afc6a6418a06459e311a610c7fd39a030a1ced1b72ce4"},
-]
-
-[package.dependencies]
-botocore = ">=1.17.63,<1.18.0"
-jmespath = ">=0.7.1,<1.0.0"
-s3transfer = ">=0.3.0,<0.4.0"
-
-[[package]]
-name = "botocore"
-version = "1.17.63"
-description = "Low-level, data-driven core of boto 3."
-optional = false
-python-versions = "*"
-groups = ["main"]
-files = [
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-    {file = "botocore-1.17.63.tar.gz", hash = "sha256:40f13f6c9c29c307a9dc5982739e537ddce55b29787b90c3447b507e3283bcd6"},
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-
-[package.dependencies]
-docutils = ">=0.10,<0.16"
-jmespath = ">=0.7.1,<1.0.0"
-python-dateutil = ">=2.1,<3.0.0"
-urllib3 = {version = ">=1.20,<1.26", markers = "python_version != \"3.4\""}
-
-[[package]]
-name = "certifi"
-version = "2026.2.25"
-description = "Python package for providing Mozilla's CA Bundle."
-optional = false
-python-versions = ">=3.7"
-groups = ["main"]
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-[[package]]
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From e416ffe45063b0a4e87718dd9a232625fb692466 Mon Sep 17 00:00:00 2001
From: Jesudas Joseph <jess.joseph@consbio.org>
Date: Thu, 23 Jul 2026 12:59:54 -0700
Subject: [PATCH 4/5] Update SQLAlchemy

---
 pyproject.toml  |  2 +-
 tablo/models.py | 27 +++++++++++++++++----------
 uv.lock         | 45 ++++++++++++++++++++++++++++++++++++++++++---
 3 files changed, 60 insertions(+), 14 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 5162c7a..adbbe4e 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -16,7 +16,7 @@ dependencies = [
   "pillow (>=9.0.1,<10.0)",
   "django-storages==1.14.*",
   "boto3==1.42.*",
-  "sqlalchemy==1.3.*",
+  "sqlalchemy==2.0.*",
   "geoalchemy2==0.7.*",
 ]
 
diff --git a/tablo/models.py b/tablo/models.py
index 2bf68cb..ed85a17 100644
--- a/tablo/models.py
+++ b/tablo/models.py
@@ -3,6 +3,7 @@
 import json
 import logging
 import re
+from sqlalchemy import text
 import sqlparse
 import uuid
 
@@ -1055,22 +1056,28 @@ def create_aggregate_database_table(row, dataset_id):
         seq_check_query = "SELECT sequence_name FROM information_schema.sequences WHERE sequence_name = '{}'".format(
             sequence_name
         )
-        if not conn.execute(seq_check_query).fetchone():
+        if not conn.execute(text(seq_check_query)).fetchone():
             conn.execute(
-                'CREATE SEQUENCE {sequence} OWNED BY {table_name}.{pk}'.format(
-                    sequence=sequence_name,
-                    table_name=table_name,
-                    pk=PRIMARY_KEY_NAME
+                text(
+                    "CREATE SEQUENCE {sequence} OWNED BY {table_name}.{pk}".format(
+                        sequence=sequence_name,
+                        table_name=table_name,
+                        pk=PRIMARY_KEY_NAME,
+                    )
                 )
             )
         conn.execute(
-            'ALTER TABLE {table} ALTER COLUMN {key} TYPE bigint USING {key}::bigint'.format(
-                table=table_name, key=PRIMARY_KEY_NAME
+            text(
+                "ALTER TABLE {table} ALTER COLUMN {key} TYPE bigint USING {key}::bigint".format(
+                    table=table_name, key=PRIMARY_KEY_NAME
+                )
             )
         )
         conn.execute(
-            'ALTER TABLE {table} ALTER COLUMN {key} SET DEFAULT nextval(\'{sequence}\')'.format(
-                table=table_name, key=PRIMARY_KEY_NAME, sequence=sequence_name
+            text(
+                "ALTER TABLE {table} ALTER COLUMN {key} SET DEFAULT nextval('{sequence}')".format(
+                    table=table_name, key=PRIMARY_KEY_NAME, sequence=sequence_name
+                )
             )
         )
     return table_name
@@ -1113,7 +1120,7 @@ def create_database_table(row_set, csv_info, dataset_id, append=False, additiona
             if c not in csv_info['optionalFields']:
                 constraints_query.append('ALTER COLUMN {} SET NOT NULL'.format(c))
         constraints_query = 'ALTER TABLE {} {}'.format(table_name, ','.join(constraints_query))
-        conn.execute(constraints_query)
+        conn.execute(text(constraints_query))
 
     return table_name
 
diff --git a/uv.lock b/uv.lock
index e67a627..d5dfa19 100644
--- a/uv.lock
+++ b/uv.lock
@@ -127,6 +127,22 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/f7/b0/5730254ba89826c2835e15c7854b1e33c3bbe0433b00a1770a962cd21a7b/GeoAlchemy2-0.7.0-py2.py3-none-any.whl", hash = "sha256:379b0fc4ca5f9b5ef625719f47e22c9b8abd347aa78344e85f99d32594cfccd4", size = 21551, upload-time = "2020-03-17T18:05:53.775Z" },
 ]
 
+[[package]]
+name = "greenlet"
+version = "3.5.4"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/a3/74/b13368064b09053253555d3f2839cc2684d22d5aed0d2ccffbf7a6736558/greenlet-3.5.4.tar.gz", hash = "sha256:0232ae1de90a8e07867bb127d7a6ba2301e859145489f25cda8a6096dabe1d20", size = 206538, upload-time = "2026-07-22T12:47:14.468Z" }
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+    { url = "https://files.pythonhosted.org/packages/36/ea/a0b19adfc35d07e10acb626e9d22a3893b95f1309c42c4a20161dec16800/greenlet-3.5.4-cp311-cp311-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:32802705c2c1ff25e8237b3bdacf2594fa02be80af8a66703eb7853ea7e68686", size = 613712, upload-time = "2026-07-22T12:26:39.375Z" },
+    { url = "https://files.pythonhosted.org/packages/54/76/a121978b3337407d05a1ce5f79b4aa5998a43a9d8422f9726029b90b4471/greenlet-3.5.4-cp311-cp311-manylinux_2_24_ppc64le.manylinux_2_28_ppc64le.whl", hash = "sha256:57aa201b351f7c7c75627c60d29e4d5b97a07d37efeb62b903466fca42c097d7", size = 625582, upload-time = "2026-07-22T12:29:00.814Z" },
+    { url = "https://files.pythonhosted.org/packages/34/c2/080f16cf870e929e592f55767f01d6c98d2ee83bfdc36c3b892f2d0459ab/greenlet-3.5.4-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl", hash = "sha256:c3fe76c2cac86b4f7a1e92865ac0a54384deb05c92986287c1a7110d9bd53071", size = 624663, upload-time = "2026-07-22T11:51:08.016Z" },
+    { url = "https://files.pythonhosted.org/packages/9e/bb/8f3ca88370b817369008faeceeee85970adc16c92a70a3e5fe5fea495a57/greenlet-3.5.4-cp311-cp311-musllinux_1_2_aarch64.whl", hash = "sha256:1e1a4a684b16c45ba324e60b32a4386a87722bcb815d2a149d2182f9b401ca72", size = 1585010, upload-time = "2026-07-22T12:25:02.539Z" },
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+    { url = "https://files.pythonhosted.org/packages/cd/7d/8711a75cb61d85246277c07ff6e1a6504621ba473d808c11ad225ffca43f/greenlet-3.5.4-cp311-cp311-win_amd64.whl", hash = "sha256:dc418cf4c873357964d6624445ed09472e50def990c65dd4e76fc3ba8cd9cef6", size = 246434, upload-time = "2026-07-22T11:43:15.557Z" },
+    { url = "https://files.pythonhosted.org/packages/00/62/e290b3bce433da8f0324ac02da0b128d683482229f1a8b789fa47818a4cd/greenlet-3.5.4-cp311-cp311-win_arm64.whl", hash = "sha256:c38c902a0986eba1f6e7ba1ab39ad5195926abde90f3fe080e08212db62176da", size = 244990, upload-time = "2026-07-22T11:39:22.626Z" },
+]
+
 [[package]]
 name = "iniconfig"
 version = "2.3.0"
@@ -347,9 +363,23 @@ wheels = [
 
 [[package]]
 name = "sqlalchemy"
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 source = { registry = "https://pypi.org/simple" }
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+    { name = "typing-extensions" },
+]
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+    { url = "https://files.pythonhosted.org/packages/ad/fd/005bf80f3cf6e5c62b5dd68616280f51cd012c60840fa74781b3ed7b1623/sqlalchemy-2.0.51-cp311-cp311-win_amd64.whl", hash = "sha256:4a011ea4510683319ce4ed274b56ee05194b39b6da9d09ca7a39388f0fa84dcc", size = 2145796, upload-time = "2026-06-15T16:13:31.283Z" },
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+]
 
 [[package]]
 name = "sqlparse"
@@ -399,7 +429,7 @@ requires-dist = [
     { name = "pillow", specifier = ">=9.0.1,<10.0" },
     { name = "psycopg2-binary" },
     { name = "pyproj", specifier = "<3.7" },
-    { name = "sqlalchemy", specifier = "==1.3.*" },
+    { name = "sqlalchemy", specifier = "==2.0.*" },
     { name = "sqlparse", specifier = ">=0.3.1" },
 ]
 
@@ -409,6 +439,15 @@ dev = [
     { name = "pytest-django", specifier = ">=4.12.0" },
 ]
 
+[[package]]
+name = "typing-extensions"
+version = "4.16.0"
+source = { registry = "https://pypi.org/simple" }
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From f3c625bf91e361cdf6e4896905ada2951b55f5cc Mon Sep 17 00:00:00 2001
From: Jesudas Joseph <jess.joseph@consbio.org>
Date: Thu, 23 Jul 2026 13:07:31 -0700
Subject: [PATCH 5/5] Make migrations

---
 ...mporaryfile_file_alter_temporaryfile_id.py | 25 +++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 tablo/migrations/0008_alter_temporaryfile_file_alter_temporaryfile_id.py

diff --git a/tablo/migrations/0008_alter_temporaryfile_file_alter_temporaryfile_id.py b/tablo/migrations/0008_alter_temporaryfile_file_alter_temporaryfile_id.py
new file mode 100644
index 0000000..5bd6c20
--- /dev/null
+++ b/tablo/migrations/0008_alter_temporaryfile_file_alter_temporaryfile_id.py
@@ -0,0 +1,25 @@
+# Generated by Django 5.2.13 on 2026-07-23 18:17
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("tablo", "0007_update_integer_columns_to_bigint"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="temporaryfile",
+            name="file",
+            field=models.FileField(max_length=1024, upload_to="storage/tablo/temp/"),
+        ),
+        migrations.AlterField(
+            model_name="temporaryfile",
+            name="id",
+            field=models.BigAutoField(
+                auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
+            ),
+        ),
+    ]