feat: get postgresql uri

README.md

@@ -86,6 +86,32 @@ from bio_data_to_db.bindingdb.fix_tables import fix_assay_table
 fix_assay_table("mysql://username:password@localhost/bind")
 ```
 
+
+### PostgreSQL Helpers (CLI)
+
+Get connection string (aka. URI) from the environment variables or `.env` file.
+
+This is useful for the above `bio-data-to-db` commands that usually require a connection string.
+
+You need to set:  
+- POSTGRESQL_HOST (default: localhost)
+- POSTGRESQL_PORT (default: 5432)
+- POSTGRESQL_USER
+- POSTGRESQL_PASSWORD
+
+```console
+$ bio-data-to-db postgresql get-uri-from-env
+postgresql://username:password@localhost:5432
+
+$ bio-data-to-db postgresql get-uri-from-env uniprot
+postgresql://username:password@localhost:5432/uniprot
+
+$ export POSTGRESQL_PASSWORD='!@#$%^&*()'
+$ bio-data-to-db postgresql get-uri-from-env uniprot
+postgresql://username:%21%40%23%24%25%5E%26%2A%28%29@localhost:5432/uniprot
+```
+
+
 ### PostgreSQL Helpers, SMILES, Polars utils and more
 
 This package also provides some useful functions to work with PostgreSQL, SMILES, Polars and more.

deps/lock/aarch64-apple-darwin/.requirements.in.sha256

@@ -1 +1 @@
-b2aeb764caf50f816850626567cb58bbe65e02c45df54e8d56b7f9e5702148c4  requirements.in
+0f0639ee4488d0173fcd2fe6da6a991d614525066cbf04ea0932c593fed75d99  requirements.in

deps/lock/aarch64-apple-darwin/requirements.txt

@@ -1,5 +1,5 @@
 # This file was autogenerated by uv via the following command:
-#    uv pip compile requirements.in -o /home/runner/work/bio-data-to-db/bio-data-to-db/deps/lock/aarch64-apple-darwin/requirements.txt --python-platform aarch64-apple-darwin --python-version 3.10
+#    uv pip compile requirements.in -o /Users/kiyoon/project/bio-data-to-db/deps/lock/aarch64-apple-darwin/requirements.txt --python-platform aarch64-apple-darwin --python-version 3.10
 click==8.1.7
     # via typer
 connectorx==0.3.3
@@ -31,6 +31,8 @@ pygments==2.18.0
     # via rich
 python-dateutil==2.9.0.post0
     # via pandas
+python-dotenv==1.0.1
+    # via -r requirements.in
 pytz==2024.1
     # via pandas
 rdkit==2024.3.3

deps/lock/aarch64-apple-darwin/requirements_dev.txt

@@ -1,5 +1,5 @@
 # This file was autogenerated by uv via the following command:
-#    uv pip compile requirements_dev.in -o /home/runner/work/bio-data-to-db/bio-data-to-db/deps/lock/aarch64-apple-darwin/requirements_dev.txt --python-platform aarch64-apple-darwin --python-version 3.10
+#    uv pip compile requirements_dev.in -o /Users/kiyoon/project/bio-data-to-db/deps/lock/aarch64-apple-darwin/requirements_dev.txt --python-platform aarch64-apple-darwin --python-version 3.10
 certifi==2024.7.4
     # via requests
 charset-normalizer==3.3.2
@@ -62,6 +62,8 @@ pytest==8.2.2
     # via -r requirements_dev.in
 python-dateutil==2.9.0.post0
     # via pandas
+python-dotenv==1.0.1
+    # via -r requirements.in
 pytz==2024.1
     # via pandas
 pyyaml==6.0.1

deps/lock/x86_64-apple-darwin/.requirements.in.sha256

@@ -1 +1 @@
-b2aeb764caf50f816850626567cb58bbe65e02c45df54e8d56b7f9e5702148c4  requirements.in
+0f0639ee4488d0173fcd2fe6da6a991d614525066cbf04ea0932c593fed75d99  requirements.in

deps/lock/x86_64-apple-darwin/requirements.txt

@@ -1,5 +1,5 @@
 # This file was autogenerated by uv via the following command:
-#    uv pip compile requirements.in -o /home/runner/work/bio-data-to-db/bio-data-to-db/deps/lock/x86_64-apple-darwin/requirements.txt --python-platform x86_64-apple-darwin --python-version 3.10
+#    uv pip compile requirements.in -o /Users/kiyoon/project/bio-data-to-db/deps/lock/x86_64-apple-darwin/requirements.txt --python-platform x86_64-apple-darwin --python-version 3.10
 click==8.1.7
     # via typer
 connectorx==0.3.3
@@ -33,6 +33,8 @@ pygments==2.18.0
     # via rich
 python-dateutil==2.9.0.post0
     # via pandas
+python-dotenv==1.0.1
+    # via -r requirements.in
 pytz==2024.1
     # via pandas
 rdkit==2024.3.3

deps/lock/x86_64-apple-darwin/requirements_dev.txt

@@ -1,5 +1,5 @@
 # This file was autogenerated by uv via the following command:
-#    uv pip compile requirements_dev.in -o /home/runner/work/bio-data-to-db/bio-data-to-db/deps/lock/x86_64-apple-darwin/requirements_dev.txt --python-platform x86_64-apple-darwin --python-version 3.10
+#    uv pip compile requirements_dev.in -o /Users/kiyoon/project/bio-data-to-db/deps/lock/x86_64-apple-darwin/requirements_dev.txt --python-platform x86_64-apple-darwin --python-version 3.10
 certifi==2024.7.4
     # via requests
 charset-normalizer==3.3.2
@@ -64,6 +64,8 @@ pytest==8.2.2
     # via -r requirements_dev.in
 python-dateutil==2.9.0.post0
     # via pandas
+python-dotenv==1.0.1
+    # via -r requirements.in
 pytz==2024.1
     # via pandas
 pyyaml==6.0.1

deps/lock/x86_64-manylinux_2_28/.requirements.in.sha256

@@ -1 +1 @@
-b2aeb764caf50f816850626567cb58bbe65e02c45df54e8d56b7f9e5702148c4  requirements.in
+0f0639ee4488d0173fcd2fe6da6a991d614525066cbf04ea0932c593fed75d99  requirements.in

deps/lock/x86_64-manylinux_2_28/requirements.txt

@@ -1,5 +1,5 @@
 # This file was autogenerated by uv via the following command:
-#    uv pip compile requirements.in -o /home/runner/work/bio-data-to-db/bio-data-to-db/deps/lock/x86_64-manylinux_2_28/requirements.txt --python-platform x86_64-manylinux_2_28 --python-version 3.10
+#    uv pip compile requirements.in -o /Users/kiyoon/project/bio-data-to-db/deps/lock/x86_64-manylinux_2_28/requirements.txt --python-platform x86_64-manylinux_2_28 --python-version 3.10
 click==8.1.7
     # via typer
 connectorx==0.3.3
@@ -33,6 +33,8 @@ pygments==2.18.0
     # via rich
 python-dateutil==2.9.0.post0
     # via pandas
+python-dotenv==1.0.1
+    # via -r requirements.in
 pytz==2024.1
     # via pandas
 rdkit==2024.3.3

deps/lock/x86_64-manylinux_2_28/requirements_dev.txt

@@ -1,5 +1,5 @@
 # This file was autogenerated by uv via the following command:
-#    uv pip compile requirements_dev.in -o /home/runner/work/bio-data-to-db/bio-data-to-db/deps/lock/x86_64-manylinux_2_28/requirements_dev.txt --python-platform x86_64-manylinux_2_28 --python-version 3.10
+#    uv pip compile requirements_dev.in -o /Users/kiyoon/project/bio-data-to-db/deps/lock/x86_64-manylinux_2_28/requirements_dev.txt --python-platform x86_64-manylinux_2_28 --python-version 3.10
 certifi==2024.7.4
     # via requests
 charset-normalizer==3.3.2
@@ -64,6 +64,8 @@ pytest==8.2.2
     # via -r requirements_dev.in
 python-dateutil==2.9.0.post0
     # via pandas
+python-dotenv==1.0.1
+    # via -r requirements.in
 pytz==2024.1
     # via pandas
 pyyaml==6.0.1

deps/lock/x86_64-pc-windows-msvc/.requirements.in.sha256

@@ -1 +1 @@
-b2aeb764caf50f816850626567cb58bbe65e02c45df54e8d56b7f9e5702148c4  requirements.in
+0f0639ee4488d0173fcd2fe6da6a991d614525066cbf04ea0932c593fed75d99  requirements.in

deps/lock/x86_64-pc-windows-msvc/requirements.txt

@@ -1,5 +1,5 @@
 # This file was autogenerated by uv via the following command:
-#    uv pip compile requirements.in -o /home/runner/work/bio-data-to-db/bio-data-to-db/deps/lock/x86_64-pc-windows-msvc/requirements.txt --python-platform x86_64-pc-windows-msvc --python-version 3.10
+#    uv pip compile requirements.in -o /Users/kiyoon/project/bio-data-to-db/deps/lock/x86_64-pc-windows-msvc/requirements.txt --python-platform x86_64-pc-windows-msvc --python-version 3.10
 click==8.1.7
     # via typer
 colorama==0.4.6
@@ -37,6 +37,8 @@ pygments==2.18.0
     # via rich
 python-dateutil==2.9.0.post0
     # via pandas
+python-dotenv==1.0.1
+    # via -r requirements.in
 pytz==2024.1
     # via pandas
 rdkit==2024.3.3

deps/lock/x86_64-pc-windows-msvc/requirements_dev.txt

@@ -1,5 +1,5 @@
 # This file was autogenerated by uv via the following command:
-#    uv pip compile requirements_dev.in -o /home/runner/work/bio-data-to-db/bio-data-to-db/deps/lock/x86_64-pc-windows-msvc/requirements_dev.txt --python-platform x86_64-pc-windows-msvc --python-version 3.10
+#    uv pip compile requirements_dev.in -o /Users/kiyoon/project/bio-data-to-db/deps/lock/x86_64-pc-windows-msvc/requirements_dev.txt --python-platform x86_64-pc-windows-msvc --python-version 3.10
 certifi==2024.7.4
     # via requests
 charset-normalizer==3.3.2
@@ -69,6 +69,8 @@ pytest==8.2.2
     # via -r requirements_dev.in
 python-dateutil==2.9.0.post0
     # via pandas
+python-dotenv==1.0.1
+    # via -r requirements.in
 pytz==2024.1
     # via pandas
 pyyaml==6.0.1

deps/requirements.in

@@ -9,3 +9,4 @@ mysqlclient>=2.2.0
 connectorx>=0.3.0
 rdkit>=2024.3.1
 tqdm>=4.62.0
+python-dotenv>=1.0.1

src/bio_data_to_db/cli/main.py

@@ -1,11 +1,12 @@
 import typer
 
-from . import bindingdb, uniprot
+from . import bindingdb, postgresql, uniprot
 
 app = typer.Typer(no_args_is_help=True)
 
 app.add_typer(uniprot.app, name="uniprot")
 app.add_typer(bindingdb.app, name="bindingdb")
+app.add_typer(postgresql.app, name="postgresql")
 
 
 def main():

src/bio_data_to_db/cli/postgresql.py

@@ -0,0 +1,62 @@
+# ruff: noqa: T201
+import os
+import urllib.parse
+from typing import Annotated
+
+import typer
+
+app = typer.Typer(no_args_is_help=True)
+
+
+@app.command()
+def get_uri_from_env(
+    db_name: Annotated[str | None, typer.Argument(..., help="Database name")] = None,
+):
+    """
+    Get connection URI from environment variables for .env file.
+
+    The following environment variables are required:
+
+    - POSTGRESQL_HOST (default: localhost)
+    - POSTGRESQL_PORT (default: 5432)
+    - POSTGRESQL_USER
+    - POSTGRESQL_PASSWORD
+    """
+    from dotenv import find_dotenv, load_dotenv
+
+    dotenv_path = find_dotenv(usecwd=True)
+    if dotenv_path != "":
+        load_dotenv(dotenv_path)
+
+    host = os.getenv("POSTGRESQL_HOST")
+    if host is None:
+        host = "localhost"
+    port = os.getenv("POSTGRESQL_PORT")
+    if port is None:
+        port = "5432"
+
+    user = os.getenv("POSTGRESQL_USER")
+    if user is None:
+        print("❌ POSTGRESQL_USER is required.")
+        typer.Exit(code=1)
+        return
+    password = os.getenv("POSTGRESQL_PASSWORD")
+    if password is None:
+        print("❌ POSTGRESQL_PASSWORD is required.")
+        typer.Exit(code=1)
+        return
+
+    if db_name is not None:
+        print(
+            f"postgresql://{user}:{urllib.parse.quote_plus(password)}@{host}:{port}/{db_name}"
+        )
+    else:
+        print(f"postgresql://{user}:{urllib.parse.quote_plus(password)}@{host}:{port}")
+
+
+def main():
+    app()
+
+
+if __name__ == "__main__":
+    main()