From ffdb0cec429fb4f3ac243d36438899ca8e35b821 Mon Sep 17 00:00:00 2001
From: Nicola Soranzo <nicola.soranzo@earlham.ac.uk>
Date: Thu, 15 Jun 2023 18:53:48 +0100
Subject: [PATCH] Replace ``urllib.parse.urljoin()`` with f-strings

because the former generate the wrong URL when passed absolute paths
for Galaxy instances served at a subdirectory, e.g.:

```python
urljoin("https://my.galaxy/subdir", "/dataset/dataset_id/display")
```

returns "https://my.galaxy/dataset/dataset_id/display" instead of
"https://my.galaxy/subdir/dataset/dataset_id/display".
---
 bioblend/_tests/TestGalaxyInstance.py  | 8 ++++++++
 bioblend/galaxy/datasets/__init__.py   | 3 +--
 bioblend/galaxy/histories/__init__.py  | 3 +--
 bioblend/galaxyclient.py               | 5 ++---
 docs/examples/objects/w5_galaxy_api.py | 5 ++---
 5 files changed, 14 insertions(+), 10 deletions(-)

diff --git a/bioblend/_tests/TestGalaxyInstance.py b/bioblend/_tests/TestGalaxyInstance.py
index 2c7f30004..54b67d343 100644
--- a/bioblend/_tests/TestGalaxyInstance.py
+++ b/bioblend/_tests/TestGalaxyInstance.py
@@ -17,6 +17,14 @@ def setUp(self):
         # "connect" to a fake Galaxy instance
         self.gi = GalaxyInstance("http://localhost:56789", key="whatever")
 
+    def test_url_attribute(self):
+        assert self.gi.base_url == "http://localhost:56789"
+        assert self.gi.url == "http://localhost:56789/api"
+        # Test instance served at a subdirectory
+        gi = GalaxyInstance("http://localhost:56789/galaxy/", key="whatever")
+        assert gi.base_url == "http://localhost:56789/galaxy"
+        assert gi.url == "http://localhost:56789/galaxy/api"
+
     def test_set_max_get_attempts(self):
         self.gi.max_get_attempts = 3
         assert 3 == self.gi.max_get_attempts
diff --git a/bioblend/galaxy/datasets/__init__.py b/bioblend/galaxy/datasets/__init__.py
index 3fef003de..f33e2582a 100644
--- a/bioblend/galaxy/datasets/__init__.py
+++ b/bioblend/galaxy/datasets/__init__.py
@@ -16,7 +16,6 @@
     TYPE_CHECKING,
     Union,
 )
-from urllib.parse import urljoin
 
 from requests import Response
 from typing_extensions import Literal
@@ -86,7 +85,7 @@ def _initiate_download(
         # does not work when using REMOTE_USER with access disabled to
         # everything but /api without auth
         download_url = dataset["download_url"] + "?to_ext=" + file_ext
-        url = urljoin(self.gi.base_url, download_url)
+        url = f"{self.gi.base_url}{download_url}"
 
         r = self.gi.make_get_request(url, stream=stream_content)
         r.raise_for_status()
diff --git a/bioblend/galaxy/histories/__init__.py b/bioblend/galaxy/histories/__init__.py
index b12737b45..72181a780 100644
--- a/bioblend/galaxy/histories/__init__.py
+++ b/bioblend/galaxy/histories/__init__.py
@@ -17,7 +17,6 @@
     Pattern,
     Union,
 )
-from urllib.parse import urljoin
 
 from typing_extensions import Literal
 
@@ -870,7 +869,7 @@ def open_history(self, history_id: str) -> None:
           any such tab is recommended.
         """
 
-        url = urljoin(self.gi.base_url, f"history/switch_to_history?hist_id={history_id}")
+        url = f"{self.gi.base_url}/history/switch_to_history?hist_id={history_id}"
         webbrowser.open_new_tab(url)
 
     def get_extra_files(self, history_id: str, dataset_id: str) -> List[str]:
diff --git a/bioblend/galaxyclient.py b/bioblend/galaxyclient.py
index a99f70c69..3a6c168e0 100644
--- a/bioblend/galaxyclient.py
+++ b/bioblend/galaxyclient.py
@@ -13,7 +13,6 @@
     Any,
     Optional,
 )
-from urllib.parse import urljoin
 
 import requests
 import tusclient.client
@@ -66,9 +65,9 @@ def __init__(
             else:
                 raise ValueError(f"Missing scheme in url {url}")
             url = found_scheme + url
+        self.base_url = url.rstrip("/")
         # All of Galaxy's and ToolShed's API's are rooted at <url>/api so make that the url
-        self.base_url = url
-        self.url = urljoin(url, "api")
+        self.url = f"{self.base_url}/api"
         # If key has been supplied, use it; otherwise just set email and
         # password and grab user's key before first request.
         if key:
diff --git a/docs/examples/objects/w5_galaxy_api.py b/docs/examples/objects/w5_galaxy_api.py
index a74534f21..d5f19897c 100644
--- a/docs/examples/objects/w5_galaxy_api.py
+++ b/docs/examples/objects/w5_galaxy_api.py
@@ -1,14 +1,13 @@
 import json
 import os
 import sys
-from urllib.parse import urljoin
 
 # This example, provided for comparison with w5_metagenomics.py,
 # contains the code required to run the metagenomics workflow
 # *without* BioBlend.
 
-URL = os.getenv("GALAXY_URL", "https://orione.crs4.it")
-API_URL = urljoin(URL, "api")
+URL = os.getenv("GALAXY_URL", "https://orione.crs4.it").rstrip("/")
+API_URL = f"{URL}/api"
 API_KEY = os.getenv("GALAXY_API_KEY", "YOUR_API_KEY")
 if API_KEY == "YOUR_API_KEY":
     sys.exit("API_KEY not set, see the README.txt file")