diff env/lib/python3.9/site-packages/bioblend/_tests/test_util.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/bioblend/_tests/test_util.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,110 @@
+""" General support infrastructure not tied to any particular test.
+"""
+import os
+import random
+import string
+import unittest
+
+import bioblend
+
+NO_CLOUDMAN_MESSAGE = "CloudMan required and no CloudMan AMI configured."
+NO_GALAXY_MESSAGE = "Externally configured Galaxy required, but not found. Set BIOBLEND_GALAXY_URL and BIOBLEND_GALAXY_API_KEY to run this test."
+OLD_GALAXY_RELEASE = "Testing on Galaxy %s, but need %s to run this test."
+MISSING_TOOL_MESSAGE = "Externally configured Galaxy instance requires tool %s to run test."
+
+
+def skip_unless_cloudman():
+    """ Decorate tests with this to skip the test if CloudMan is not
+    configured.
+    """
+    if 'BIOBLEND_AMI_ID' not in os.environ:
+        return unittest.skip(NO_CLOUDMAN_MESSAGE)
+    else:
+        return lambda f: f
+
+
+def skip_unless_galaxy(min_release=None):
+    """ Decorate tests with this to skip the test if Galaxy is not
+    configured.
+    """
+    if min_release is not None:
+        galaxy_release = os.environ.get('GALAXY_VERSION', None)
+        if galaxy_release is not None and galaxy_release != 'dev':
+            if not galaxy_release.startswith('release_'):
+                raise ValueError("The value of GALAXY_VERSION environment variable should start with 'release_'")
+            if not min_release.startswith('release_'):
+                raise Exception("min_release should start with 'release_'")
+            if galaxy_release[8:] < min_release[8:]:
+                return unittest.skip(OLD_GALAXY_RELEASE % (galaxy_release, min_release))
+
+    if 'BIOBLEND_GALAXY_URL' not in os.environ:
+        return unittest.skip(NO_GALAXY_MESSAGE)
+
+    if 'BIOBLEND_GALAXY_API_KEY' not in os.environ and 'BIOBLEND_GALAXY_MASTER_API_KEY' in os.environ:
+        galaxy_url = os.environ['BIOBLEND_GALAXY_URL']
+        galaxy_master_api_key = os.environ['BIOBLEND_GALAXY_MASTER_API_KEY']
+        gi = bioblend.galaxy.GalaxyInstance(galaxy_url, galaxy_master_api_key)
+
+        if 'BIOBLEND_GALAXY_USER_EMAIL' in os.environ:
+            galaxy_user_email = os.environ['BIOBLEND_GALAXY_USER_EMAIL']
+        else:
+            galaxy_user_email = ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(5)) + "@localhost.localdomain"
+
+        galaxy_user_id = None
+        for user in gi.users.get_users():
+            if user["email"] == galaxy_user_email:
+                galaxy_user_id = user["id"]
+                break
+
+        if galaxy_user_id is None:
+            try:
+                config = gi.config.get_config()
+            except Exception:
+                # If older Galaxy for instance just assume use_remote_user is False.
+                config = {}
+
+            if config.get("use_remote_user", False):
+                new_user = gi.users.create_remote_user(galaxy_user_email)
+            else:
+                galaxy_user = galaxy_user_email.split("@", 1)[0]
+                galaxy_password = ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(20))
+
+                # Create a new user and get a new API key for her
+                new_user = gi.users.create_local_user(galaxy_user, galaxy_user_email, galaxy_password)
+            galaxy_user_id = new_user["id"]
+
+        api_key = gi.users.create_user_apikey(galaxy_user_id)
+        os.environ["BIOBLEND_GALAXY_API_KEY"] = api_key
+
+    if 'BIOBLEND_GALAXY_API_KEY' not in os.environ:
+        return unittest.skip(NO_GALAXY_MESSAGE)
+
+    return lambda f: f
+
+
+def skip_unless_tool(tool_id):
+    """ Decorate a Galaxy test method as requiring a specific tool,
+    skip the test case if the tool is unavailable.
+    """
+
+    def method_wrapper(method):
+
+        def wrapped_method(has_gi, *args, **kwargs):
+            tools = has_gi.gi.tools.get_tools()
+            # In panels by default, so flatten out sections...
+            tool_ids = [_['id'] for _ in tools]
+            if tool_id not in tool_ids:
+                raise unittest.SkipTest(MISSING_TOOL_MESSAGE % tool_id)
+
+            return method(has_gi, *args, **kwargs)
+
+        # Must preserve method name so nose can detect and report tests by
+        # name.
+        wrapped_method.__name__ = method.__name__
+        return wrapped_method
+
+    return method_wrapper
+
+
+def get_abspath(path):
+    return os.path.abspath(os.path.join(os.path.dirname(__file__), path))