diff env/lib/python3.9/site-packages/ephemeris/__init__.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/ephemeris/__init__.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,66 @@
+
+# -*- coding: utf-8 -*-
+
+import yaml
+from bioblend import galaxy
+
+__version__ = '0.10.6'
+
+PROJECT_NAME = "ephemeris"
+PROJECT_OWNER = PROJECT_USERAME = "galaxyproject"
+PROJECT_URL = "https://github.com/galaxyproject/ephemeris"
+PROJECT_AUTHOR = 'Galaxy Project and Community'
+PROJECT_EMAIL = '[e-mail]'
+RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % (
+    PROJECT_USERAME, PROJECT_NAME
+)
+
+
+def check_url(url, log=None):
+    if not url.startswith('http'):
+        if log:
+            log.warning('URL should start with http:// or https://. https:// chosen by default.')
+        url = 'https://' + url
+    return url
+
+
+def get_galaxy_connection(args, file=None, log=None, login_required=True):
+    """
+    Return a Galaxy connection, given a user or an API key.
+    If not given gets the arguments from the file.
+    If either is missing raise ValueError.
+    """
+    if file:
+        file_content = load_yaml_file(file)
+    else:
+        file_content = dict()
+
+    url = args.galaxy or file_content.get('galaxy_instance')
+    galaxy_url = check_url(url, log)
+    api_key = args.api_key or file_content.get('api_key')
+
+    if args.user and args.password:
+        return galaxy.GalaxyInstance(url=galaxy_url, email=args.user, password=args.password)
+    elif api_key:
+        return galaxy.GalaxyInstance(url=galaxy_url, key=api_key)
+    elif not login_required:
+        return galaxy.GalaxyInstance(url=galaxy_url)
+    else:
+        raise ValueError("Missing api key or user & password combination, in order to make a galaxy connection.")
+
+
+def load_yaml_file(filename):
+    """
+    Load YAML from the `tool_list_file` and return a dict with the content.
+    """
+    with open(filename, 'r') as f:
+        dictionary = yaml.safe_load(f)
+    return dictionary
+
+
+def dump_to_yaml_file(content, file_name):
+    """
+    Dump YAML-compatible `content` to `file_name`.
+    """
+    with open(file_name, 'w') as f:
+        yaml.dump(content, f, default_flow_style=False)