diff util.py @ 14:a38315ecf593 draft

planemo upload for repository https://github.com/Alveo/alveo-galaxy-tools commit b5b26e9118f2ad8af109d606746b39a5588f0511-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/util.py	Wed Nov 01 01:18:15 2017 -0400
@@ -0,0 +1,55 @@
+"""
+Utility functions and settings for API tools
+"""
+import pyalveo
+import csv
+
+# this should be in a config file
+API_URL = 'https://app.alveo.edu.au'
+
+
+def write_key(api_key, output_path, client_module=pyalveo):
+    """Tests whether an API key is valid and writes it to a file.
+
+    :type api_key: String
+    :param api_key: Alveo API key
+
+    :type output_path: String
+    :param output_path: Path to the file to store the API key in
+
+    :type client_module: pyalveo.Client
+    :param client_module: Module providing the client (used for testing purposes),
+        defaults to pyalveo
+
+    :raises: pyalveo.APIError if the API request is not successful
+
+    """
+    # validate the client key, raises an exception if it is not valid
+    client_module.Client(api_key, API_URL, use_cache=False)
+    outfile = open(output_path, 'w')
+    outfile.write(api_key)
+    outfile.close()
+
+
+def get_item_lists(api_key):
+    client = pyalveo.Client(api_key=api_key, api_url=API_URL, use_cache=False)
+    return client.get_item_lists()
+
+
+def read_item_list(filename, client):
+    """Read an item list from a file
+    which should be a tabular formatted file
+    with one column header ItemURL.
+    Return an instance of ItemGroup"""
+
+    with open(filename) as fd:
+        csvreader = csv.DictReader(fd, dialect='excel-tab')
+        if 'ItemURL' not in csvreader.fieldnames:
+            return None
+        itemurls = []
+        for row in csvreader:
+            itemurls.append(row['ItemURL'])
+
+    itemlist = pyalveo.ItemGroup(itemurls, client)
+
+    return itemlist