Mercurial > repos > fubar > tool_factory_2

annotate toolfactory/galaxyxml/__init__.py @ 35:5d38cb3d9be8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
added patched galaxyxml code temporarily until PR accepted
author fubar
date Sat, 08 Aug 2020 19:55:55 -0400
parents
children ce2b1f8ea68d
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
35
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
1 from builtins import str
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
2 from builtins import object
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
3 from lxml import etree
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
4
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
5
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
6 class GalaxyXML(object):
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
7
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
8 def __init__(self):
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
9 self.root = etree.Element('root')
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
10
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
11 def export(self):
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
12 return etree.tostring(self.root, pretty_print=True, encoding='unicode')
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
13
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
14
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
15 class Util(object):
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
16
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
17 @classmethod
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
18 def coerce(cls, data, kill_lists=False):
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
19 """Recursive data sanitisation
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
20 """
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
21 if isinstance(data, dict):
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
22 return {k: cls.coerce(v, kill_lists=kill_lists) for k, v in
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
23 list(data.items()) if v is not None}
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
24 elif isinstance(data, list):
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
25 if kill_lists:
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
26 return cls.coerce(data[0])
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
27 else:
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
28 return [cls.coerce(v, kill_lists=kill_lists) for v in data]
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
29 else:
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
30 return cls.coerce_value(data)
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
31
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
32 @classmethod
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
33 def coerce_value(cls, obj):
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
34 """Make everything a string!
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
35 """
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
36 if isinstance(obj, bool):
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
37 if obj:
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
38 return "true"
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
39 else:
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
40 return "false"
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
41 elif isinstance(obj, str):
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
42 return obj
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
43 else:
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
44 return str(obj)
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
45
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
46 @classmethod
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
47 def clean_kwargs(cls, params, final=False):
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
48 if 'kwargs' in params:
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
49 kwargs = params['kwargs']
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
50 for k in kwargs:
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
51 params[k] = kwargs[k]
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
52 del params['kwargs']
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
53 if 'self' in params:
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
54 del params['self']
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
55
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
56 if '__class__' in params:
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
57 del params['__class__']
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
58
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
59 # There will be more params, it would be NICE to use a whitelist
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
60 # instead of a blacklist, but until we have more data let's just
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
61 # blacklist stuff we see commonly.
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
62 if final:
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
63 for blacklist in ('positional',):
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
64 if blacklist in params:
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
65 del params[blacklist]
5d38cb3d9be8 added patched galaxyxml code temporarily until PR accepted
fubar
parents:
diff changeset
66 return params