Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/galaxy/util/yaml_util.py @ 2:6af9afd405e9 draft

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"planemo upload commit 0a63dd5f4d38a1f6944587f52a8cd79874177fc1"
author shellac
date Thu, 14 May 2020 14:56:58 -0400
parents 26e78fe6e8c4
children
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1 from __future__ import absolute_import
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2
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3 import logging
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4 import os
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5 from collections import OrderedDict
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6
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7 import yaml
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8 from yaml.constructor import ConstructorError
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9
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10
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11 log = logging.getLogger(__name__)
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12
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13 OPTION_DEFAULTS = {
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14 "type": "str",
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15 "unknown_option": False,
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16 "default": None,
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17 "desc": None,
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18 }
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19
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20
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21 class OrderedLoader(yaml.SafeLoader):
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22 # This class was pulled out of ordered_load() for the sake of
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23 # mocking __init__ in a unit test.
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24 def __init__(self, stream):
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25 self._root = os.path.split(stream.name)[0]
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26 super(OrderedLoader, self).__init__(stream)
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27
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28 def include(self, node):
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29 filename = os.path.join(self._root, self.construct_scalar(node))
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30 with open(filename, 'r') as f:
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31 return yaml.load(f, OrderedLoader)
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32
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33
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34 def ordered_load(stream, merge_duplicate_keys=False):
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35 """
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36 Parse the first YAML document in a stream and produce the corresponding
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37 Python object, using OrderedDicts instead of dicts.
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38
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39 If merge_duplicate_keys is True, merge the values of duplicate mapping keys
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40 into a list, as the uWSGI "dumb" YAML parser would do.
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41 Otherwise, following YAML 1.2 specification which says that "each key is
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42 unique in the association", raise a ConstructionError exception.
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43 """
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44 def construct_mapping(loader, node, deep=False):
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45 loader.flatten_mapping(node)
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46 mapping = OrderedDict()
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47 merged_duplicate = {}
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48 for key_node, value_node in node.value:
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49 key = loader.construct_object(key_node, deep=deep)
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50 value = loader.construct_object(value_node, deep=deep)
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51 if key in mapping:
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52 if not merge_duplicate_keys:
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53 raise ConstructorError("while constructing a mapping", node.start_mark,
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54 "found duplicated key (%s)" % key, key_node.start_mark)
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55 log.debug("Merging values for duplicate key '%s' into a list", key)
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56 if merged_duplicate.get(key):
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57 mapping[key].append(value)
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58 else:
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59 mapping[key] = [mapping[key], value]
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60 merged_duplicate[key] = True
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61 else:
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62 mapping[key] = value
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63 return mapping
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64
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65 OrderedLoader.add_constructor(
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66 yaml.resolver.BaseResolver.DEFAULT_MAPPING_TAG,
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67 construct_mapping)
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68 OrderedLoader.add_constructor('!include', OrderedLoader.include)
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69
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70 return yaml.load(stream, OrderedLoader)
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71
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72
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73 def ordered_dump(data, stream=None, Dumper=yaml.Dumper, **kwds):
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74 class OrderedDumper(Dumper):
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75 pass
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76
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77 def _dict_representer(dumper, data):
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78 return dumper.represent_mapping(
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79 yaml.resolver.BaseResolver.DEFAULT_MAPPING_TAG,
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80 list(data.items()))
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81 OrderedDumper.add_representer(OrderedDict, _dict_representer)
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82 return yaml.dump(data, stream, OrderedDumper, **kwds)