Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/galaxy/util/yaml_util.py @ 0:4f3585e2f14b draft default tip
"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"
author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 import logging |
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2 import os |
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3 from collections import OrderedDict |
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4 |
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5 import yaml |
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6 try: |
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7 from yaml import CSafeLoader as SafeLoader |
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8 except ImportError: |
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9 from yaml import SafeLoader # type: ignore |
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10 from yaml.constructor import ConstructorError |
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11 |
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12 |
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13 log = logging.getLogger(__name__) |
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14 |
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15 |
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16 class OrderedLoader(SafeLoader): |
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17 # This class was pulled out of ordered_load() for the sake of |
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18 # mocking __init__ in a unit test. |
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19 def __init__(self, stream): |
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20 self._root = os.path.split(stream.name)[0] |
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21 super().__init__(stream) |
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22 |
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23 def include(self, node): |
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24 filename = os.path.join(self._root, self.construct_scalar(node)) |
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25 with open(filename) as f: |
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26 return yaml.load(f, OrderedLoader) |
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27 |
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28 |
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29 def ordered_load(stream, merge_duplicate_keys=False): |
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30 """ |
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31 Parse the first YAML document in a stream and produce the corresponding |
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32 Python object. |
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33 |
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34 If merge_duplicate_keys is True, merge the values of duplicate mapping keys |
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35 into a list, as the uWSGI "dumb" YAML parser would do. |
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36 Otherwise, following YAML 1.2 specification which says that "each key is |
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37 unique in the association", raise a ConstructionError exception. |
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38 """ |
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39 def construct_mapping(loader, node, deep=False): |
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40 loader.flatten_mapping(node) |
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41 mapping = {} |
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42 merged_duplicate = {} |
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43 for key_node, value_node in node.value: |
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44 key = loader.construct_object(key_node, deep=deep) |
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45 value = loader.construct_object(value_node, deep=deep) |
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46 if key in mapping: |
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47 if not merge_duplicate_keys: |
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48 raise ConstructorError("while constructing a mapping", node.start_mark, |
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49 "found duplicated key (%s)" % key, key_node.start_mark) |
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50 log.debug("Merging values for duplicate key '%s' into a list", key) |
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51 if merged_duplicate.get(key): |
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52 mapping[key].append(value) |
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53 else: |
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54 mapping[key] = [mapping[key], value] |
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55 merged_duplicate[key] = True |
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56 else: |
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57 mapping[key] = value |
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58 return mapping |
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59 |
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60 OrderedLoader.add_constructor( |
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61 yaml.resolver.BaseResolver.DEFAULT_MAPPING_TAG, |
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62 construct_mapping) |
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63 OrderedLoader.add_constructor('!include', OrderedLoader.include) |
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64 |
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65 return yaml.load(stream, OrderedLoader) |
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66 |
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67 |
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68 def ordered_dump(data, stream=None, Dumper=yaml.Dumper, **kwds): |
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69 class OrderedDumper(Dumper): |
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70 pass |
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71 |
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72 def _dict_representer(dumper, data): |
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73 return dumper.represent_mapping( |
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74 yaml.resolver.BaseResolver.DEFAULT_MAPPING_TAG, |
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75 list(data.items())) |
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76 OrderedDumper.add_representer(OrderedDict, _dict_representer) |
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77 return yaml.dump(data, stream, OrderedDumper, **kwds) |