Mercurial > repos > guerler > springsuite

annotate planemo/lib/python3.7/site-packages/galaxy/tool_util/provided_metadata.py @ 1:56ad4e20f292 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:32:28 -0400
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1
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1 import json
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2 import logging
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3 import os
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4 import re
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5
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6 from galaxy.util import stringify_dictionary_keys
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7
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8 log = logging.getLogger(__name__)
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9
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10
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11 def parse_tool_provided_metadata(meta_file, provided_metadata_style=None, job_wrapper=None):
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12 """Return a ToolProvidedMetadata object for specified file path.
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13
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14 If meta_file is absent, return a NullToolProvidedMetadata. If provided_metadata_style is None
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15 attempt to guess tool provided metadata type.
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16 """
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17 if not os.path.exists(meta_file):
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18 return NullToolProvidedMetadata()
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19 if provided_metadata_style is None:
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20 provided_metadata_style = _guess_tool_provided_metadata_style(meta_file)
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21
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22 assert provided_metadata_style in ["legacy", "default"]
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23
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24 if provided_metadata_style == "legacy":
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25 return LegacyToolProvidedMetadata(meta_file, job_wrapper=job_wrapper)
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26 elif provided_metadata_style == "default":
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27 return ToolProvidedMetadata(meta_file)
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28
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29
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30 def _guess_tool_provided_metadata_style(path):
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31 try:
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32 with open(path, "r") as f:
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33 metadata = json.load(f)
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34 metadata_type = metadata.get("type", None)
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35 return "legacy" if metadata_type in ["dataset", "new_primary_dataset"] else "default"
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36 except ValueError:
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37 # Either empty or multiple JSON lines, either way we can safely treat
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38 # it as legacy style.
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39 return "legacy"
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40
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41
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42 class BaseToolProvidedMetadata(object):
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43
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44 def get_new_datasets(self, output_name):
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45 """Find new datasets for dataset discovery for specified output.
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46
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47 Return a list of such datasets.
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48
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49 Called only in the context of discovering datasets when
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50 discover_via="tool_provided_metadata" is defined in the tool.
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51 """
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52 return []
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53
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54 def has_failed_outputs(self):
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55 """Determine if generation of any of the outputs failed.
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56
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57 If True, this method should also log information about at least the first such failed output.
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58 """
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59 return False
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60
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61 def get_new_dataset_meta_by_basename(self, output_name, basename):
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62 """For a discovered dataset, get the corresponding metadata entry.
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63
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64 The discovery may have been from explicit listing in this file (returned
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65 from get_new_datasets) or via file regex, either way the basename of the
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66 file is used to index the fetching of the metadata entry.
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67 """
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68 return {}
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69
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70 def get_unnamed_outputs(self):
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71 """Return unnamed outputs dataset introduced for upload 2.0.
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72
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73 Needs more formal specification but see output_collect for how destinations,
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74 types, elements, etc... are consumed.
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75 """
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76 return []
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77
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78 def get_dataset_meta(self, output_name, dataset_id, dataset_uuid):
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79 """Return primary dataset metadata for specified output.
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80 """
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81 return {}
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82
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83 def rewrite(self):
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84 """Write metadata back to the file system.
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85
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86 If metadata has not changed via outputs specified as mutable, the
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87 implementation class may opt to not re-write the file.
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88 """
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89 return None
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90
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91 def get_new_datasets_for_metadata_collection(self):
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92 """Return all datasets tracked that are not explicit primary outputs.
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93 """
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94 return []
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95
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96
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97 class NullToolProvidedMetadata(BaseToolProvidedMetadata):
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98 pass
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99
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100
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101 class LegacyToolProvidedMetadata(BaseToolProvidedMetadata):
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102
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103 def __init__(self, meta_file, job_wrapper=None):
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104 self.meta_file = meta_file
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105 self.tool_provided_job_metadata = []
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106
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107 with open(meta_file, 'r') as f:
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108 for line in f:
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109 try:
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110 line = stringify_dictionary_keys(json.loads(line))
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111 assert 'type' in line
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112 except Exception:
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113 log.exception('(%s) Got JSON data from tool, but data is improperly formatted or no "type" key in data' % getattr(job_wrapper, "job_id", None))
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114 log.debug('Offending data was: %s' % line)
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115 continue
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116 # Set the dataset id if it's a dataset entry and isn't set.
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117 # This isn't insecure. We loop the job's output datasets in
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118 # the finish method, so if a tool writes out metadata for a
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119 # dataset id that it doesn't own, it'll just be ignored.
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120 dataset_id_not_specified = line['type'] == 'dataset' and 'dataset_id' not in line
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121 if dataset_id_not_specified:
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122 dataset_basename = line['dataset']
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123 if job_wrapper:
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124 try:
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125 line['dataset_id'] = job_wrapper.get_output_file_id(dataset_basename)
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126 except KeyError:
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127 log.warning('(%s) Tool provided job dataset-specific metadata without specifying a dataset' % job_wrapper.job_id)
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128 continue
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129 else:
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130 match = re.match(r'(galaxy_)?dataset_(.*)\.dat', dataset_basename)
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131 if match is None:
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132 raise Exception("processing tool_provided_metadata (e.g. galaxy.json) entry with invalid dataset name [%s]" % dataset_basename)
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133 dataset_id = match.group(2)
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134 if dataset_id.isdigit():
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135 line['dataset_id'] = dataset_id
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136 else:
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137 line['dataset_uuid'] = dataset_id
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138
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139 self.tool_provided_job_metadata.append(line)
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140
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141 def get_dataset_meta(self, output_name, dataset_id, dataset_uuid):
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142 for meta in self.tool_provided_job_metadata:
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143 if meta['type'] == 'dataset' and 'dataset_id' in meta and int(meta['dataset_id']) == dataset_id:
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144 return meta
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145 if meta['type'] == 'dataset' and 'dataset_uuid' in meta and meta['dataset_uuid'] == dataset_uuid:
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146 return meta
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147 return {}
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148
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149 def get_new_dataset_meta_by_basename(self, output_name, basename):
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150 for meta in self.tool_provided_job_metadata:
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151 if meta['type'] == 'new_primary_dataset' and meta['filename'] == basename:
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152 return meta
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153
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154 def get_new_datasets(self, output_name):
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155 log.warning("Called get_new_datasets with legacy tool metadata provider - that is unimplemented.")
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156 return []
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157
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158 def has_failed_outputs(self):
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159 found_failed = False
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160 for meta in self.tool_provided_job_metadata:
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161 if meta.get("failed", False):
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162 log.info("One or more tool outputs is marked as failed (%s)." % meta)
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163 found_failed = True
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164
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165 return found_failed
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166
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167 def get_unnamed_outputs(self):
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168 return []
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169
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170 def rewrite(self):
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171 with open(self.meta_file, 'wt') as job_metadata_fh:
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172 for meta in self.tool_provided_job_metadata:
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173 job_metadata_fh.write("%s\n" % (json.dumps(meta)))
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174
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175 def get_new_datasets_for_metadata_collection(self):
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176 for meta in self.tool_provided_job_metadata:
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177 if meta['type'] == 'new_primary_dataset':
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178 yield meta
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179
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180
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181 class ToolProvidedMetadata(BaseToolProvidedMetadata):
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182
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183 def __init__(self, meta_file):
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184 self.meta_file = meta_file
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185 with open(meta_file, 'r') as f:
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186 self.tool_provided_job_metadata = json.load(f)
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187
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188 def get_dataset_meta(self, output_name, dataset_id, dataset_uuid):
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189 return self.tool_provided_job_metadata.get(output_name, {})
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190
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191 def get_new_dataset_meta_by_basename(self, output_name, basename):
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192 datasets = self.tool_provided_job_metadata.get(output_name, {}).get("datasets", [])
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193 for meta in datasets:
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194 if meta['filename'] == basename:
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195 return meta
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196
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197 def get_new_datasets(self, output_name):
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198 datasets = self.tool_provided_job_metadata.get(output_name, {}).get("datasets", [])
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199 if not datasets:
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200 elements = self.tool_provided_job_metadata.get(output_name, {}).get("elements", [])
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201 if elements:
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202 datasets = self._elements_to_datasets(elements)
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203 return datasets
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204
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205 def _elements_to_datasets(self, elements, level=0):
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206 for element in elements:
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207 extra_kwds = {"identifier_%d" % level: element["name"]}
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208 if "elements" in element:
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209 for inner_element in self._elements_to_datasets(element["elements"], level=level + 1):
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210 dataset = extra_kwds.copy()
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211 dataset.update(inner_element)
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212 yield dataset
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213 else:
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214 dataset = extra_kwds
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215 extra_kwds.update(element)
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216 yield extra_kwds
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217
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218 def has_failed_outputs(self):
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219 found_failed = False
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220 for output_name, meta in self.tool_provided_job_metadata.items():
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221 if output_name == "__unnamed_outputs":
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222 continue
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223
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224 if meta.get("failed", False):
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225 log.info("One or more tool outputs is marked as failed (%s)." % meta)
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226 found_failed = True
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227
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228 return found_failed
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229
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230 def get_unnamed_outputs(self):
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231 log.debug("unnamed outputs [%s]" % self.tool_provided_job_metadata)
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232 return self.tool_provided_job_metadata.get("__unnamed_outputs", [])
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233
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234 def rewrite(self):
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235 with open(self.meta_file, 'wt') as job_metadata_fh:
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236 json.dump(self.tool_provided_job_metadata, job_metadata_fh)