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annotate planemo/lib/python3.7/site-packages/galaxy/tool_util/cwl/util.py @ 0:d30785e31577 draft

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"planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
author guerler
date Fri, 31 Jul 2020 00:18:57 -0400
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1 """Client-centric CWL-related utilities.
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2
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3 Used to share code between the Galaxy test framework
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4 and other Galaxy CWL clients (e.g. Planemo)."""
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5 import hashlib
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6 import json
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7 import os
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8 import tarfile
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9 import tempfile
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10 from collections import namedtuple
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11
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12 import yaml
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13 from six import (
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14 BytesIO,
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15 iteritems,
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16 python_2_unicode_compatible
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17 )
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18
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19 from galaxy.util import unicodify
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20
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21 STORE_SECONDARY_FILES_WITH_BASENAME = True
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22 SECONDARY_FILES_EXTRA_PREFIX = "__secondary_files__"
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23 SECONDARY_FILES_INDEX_PATH = "__secondary_files_index.json"
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24
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25
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26 def set_basename_and_derived_properties(properties, basename):
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27 properties["basename"] = basename
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28 properties["nameroot"], properties["nameext"] = os.path.splitext(basename)
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29 return properties
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30
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31
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32 def output_properties(path=None, content=None, basename=None, pseduo_location=False):
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33 checksum = hashlib.sha1()
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34 properties = {
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35 "class": "File",
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36 }
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37 if path is not None:
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38 properties["path"] = path
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39 f = open(path, "rb")
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40 else:
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41 f = BytesIO(content)
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42
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43 try:
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44 contents = f.read(1024 * 1024)
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45 filesize = 0
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46 while contents:
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47 checksum.update(contents)
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48 filesize += len(contents)
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49 contents = f.read(1024 * 1024)
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50 finally:
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51 f.close()
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52 properties["checksum"] = "sha1$%s" % checksum.hexdigest()
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53 properties["size"] = filesize
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54 set_basename_and_derived_properties(properties, basename)
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55 _handle_pseudo_location(properties, pseduo_location)
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56 return properties
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57
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58
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59 def _handle_pseudo_location(properties, pseduo_location):
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60 if pseduo_location:
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61 properties["location"] = properties["basename"]
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62
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63
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64 def abs_path_or_uri(path_or_uri, relative_to):
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65 """Return an absolute path if this isn't a URI, otherwise keep the URI the same.
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66 """
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67 is_uri = "://" in path_or_uri
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68 if not is_uri and not os.path.isabs(path_or_uri):
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69 path_or_uri = os.path.join(relative_to, path_or_uri)
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70 if not is_uri:
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71 _ensure_file_exists(path_or_uri)
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72 return path_or_uri
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73
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74
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75 def abs_path(path_or_uri, relative_to):
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76 path_or_uri = abs_path_or_uri(path_or_uri, relative_to)
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77 if path_or_uri.startswith("file://"):
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78 path_or_uri = path_or_uri[len("file://"):]
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79
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80 return path_or_uri
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81
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82
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83 def path_or_uri_to_uri(path_or_uri):
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84 if "://" not in path_or_uri:
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85 return "file://%s" % path_or_uri
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86 else:
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87 return path_or_uri
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88
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89
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90 def galactic_job_json(
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91 job, test_data_directory, upload_func, collection_create_func, tool_or_workflow="workflow"
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92 ):
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93 """Adapt a CWL job object to the Galaxy API.
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94
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95 CWL derived tools in Galaxy can consume a job description sort of like
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96 CWL job objects via the API but paths need to be replaced with datasets
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97 and records and arrays with collection references. This function will
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98 stage files and modify the job description to adapt to these changes
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99 for Galaxy.
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100 """
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101
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102 datasets = []
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103 dataset_collections = []
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104
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105 def response_to_hda(target, upload_response):
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106 assert isinstance(upload_response, dict), upload_response
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107 assert "outputs" in upload_response, upload_response
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108 assert len(upload_response["outputs"]) > 0, upload_response
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109 dataset = upload_response["outputs"][0]
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110 datasets.append((dataset, target))
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111 dataset_id = dataset["id"]
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112 return {"src": "hda", "id": dataset_id}
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113
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114 def upload_file(file_path, secondary_files, **kwargs):
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115 file_path = abs_path_or_uri(file_path, test_data_directory)
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116 target = FileUploadTarget(file_path, secondary_files, **kwargs)
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117 upload_response = upload_func(target)
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118 return response_to_hda(target, upload_response)
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119
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120 def upload_file_literal(contents, **kwd):
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121 target = FileLiteralTarget(contents, **kwd)
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122 upload_response = upload_func(target)
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123 return response_to_hda(target, upload_response)
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124
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125 def upload_tar(file_path):
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126 file_path = abs_path_or_uri(file_path, test_data_directory)
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127 target = DirectoryUploadTarget(file_path)
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128 upload_response = upload_func(target)
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129 return response_to_hda(target, upload_response)
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130
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131 def upload_file_with_composite_data(file_path, composite_data, **kwargs):
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132 if file_path is not None:
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133 file_path = abs_path_or_uri(file_path, test_data_directory)
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134 composite_data_resolved = []
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135 for cd in composite_data:
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136 composite_data_resolved.append(abs_path_or_uri(cd, test_data_directory))
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137 target = FileUploadTarget(file_path, composite_data=composite_data_resolved, **kwargs)
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138 upload_response = upload_func(target)
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139 return response_to_hda(target, upload_response)
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140
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141 def upload_object(the_object):
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142 target = ObjectUploadTarget(the_object)
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143 upload_response = upload_func(target)
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144 return response_to_hda(target, upload_response)
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145
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146 def replacement_item(value, force_to_file=False):
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147 is_dict = isinstance(value, dict)
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148 item_class = None if not is_dict else value.get("class", None)
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149 is_file = item_class == "File"
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150 is_directory = item_class == "Directory"
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151 is_collection = item_class == "Collection" # Galaxy extension.
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152
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153 if force_to_file:
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154 if is_file:
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155 return replacement_file(value)
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156 else:
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157 return upload_object(value)
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158
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159 if isinstance(value, list):
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160 return replacement_list(value)
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161 elif not isinstance(value, dict):
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162 if tool_or_workflow == "workflow":
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163 # All inputs represented as dataset or collection parameters
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164 return upload_object(value)
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165 else:
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166 return value
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167
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168 if is_file:
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169 return replacement_file(value)
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170 elif is_directory:
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171 return replacement_directory(value)
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172 elif is_collection:
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173 return replacement_collection(value)
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174 else:
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175 return replacement_record(value)
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176
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177 def replacement_file(value):
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178 file_path = value.get("location", None) or value.get("path", None)
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179 # format to match output definitions in tool, where did filetype come from?
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180 filetype = value.get("filetype", None) or value.get("format", None)
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181 composite_data_raw = value.get("composite_data", None)
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182 kwd = {}
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183 if "tags" in value:
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184 kwd["tags"] = value.get("tags")
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185 if composite_data_raw:
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186 composite_data = []
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187 for entry in composite_data_raw:
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188 path = None
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189 if isinstance(entry, dict):
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190 path = entry.get("location", None) or entry.get("path", None)
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191 else:
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192 path = entry
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193 composite_data.append(path)
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194 rval_c = upload_file_with_composite_data(None, composite_data, filetype=filetype, **kwd)
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195 return rval_c
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196
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197 if file_path is None:
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198 contents = value.get("contents", None)
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199 if contents is not None:
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200 return upload_file_literal(contents, **kwd)
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201
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202 return value
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203
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204 secondary_files = value.get("secondaryFiles", [])
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205 secondary_files_tar_path = None
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206 if secondary_files:
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207 tmp = tempfile.NamedTemporaryFile(delete=False)
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208 tf = tarfile.open(fileobj=tmp, mode='w:')
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209 order = []
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210 index_contents = {
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211 "order": order
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212 }
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213 for secondary_file in secondary_files:
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214 secondary_file_path = secondary_file.get("location", None) or secondary_file.get("path", None)
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215 assert secondary_file_path, "Invalid secondaryFile entry found [%s]" % secondary_file
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216 full_secondary_file_path = os.path.join(test_data_directory, secondary_file_path)
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217 basename = secondary_file.get("basename") or os.path.basename(secondary_file_path)
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218 order.append(unicodify(basename))
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219 tf.add(full_secondary_file_path, os.path.join(SECONDARY_FILES_EXTRA_PREFIX, basename))
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220 tmp_index = tempfile.NamedTemporaryFile(delete=False, mode="w")
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221 json.dump(index_contents, tmp_index)
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222 tmp_index.close()
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223 tf.add(tmp_index.name, SECONDARY_FILES_INDEX_PATH)
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224 tf.close()
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225 secondary_files_tar_path = tmp.name
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226
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227 return upload_file(file_path, secondary_files_tar_path, filetype=filetype, **kwd)
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228
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229 def replacement_directory(value):
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230 file_path = value.get("location", None) or value.get("path", None)
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231 if file_path is None:
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232 return value
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233
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234 if not os.path.isabs(file_path):
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235 file_path = os.path.join(test_data_directory, file_path)
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236
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237 tmp = tempfile.NamedTemporaryFile(delete=False)
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238 tf = tarfile.open(fileobj=tmp, mode='w:')
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239 tf.add(file_path, '.')
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240 tf.close()
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241
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242 return upload_tar(tmp.name)
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243
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244 def replacement_list(value):
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245 collection_element_identifiers = []
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246 for i, item in enumerate(value):
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247 dataset = replacement_item(item, force_to_file=True)
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248 collection_element = dataset.copy()
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249 collection_element["name"] = str(i)
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250 collection_element_identifiers.append(collection_element)
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251
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252 # TODO: handle nested lists/arrays
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253 collection = collection_create_func(collection_element_identifiers, "list")
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254 dataset_collections.append(collection)
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255 hdca_id = collection["id"]
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256 return {"src": "hdca", "id": hdca_id}
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257
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258 def to_elements(value, rank_collection_type):
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259 collection_element_identifiers = []
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260 assert "elements" in value
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261 elements = value["elements"]
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262
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263 is_nested_collection = ":" in rank_collection_type
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264 for element in elements:
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265 if not is_nested_collection:
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266 # flat collection
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267 dataset = replacement_item(element, force_to_file=True)
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268 collection_element = dataset.copy()
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269 collection_element["name"] = element["identifier"]
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270 collection_element_identifiers.append(collection_element)
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271 else:
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272 # nested collection
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273 sub_collection_type = rank_collection_type[rank_collection_type.find(":") + 1:]
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274 collection_element = {
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275 "name": element["identifier"],
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276 "src": "new_collection",
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277 "collection_type": sub_collection_type,
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278 "element_identifiers": to_elements(element, sub_collection_type)
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279 }
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280 collection_element_identifiers.append(collection_element)
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281
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282 return collection_element_identifiers
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283
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284 def replacement_collection(value):
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285 assert "collection_type" in value
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286 collection_type = value["collection_type"]
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287 elements = to_elements(value, collection_type)
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288
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289 collection = collection_create_func(elements, collection_type)
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290 dataset_collections.append(collection)
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291 hdca_id = collection["id"]
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292 return {"src": "hdca", "id": hdca_id}
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293
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294 def replacement_record(value):
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295 collection_element_identifiers = []
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296 for record_key, record_value in value.items():
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297 if not isinstance(record_value, dict) or record_value.get("class") != "File":
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298 dataset = replacement_item(record_value, force_to_file=True)
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299 collection_element = dataset.copy()
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300 else:
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301 dataset = upload_file(record_value["location"], [])
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302 collection_element = dataset.copy()
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303
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304 collection_element["name"] = record_key
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305 collection_element_identifiers.append(collection_element)
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306
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307 collection = collection_create_func(collection_element_identifiers, "record")
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308 dataset_collections.append(collection)
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309 hdca_id = collection["id"]
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310 return {"src": "hdca", "id": hdca_id}
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311
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312 replace_keys = {}
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313 for key, value in iteritems(job):
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314 replace_keys[key] = replacement_item(value)
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315
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316 job.update(replace_keys)
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317 return job, datasets
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318
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319
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320 def _ensure_file_exists(file_path):
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321 if not os.path.exists(file_path):
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322 template = "File [%s] does not exist - parent directory [%s] does %sexist, cwd is [%s]"
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323 parent_directory = os.path.dirname(file_path)
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324 message = template % (
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325 file_path,
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326 parent_directory,
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327 "" if os.path.exists(parent_directory) else "not ",
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328 os.getcwd(),
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329 )
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330 raise Exception(message)
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331
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332
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333 @python_2_unicode_compatible
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334 class FileLiteralTarget(object):
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335
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336 def __init__(self, contents, **kwargs):
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337 self.contents = contents
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338 self.properties = kwargs
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339
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340 def __str__(self):
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341 return "FileLiteralTarget[path=%s] with %s" % (self.path, self.properties)
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342
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343
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344 @python_2_unicode_compatible
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345 class FileUploadTarget(object):
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346
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347 def __init__(self, path, secondary_files=None, **kwargs):
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348 self.path = path
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349 self.secondary_files = secondary_files
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350 self.composite_data = kwargs.get("composite_data", [])
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351 self.properties = kwargs
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352
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353 def __str__(self):
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354 return "FileUploadTarget[path=%s] with %s" % (self.path, self.properties)
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355
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356
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357 @python_2_unicode_compatible
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358 class ObjectUploadTarget(object):
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359
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360 def __init__(self, the_object):
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361 self.object = the_object
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362
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363 def __str__(self):
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364 return "ObjectUploadTarget[object=%s]" % self.object
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365
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366
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367 @python_2_unicode_compatible
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368 class DirectoryUploadTarget(object):
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369
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370 def __init__(self, tar_path):
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371 self.tar_path = tar_path
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372
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373 def __str__(self):
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374 return "DirectoryUploadTarget[tar_path=%s]" % self.tar_path
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375
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376
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377 GalaxyOutput = namedtuple("GalaxyOutput", ["history_id", "history_content_type", "history_content_id", "metadata"])
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378
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379
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380 def tool_response_to_output(tool_response, history_id, output_id):
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381 for output in tool_response["outputs"]:
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382 if output["output_name"] == output_id:
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383 return GalaxyOutput(history_id, "dataset", output["id"], None)
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384
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385 for output_collection in tool_response["output_collections"]:
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386 if output_collection["output_name"] == output_id:
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387 return GalaxyOutput(history_id, "dataset_collection", output_collection["id"], None)
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388
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389 raise Exception("Failed to find output with label [%s]" % output_id)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
390
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
391
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
392 def invocation_to_output(invocation, history_id, output_id):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
393 if output_id in invocation["outputs"]:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
394 dataset = invocation["outputs"][output_id]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
395 galaxy_output = GalaxyOutput(history_id, "dataset", dataset["id"], None)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
396 elif output_id in invocation["output_collections"]:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
397 collection = invocation["output_collections"][output_id]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
398 galaxy_output = GalaxyOutput(history_id, "dataset_collection", collection["id"], None)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
399 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
400 raise Exception("Failed to find output with label [%s] in [%s]" % (output_id, invocation))
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
401
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
402 return galaxy_output
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
403
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
404
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
405 def output_to_cwl_json(
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
406 galaxy_output, get_metadata, get_dataset, get_extra_files, pseduo_location=False,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
407 ):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
408 """Convert objects in a Galaxy history into a CWL object.
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
409
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
410 Useful in running conformance tests and implementing the cwl-runner
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
411 interface via Galaxy.
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
412 """
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
413 def element_to_cwl_json(element):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
414 object = element["object"]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
415 content_type = object.get("history_content_type")
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
416 metadata = None
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
417 if content_type is None:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
418 content_type = "dataset_collection"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
419 metadata = element["object"]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
420 metadata["history_content_type"] = content_type
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
421 element_output = GalaxyOutput(
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
422 galaxy_output.history_id,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
423 content_type,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
424 object["id"],
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
425 metadata,
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
426 )
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
427 return output_to_cwl_json(element_output, get_metadata, get_dataset, get_extra_files, pseduo_location=pseduo_location)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
428
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
429 output_metadata = galaxy_output.metadata
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
430 if output_metadata is None:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
431 output_metadata = get_metadata(galaxy_output.history_content_type, galaxy_output.history_content_id)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
432
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
433 def dataset_dict_to_json_content(dataset_dict):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
434 if "content" in dataset_dict:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
435 return json.loads(dataset_dict["content"])
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
436 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
437 with open(dataset_dict["path"]) as f:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
438 return json.safe_load(f)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
439
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
440 if output_metadata["history_content_type"] == "dataset":
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
441 ext = output_metadata["file_ext"]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
442 assert output_metadata["state"] == "ok"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
443 if ext == "expression.json":
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
444 dataset_dict = get_dataset(output_metadata)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
445 return dataset_dict_to_json_content(dataset_dict)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
446 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
447 file_or_directory = "Directory" if ext == "directory" else "File"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
448 secondary_files = []
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
449
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
450 if file_or_directory == "File":
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
451 dataset_dict = get_dataset(output_metadata)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
452 properties = output_properties(pseduo_location=pseduo_location, **dataset_dict)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
453 basename = properties["basename"]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
454 extra_files = get_extra_files(output_metadata)
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parents:
diff changeset
455 found_index = False
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
456 for extra_file in extra_files:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
457 if extra_file["class"] == "File":
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
458 path = extra_file["path"]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
459 if path == SECONDARY_FILES_INDEX_PATH:
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parents:
diff changeset
460 found_index = True
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
461
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
462 if found_index:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
463 ec = get_dataset(output_metadata, filename=SECONDARY_FILES_INDEX_PATH)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
464 index = dataset_dict_to_json_content(ec)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
465
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
466 def dir_listing(dir_path):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
467 listing = []
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
468 for extra_file in extra_files:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
469 path = extra_file["path"]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
470 extra_file_class = extra_file["class"]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
diff changeset
471 extra_file_basename = os.path.basename(path)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
472 if os.path.join(dir_path, extra_file_basename) != path:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
473 continue
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
474
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
475 if extra_file_class == "File":
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
476 ec = get_dataset(output_metadata, filename=path)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
477 ec["basename"] = extra_file_basename
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
478 ec_properties = output_properties(pseduo_location=pseduo_location, **ec)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
479 elif extra_file_class == "Directory":
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
480 ec_properties = {}
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
481 ec_properties["class"] = "Directory"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
482 ec_properties["location"] = ec_basename
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
483 ec_properties["listing"] = dir_listing(path)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
484 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
485 raise Exception("Unknown output type encountered....")
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
486 listing.append(ec_properties)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
487 return listing
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
488
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
489 for basename in index["order"]:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
490 for extra_file in extra_files:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
491 path = extra_file["path"]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
492 if path != os.path.join(SECONDARY_FILES_EXTRA_PREFIX, basename):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
493 continue
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
494
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
495 extra_file_class = extra_file["class"]
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
496
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
497 # This is wrong...
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
498 if not STORE_SECONDARY_FILES_WITH_BASENAME:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
499 ec_basename = basename + os.path.basename(path)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
500 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
501 ec_basename = os.path.basename(path)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
502
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
503 if extra_file_class == "File":
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
504 ec = get_dataset(output_metadata, filename=path)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
505 ec["basename"] = ec_basename
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
506 ec_properties = output_properties(pseduo_location=pseduo_location, **ec)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
507 elif extra_file_class == "Directory":
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
508 ec_properties = {}
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
509 ec_properties["class"] = "Directory"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
510 ec_properties["location"] = ec_basename
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
511 ec_properties["listing"] = dir_listing(path)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
512 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
513 raise Exception("Unknown output type encountered....")
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
514 secondary_files.append(ec_properties)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
515
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
516 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
517 basename = output_metadata.get("created_from_basename")
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
518 if not basename:
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parents:
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519 basename = output_metadata.get("name")
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520
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521 listing = []
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522 properties = {
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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parents:
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523 "class": "Directory",
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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diff changeset
524 "basename": basename,
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525 "listing": listing,
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parents:
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526 }
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527
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528 extra_files = get_extra_files(output_metadata)
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guerler
parents:
diff changeset
529 for extra_file in extra_files:
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guerler
parents:
diff changeset
530 if extra_file["class"] == "File":
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parents:
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531 path = extra_file["path"]
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parents:
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532 ec = get_dataset(output_metadata, filename=path)
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guerler
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533 ec["basename"] = os.path.basename(path)
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guerler
parents:
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534 ec_properties = output_properties(pseduo_location=pseduo_location, **ec)
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guerler
parents:
diff changeset
535 listing.append(ec_properties)
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536
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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537 if secondary_files:
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guerler
parents:
diff changeset
538 properties["secondaryFiles"] = secondary_files
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
539 return properties
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guerler
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540
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parents:
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541 elif output_metadata["history_content_type"] == "dataset_collection":
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guerler
parents:
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542 rval = None
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guerler
parents:
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543 collection_type = output_metadata["collection_type"].split(":", 1)[0]
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guerler
parents:
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544 if collection_type in ["list", "paired"]:
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guerler
parents:
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545 rval = []
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
546 for element in output_metadata["elements"]:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
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547 rval.append(element_to_cwl_json(element))
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
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548 elif collection_type == "record":
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guerler
parents:
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549 rval = {}
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
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550 for element in output_metadata["elements"]:
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guerler
parents:
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551 rval[element["element_identifier"]] = element_to_cwl_json(element)
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guerler
parents:
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552 return rval
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
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553 else:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
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554 raise NotImplementedError("Unknown history content type encountered")
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guerler
parents:
diff changeset
555
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guerler
parents:
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556
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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557 def download_output(galaxy_output, get_metadata, get_dataset, get_extra_files, output_path):
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558 output_metadata = get_metadata(galaxy_output.history_content_type, galaxy_output.history_content_id)
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guerler
parents:
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559 dataset_dict = get_dataset(output_metadata)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
diff changeset
560 with open(output_path, 'wb') as fh:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
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561 fh.write(dataset_dict['content'])
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guerler
parents:
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562
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
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563
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
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564 def guess_artifact_type(path):
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
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565 # TODO: Handle IDs within files.
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guerler
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566 tool_or_workflow = "workflow"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
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567 try:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
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568 with open(path, "r") as f:
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guerler
parents:
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569 artifact = yaml.safe_load(f)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
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570
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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571 tool_or_workflow = "tool" if artifact["class"] != "Workflow" else "workflow"
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
parents:
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572
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
guerler
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573 except Exception as e:
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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574 print(e)
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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575
d30785e31577 "planemo upload commit 6eee67778febed82ddd413c3ca40b3183a3898f1"
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576 return tool_or_workflow