Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/ephemeris/setup_data_libraries.py @ 4:79f47841a781 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:47:39 -0400
parents 26e78fe6e8c4
children
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0
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1 #!/usr/bin/env python
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2 '''Tool to setup data libraries on a galaxy instance'''
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3 import argparse
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4 import logging as log
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5 import sys
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6 import time
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7
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8 import yaml
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9 from bioblend import galaxy
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10
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11 from .common_parser import get_common_args
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12
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13
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14 def create_legacy(gi, desc):
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15 destination = desc["destination"]
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16 if destination["type"] != "library":
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17 raise Exception("Only libraries may be created with pre-18.05 Galaxies using this script.")
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18 library_name = destination.get("name")
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19 library_description = destination.get("description")
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20 library_synopsis = destination.get("synopsis")
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21
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22 # Check to see if the library already exists. If it does, do not recreate it. If it doesn't, create it.
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23 lib_id = None
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24 print("Library name: " + str(library_name))
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25 rmt_lib_list = gi.libraries.get_libraries(name=library_name, deleted=False)
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26 # Now we need to check if the library has been deleted since deleted=False still returns the deleted libraries!
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27 not_deleted_rmt_lib_list = []
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28 folder_id = None
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29
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30 if rmt_lib_list:
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31 for x in rmt_lib_list:
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32 if not x['deleted']:
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33 not_deleted_rmt_lib_list.append(x)
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34 if not_deleted_rmt_lib_list:
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35 lib_id = not_deleted_rmt_lib_list[0]['id']
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36 print("Library already exists! id: " + str(lib_id))
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37 folder_id = gi.libraries.show_library(lib_id)['root_folder_id']
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38 else:
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39 lib = gi.libraries.create_library(library_name, library_description, library_synopsis)
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40 lib_id = lib['id']
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41 folder_id = lib['root_folder_id']
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42
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43 def populate_items(base_folder_id, has_items):
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44 if "items" in has_items:
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45 name = has_items.get("name")
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46 description = has_items.get("description")
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47 folder_id = base_folder_id
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48 if name:
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49 # Check to see if the folder already exists, if it doesn't create it.
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50 rmt_folder_list = []
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51 folder = gi.libraries.get_folders(lib_id, folder_id)
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52 new_folder_name = "/" + name
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53 if folder and not folder[0]['name'] == "/":
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54 new_folder_name = folder[0]['name'] + "/" + name
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55 rmt_folder_list = gi.libraries.get_folders(lib_id, name=new_folder_name)
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56 if rmt_folder_list:
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57 folder_id = rmt_folder_list[0]['id']
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58 else:
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59 folder = gi.libraries.create_folder(lib_id, name, description, base_folder_id=base_folder_id)
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60 folder_id = folder[0]["id"]
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61 for item in has_items["items"]:
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62 populate_items(folder_id, item)
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63 else:
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64 src = has_items["src"]
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65 if src != "url":
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66 raise Exception("For pre-18.05 Galaxies only support URLs src items are supported.")
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67 rmt_library_files = gi.folders.show_folder(base_folder_id, contents=True)['folder_contents']
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68 file_names = []
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69 for item in rmt_library_files:
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70 if item['type'] == 'file':
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71 file_names.append(item['name'])
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72 if has_items['url'] not in file_names:
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73 try:
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74 gi.libraries.upload_file_from_url(
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75 lib_id,
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76 has_items['url'],
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77 folder_id=base_folder_id,
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78 file_type=has_items['ext']
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79 )
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80 except Exception:
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81 log.exception("Could not upload %s to %s/%s", has_items['url'], lib_id, base_folder_id)
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82 return None
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83
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84 populate_items(folder_id, desc)
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85 return []
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86
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87
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88 def create_batch_api(gi, desc):
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89 hc = galaxy.histories.HistoryClient(gi)
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90 tc = galaxy.tools.ToolClient(gi)
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91
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92 history = hc.create_history()
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93 url = "%s/tools/fetch" % gi.url
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94 payload = {
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95 'targets': [desc],
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96 'history_id': history["id"]
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97 }
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98 yield tc._post(payload=payload, url=url)
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99
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100
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101 def setup_data_libraries(gi, data, training=False, legacy=False):
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102 """
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103 Load files into a Galaxy data library.
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104 By default all test-data tools from all installed tools
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105 will be linked into a data library.
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106 """
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107
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108 log.info("Importing data libraries.")
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109 jc = galaxy.jobs.JobsClient(gi)
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110 config = galaxy.config.ConfigClient(gi)
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111 version = config.get_version()
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112
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113 if legacy:
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114 create_func = create_legacy
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115 else:
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116 version_major = version.get("version_major", "16.01")
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117 create_func = create_batch_api if version_major >= "18.05" else create_legacy
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118
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119 library_def = yaml.safe_load(data)
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120
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121 def normalize_items(has_items):
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122 # Synchronize Galaxy batch format with older training material style.
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123 if "files" in has_items:
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124 items = has_items.pop("files")
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125 has_items["items"] = items
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126
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127 items = has_items.get("items", [])
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128 for item in items:
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129 normalize_items(item)
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130 src = item.get("src")
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131 url = item.get("url")
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132 if src is None and url:
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133 item["src"] = "url"
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134 if "file_type" in item:
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135 ext = item.pop("file_type")
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136 item["ext"] = ext
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137
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138 # Normalize library definitions to allow older ephemeris style and native Galaxy batch
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139 # upload formats.
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140 if "libraries" in library_def:
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141 # File contains multiple definitions.
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142 library_def["items"] = library_def.pop("libraries")
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143
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144 if "destination" not in library_def:
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145 library_def["destination"] = {"type": "library"}
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146 destination = library_def["destination"]
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147
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148 if training:
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149 destination["name"] = destination.get("name", 'Training Data')
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150 destination["description"] = destination.get("description", 'Data pulled from online archives.')
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151 else:
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152 destination["name"] = destination.get("name", 'New Data Library')
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153 destination["description"] = destination.get("description", '')
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154
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155 normalize_items(library_def)
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156
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157 if library_def:
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158 jobs = list(create_func(gi, library_def))
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159
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160 job_ids = []
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161 if legacy:
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162 for job in jc.get_jobs():
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163 # Fetch all upload job IDs, ignoring complete ones.
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164 if job['tool_id'] == 'upload1' and job['state'] not in ('ok', 'error'):
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165 job_ids.append(job['id'])
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166
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167 # Just have to check that all upload1 jobs are termianl.
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168 else:
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169 # Otherwise get back an actual list of jobs
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170 for job in jobs:
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171 if 'jobs' in job:
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172 for subjob in job['jobs']:
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173 job_ids.append(subjob['id'])
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174
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175 while True:
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176 job_states = [jc.get_state(job) in ('ok', 'error', 'deleted') for job in job_ids]
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177 log.debug('Job states: %s' % ','.join([
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178 '%s=%s' % (job_id, job_state) for (job_id, job_state) in zip(job_ids, job_states)]))
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179
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180 if all(job_states):
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181 break
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182 time.sleep(3)
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183
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184 log.info("Finished importing test data.")
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185
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186
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187 def _parser():
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188 '''Constructs the parser object'''
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189 parent = get_common_args()
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190 parser = argparse.ArgumentParser(
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191 parents=[parent],
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192 description='Populate the Galaxy data library with data.'
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193 )
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194 parser.add_argument('-i', '--infile', required=True, type=argparse.FileType('r'))
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195 parser.add_argument('--training', default=False, action="store_true",
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196 help="Set defaults that make sense for training data.")
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197 parser.add_argument('--legacy', default=False, action="store_true",
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198 help="Use legacy APIs even for newer Galaxies that should have a batch upload API enabled.")
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199 return parser
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200
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201
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202 def main():
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203 args = _parser().parse_args()
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204 if args.user and args.password:
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205 gi = galaxy.GalaxyInstance(url=args.galaxy, email=args.user, password=args.password)
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206 elif args.api_key:
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207 gi = galaxy.GalaxyInstance(url=args.galaxy, key=args.api_key)
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208 else:
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209 sys.exit('Please specify either a valid Galaxy username/password or an API key.')
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210
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211 if args.verbose:
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212 log.basicConfig(level=log.DEBUG)
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213
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214 setup_data_libraries(gi, args.infile, training=args.training, legacy=args.legacy)
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215
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216
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217 if __name__ == '__main__':
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218 main()