Mercurial > repos > rnateam > data_manager_sortmerna_database_downloader

annotate data_manager/data_manager_sortmerna_download.py @ 1:30bb49887172 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sortmerna_database_downloader commit 044a991b45c9135339daf138929887cd8e93a1bf
author rnateam
date Tue, 06 Jun 2017 13:40:27 -0400
parents 765f4ec851f0
children 7d2252852f96
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765f4ec851f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sortmerna_database_downloader commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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1 #!/usr/bin/env python
765f4ec851f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sortmerna_database_downloader commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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2 # Data manager for reference data for the SortMeRNA Galaxy tools
765f4ec851f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sortmerna_database_downloader commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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4 import argparse
765f4ec851f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sortmerna_database_downloader commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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5 import json
765f4ec851f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sortmerna_database_downloader commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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6 import os
765f4ec851f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sortmerna_database_downloader commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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7 import tarfile
765f4ec851f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sortmerna_database_downloader commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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8 import requests
765f4ec851f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sortmerna_database_downloader commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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9 import subprocess
765f4ec851f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sortmerna_database_downloader commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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765f4ec851f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sortmerna_database_downloader commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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12 # Utility functions for interacting with Galaxy JSON
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13 def read_input_json(jsonfile):
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14 """Read the JSON supplied from the data manager tool
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16 Returns a tuple (param_dict,extra_files_path)
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18 'param_dict' is an arbitrary dictionary of parameters
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19 input into the tool; 'extra_files_path' is the path
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20 to a directory where output files must be put for the
765f4ec851f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sortmerna_database_downloader commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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21 receiving data manager to pick them up.
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23 NB the directory pointed to by 'extra_files_path'
765f4ec851f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sortmerna_database_downloader commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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24 doesn't exist initially, it is the job of the script
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25 to create it if necessary.
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27 """
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28 params = json.loads(open(jsonfile).read())
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29 return (params['param_dict'],
765f4ec851f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sortmerna_database_downloader commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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30 params['output_data'][0]['extra_files_path'])
765f4ec851f0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sortmerna_database_downloader commit 65d322f9ab2f24d65b307f3553589149a1d678d5
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33 # Utility functions for creating data table dictionaries
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34 #
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35 # Example usage:
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36 # >>> d = create_data_tables_dict()
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37 # >>> add_data_table(d,'my_data')
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38 # >>> add_data_table_entry(dict(dbkey='hg19',value='human'))
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39 # >>> add_data_table_entry(dict(dbkey='mm9',value='mouse'))
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40 # >>> print str(json.dumps(d))
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41 def create_data_tables_dict():
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42 """Return a dictionary for storing data table information
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43
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44 Returns a dictionary that can be used with 'add_data_table'
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45 and 'add_data_table_entry' to store information about a
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46 data table. It can be converted to JSON to be sent back to
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47 the data manager.
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48
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49 """
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50 d = {}
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51 d['data_tables'] = {}
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52 return d
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55 def add_data_table(d, table):
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56 """Add a data table to the data tables dictionary
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58 Creates a placeholder for a data table called 'table'.
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60 """
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61 d['data_tables'][table] = []
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64 def add_data_table_entry(d, table, entry):
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65 """Add an entry to a data table
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67 Appends an entry to the data table 'table'. 'entry'
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68 should be a dictionary where the keys are the names of
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69 columns in the data table.
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71 Raises an exception if the named data table doesn't
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72 exist.
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74 """
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75 try:
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76 d['data_tables'][table].append(entry)
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77 except KeyError:
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78 raise Exception("add_data_table_entry: no table '%s'" % table)
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81 def download_archive(version):
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82 """
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83
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84 """
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85 filepath = "%s.tar.gz" % (version)
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86 url = "https://github.com/biocore/sortmerna/archive/%s.tar.gz" % (version)
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87 r = requests.get(url, stream=True)
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88 r.raise_for_status()
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89 with open(filepath, "wb") as fd:
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90 for chunk in r.iter_content(chunk_size=128):
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91 fd.write(chunk)
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92 return filepath
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93
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94
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95 def find_archive_content_path(archive_content_path):
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96 """
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97 """
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98 content = os.listdir(archive_content_path)
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99 archive_content = []
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100 for x in content:
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101 if not x.startswith(".") and not x.startswith("_"):
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102 archive_content.append(x)
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103 if len(archive_content) == 1:
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104 archive_content_path = os.path.join(
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105 archive_content_path,
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106 archive_content[0])
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107 return archive_content_path
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108
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109
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110 def extract_archive(filepath):
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111 """
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112 """
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113 archive_content_path = "tmp"
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114 tar = tarfile.open(filepath)
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115 tar.extractall(path=archive_content_path)
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116 tar.close()
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117 archive_content_path = find_archive_content_path(archive_content_path)
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118 return archive_content_path
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119
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120
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121 def move_index_files(archive_content_path, target_dir, data_tables, version):
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122 """
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123 """
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124 file_dir = os.path.join(archive_content_path, "rRNA_databases")
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125 for filename in os.listdir(file_dir):
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126 if not filename.endswith("fasta"):
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127 continue
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128 input_filepath = os.path.join(file_dir, filename)
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129 output_filepath = os.path.join(target_dir, filename)
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130 # Move file
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131 os.rename(input_filepath, output_filepath)
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132 # Index the file with indexdb_rna
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133 command = "indexdb_rna --ref %s,%s" % (
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134 output_filepath,
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135 os.path.splitext(output_filepath)[0])
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136 process = subprocess.call(command, shell=True )
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137 # Add entry in the data table
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138 db_name = os.path.splitext(filename)[0]
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139 add_data_table_entry(
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140 data_tables,
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141 "rRNA_databases",
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142 dict(
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143 value=version,
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144 name=db_name,
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145 path=output_filepath))
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146
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147
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148 def download_db(data_tables, version, target_dir):
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149 """Download SortMeRNA database
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150
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151 Creates references to the specified file(s) on the Galaxy
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152 server in the appropriate data table (determined from the
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153 file extension).
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154
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155 The 'data_tables' dictionary should have been created using
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156 the 'create_data_tables_dict' and 'add_data_table' functions.
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157
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158 Arguments:
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159 data_tables: a dictionary containing the data table info
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160 version: version of the database
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161 table_name: name of the table
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162 target_dir: directory to put copy or link to the data file
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163 """
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164 print("Download archive")
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165 filepath = download_archive(version)
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166
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167 print("Extract archive %s" % filepath)
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168 archive_content_path = extract_archive(filepath)
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169
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170 print("Moving fasta file from %s and index them" % archive_content_path)
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171 move_index_files(
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172 archive_content_path,
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173 target_dir,
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174 data_tables,
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175 version)
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176
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177
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178 if __name__ == "__main__":
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179 print("Starting...")
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180
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181 # Read command line
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182 parser = argparse.ArgumentParser(
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183 description='Download QIIME reference database')
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184 parser.add_argument('--version', help="Database version")
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185 parser.add_argument('--jsonfile', help="Output JSON file")
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186 args = parser.parse_args()
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187
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188 jsonfile = args.jsonfile
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189
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190 # Read the input JSON
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191 params, target_dir = read_input_json(jsonfile)
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192
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193 # Make the target directory
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194 print("Making %s" % target_dir)
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195 os.mkdir(target_dir)
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196 os.mkdir(os.path.join(target_dir, "rRNA_databases"))
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197 target_dir = os.path.join(target_dir, "rRNA_databases")
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198
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199 # Set up data tables dictionary
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200 data_tables = create_data_tables_dict()
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201 add_data_table(data_tables, "rRNA_databases")
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202
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203 # Fetch data from specified data sources
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204 download_db(
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205 data_tables,
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206 args.version,
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207 target_dir)
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208
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209 # Write output JSON
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210 print("Outputting JSON")
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211 print(str(json.dumps(data_tables)))
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212 with open(jsonfile, 'w') as out:
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213 json.dump(data_tables, out)
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214 print("Done.")