Mercurial > repos > rnateam > data_manager_sortmerna_database_downloader

annotate data_manager/data_manager_sortmerna_download.py @ 2:7d2252852f96 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sortmerna_database_downloader commit 4241c1d4b05a177bd2c74f5a139f51d4f65e0b55
author rnateam
date Tue, 13 Jun 2017 12:03:08 -0400
parents 30bb49887172
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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
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7d2252852f96 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_sortmerna_database_downloader commit 4241c1d4b05a177bd2c74f5a139f51d4f65e0b55
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7 import shutil
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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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8 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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9 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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10 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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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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13 # Utility functions for interacting with Galaxy JSON
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14 def read_input_json(jsonfile):
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15 """Read the JSON supplied from the data manager tool
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17 Returns a tuple (param_dict,extra_files_path)
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19 'param_dict' is an arbitrary dictionary of parameters
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20 input into the tool; 'extra_files_path' is the 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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21 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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22 receiving data manager to pick them up.
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 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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25 doesn't exist initially, it is the job of the script
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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26 to create it if necessary.
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28 """
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29 params = json.loads(open(jsonfile).read())
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 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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31 params['output_data'][0]['extra_files_path'])
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34 # Utility functions for creating data table dictionaries
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35 #
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36 # Example usage:
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37 # >>> d = create_data_tables_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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38 # >>> add_data_table(d,'my_data')
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39 # >>> add_data_table_entry(dict(dbkey='hg19',value='human'))
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40 # >>> add_data_table_entry(dict(dbkey='mm9',value='mouse'))
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41 # >>> print str(json.dumps(d))
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42 def create_data_tables_dict():
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43 """Return a dictionary for storing data table information
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44
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45 Returns a dictionary that can be used with 'add_data_table'
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46 and 'add_data_table_entry' to store information about a
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47 data table. It can be converted to JSON to be sent back to
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48 the data manager.
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49
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50 """
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51 d = {}
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52 d['data_tables'] = {}
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53 return d
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56 def add_data_table(d, table):
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57 """Add a data table to the data tables dictionary
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58
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59 Creates a placeholder for a data table called 'table'.
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61 """
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62 d['data_tables'][table] = []
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65 def add_data_table_entry(d, table, entry):
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66 """Add an entry to a data table
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67
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68 Appends an entry to the data table 'table'. 'entry'
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69 should be a dictionary where the keys are the names of
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70 columns in the data table.
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71
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72 Raises an exception if the named data table doesn't
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73 exist.
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74
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75 """
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76 try:
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77 d['data_tables'][table].append(entry)
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78 except KeyError:
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79 raise Exception("add_data_table_entry: no table '%s'" % table)
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80
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81
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82 def download_archive(version):
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83 """
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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84
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85 """
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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86 filepath = "%s.tar.gz" % (version)
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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87 url = "https://github.com/biocore/sortmerna/archive/%s.tar.gz" % (version)
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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88 r = requests.get(url, stream=True)
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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89 r.raise_for_status()
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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90 with open(filepath, "wb") as fd:
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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91 for chunk in r.iter_content(chunk_size=128):
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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92 fd.write(chunk)
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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93 return filepath
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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94
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95
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96 def find_archive_content_path(archive_content_path):
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97 """
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98 """
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99 content = os.listdir(archive_content_path)
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100 archive_content = []
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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101 for x in content:
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102 if not x.startswith(".") and not x.startswith("_"):
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103 archive_content.append(x)
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104 if len(archive_content) == 1:
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105 archive_content_path = os.path.join(
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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106 archive_content_path,
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107 archive_content[0])
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108 return archive_content_path
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109
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110
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111 def extract_archive(filepath):
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112 """
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113 """
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114 archive_content_path = "tmp"
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115 tar = tarfile.open(filepath)
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116 tar.extractall(path=archive_content_path)
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117 tar.close()
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118 archive_content_path = find_archive_content_path(archive_content_path)
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119 return archive_content_path
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120
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121
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122 def move_index_files(archive_content_path, target_dir, data_tables, version):
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123 """
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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124 """
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125 file_dir = os.path.join(archive_content_path, "rRNA_databases")
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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126 for filename in os.listdir(file_dir):
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127 if not filename.endswith("fasta"):
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128 continue
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129 input_filepath = os.path.join(file_dir, filename)
2
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130 # Extract the db name
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131 db_name = os.path.splitext(filename)[0]
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132 # Create the directory where to put the fasta files and indexed files
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133 filedir = os.path.join(target_dir, db_name)
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134 os.mkdir(filedir)
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135 fasta_filepath = os.path.join(filedir, "%s.fasta" % db_name)
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136 indexed_filepath = os.path.join(filedir, db_name)
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137 # Move the fasta file
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138 shutil.move(input_filepath, fasta_filepath)
0
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139 # Index the file with indexdb_rna
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140 command = "indexdb_rna --ref %s,%s" % (
2
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141 fasta_filepath,
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142 indexed_filepath)
0
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143 process = subprocess.call(command, shell=True )
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144 # Add entry in the data table
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145 add_data_table_entry(
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146 data_tables,
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147 "rRNA_databases",
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148 dict(
2
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149 value="%s-%s" %(version, db_name),
0
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150 name=db_name,
2
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151 path=filedir))
0
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152
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153
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154 def download_db(data_tables, version, target_dir):
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155 """Download SortMeRNA database
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156
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157 Creates references to the specified file(s) on the Galaxy
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158 server in the appropriate data table (determined from the
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159 file extension).
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160
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161 The 'data_tables' dictionary should have been created using
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162 the 'create_data_tables_dict' and 'add_data_table' functions.
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163
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164 Arguments:
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165 data_tables: a dictionary containing the data table info
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166 version: version of the database
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167 table_name: name of the table
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168 target_dir: directory to put copy or link to the data file
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169 """
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170 print("Download archive")
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171 filepath = download_archive(version)
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172
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173 print("Extract archive %s" % filepath)
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174 archive_content_path = extract_archive(filepath)
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175
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176 print("Moving fasta file from %s and index them" % archive_content_path)
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177 move_index_files(
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178 archive_content_path,
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179 target_dir,
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180 data_tables,
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181 version)
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182
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183
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184 if __name__ == "__main__":
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185 print("Starting...")
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186
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187 # Read command line
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188 parser = argparse.ArgumentParser(
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189 description='Download QIIME reference database')
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190 parser.add_argument('--version', help="Database version")
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191 parser.add_argument('--jsonfile', help="Output JSON file")
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192 args = parser.parse_args()
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193
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194 jsonfile = args.jsonfile
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195
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196 # Read the input JSON
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197 params, target_dir = read_input_json(jsonfile)
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198
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199 # Make the target directory
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200 print("Making %s" % target_dir)
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201 os.mkdir(target_dir)
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202 os.mkdir(os.path.join(target_dir, "rRNA_databases"))
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203 target_dir = os.path.join(target_dir, "rRNA_databases")
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204
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205 # Set up data tables dictionary
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206 data_tables = create_data_tables_dict()
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207 add_data_table(data_tables, "rRNA_databases")
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208
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209 # Fetch data from specified data sources
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210 download_db(
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211 data_tables,
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212 args.version,
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213 target_dir)
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214
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215 # Write output JSON
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216 print("Outputting JSON")
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217 print(str(json.dumps(data_tables)))
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218 with open(jsonfile, 'w') as out:
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219 json.dump(data_tables, out)
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220 print("Done.")