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1 #!/usr/bin/env python
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2 # ref: https://galaxyproject.org/admin/tools/data-managers/how-to/define/
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3
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4 # Rewritten by H.E. Cicada Brokaw Dennis from a source downloaded from the toolshed and
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5 # other example code on the web.
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6 # This file downloads annotations for lncrna (slncky tool)
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7
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8 import argparse
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9 import os
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10 import subprocess
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11
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12 # The following is used to generate a unique_id value
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13 from datetime import *
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14
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15 # Remove the following line when testing without galaxy package:
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16 # from galaxy.util.json import to_json_string
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17 # Am not using the following:
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18 # from galaxy.util.json import from_json_string
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19
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20 # The FileListParser is used by get_ctat_genome_filenames(),
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21 # which is called by the Data Manager interface (.xml file) to get
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22 # the filenames that are available online at broadinstitute.org
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23 # Not sure best way to do it.
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24 # This object uses HTMLParser to look through the html
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25 # searching for the filenames within anchor tags.
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26 import urllib2
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27 from HTMLParser import HTMLParser
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28
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29 _CTAT_lncrnaIndexPage_URL = 'https://data.broadinstitute.org/Trinity/CTAT/lncrna'
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30 _CTAT_lncrnaDownload_URL = 'https://data.broadinstitute.org/Trinity/CTAT/lncrna/annotations.tar.gz'
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31 _CTAT_lncrnaTableName = 'ctat_lncrna_annotations'
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32 _CTAT_lncrnaDir_Name = 'annotations'
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33 _CTAT_lncrna_DisplayNamePrefix = 'CTAT_lncrna_annotations_'
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34 _lncrnaFileExtension = 'lc'
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35 _NumBytesNeededForAnnotations = 2147483648 # Number of bytes
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36 #_DownloadFileSize = 5790678746 # 5.4 Gigabytes.
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37 _Download_TestFile = 'write_testfile.txt'
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38 _DownloadSuccessFile = 'download_succeeded.txt'
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39
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40 '''
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41 class FileListParser(HTMLParser):
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42 def __init__(self):
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43 # Have to use direct call to super class rather than using super():
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44 # super(FileListParser, self).__init__()
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45 # because HTMLParser is an "old style" class and its inheritance chain does not include object.
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46 HTMLParser.__init__(self)
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47 self.filenames = set()
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48 def handle_starttag(self, tag, attrs):
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49 # Look for filename references in anchor tags and add them to filenames.
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50 if tag == "a":
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51 # The tag is an anchor tag.
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52 for attribute in attrs:
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53 # print "Checking: {:s}".format(str(attribute))
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54 if attribute[0] == "href":
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55 # Does the href have a tar.gz in it?
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56 if ("tar.gz" in attribute[1]) and ("md5" not in attribute[1]):
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57 # Add the value to filenames.
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58 self.filenames.add(attribute[1])
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59 # End of class FileListParser
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60 '''
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61
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62
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63 def get_ctat_lncrna_annotations_locations():
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64 # For dynamic options need to return an interable with contents that are tuples with 3 items.
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65 # Item one is a string that is the display name put into the option list.
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66 # Item two is the value that is put into the parameter associated with the option list.
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67 # Item three is a True or False value, indicating whether the item is selected.
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68 options = []
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69 # open the url and retrieve the filenames of the files in the directory.
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70 resource = urllib2.urlopen(_CTAT_lncrnaIndexPage_URL)
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71 theHTML = resource.read()
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72 filelist_parser = FileListParser()
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73 filelist_parser.feed(theHTML)
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74 options.append((_CTAT_lncrnaDir_Name, _CTAT_lncrnaDownload_URL, True))
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75 print "The list of items being returned for the option menu is:"
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76 print str(options)
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77 return options
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78
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79 def download_annotations(src_location, destination, force_download):
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80 # We do not know if the annotations has been downloaded already.
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81 # This function returns whether or not the annotations actually gets downloaded.
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82 annotations_was_downloaded = False
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83 # Get the root filename of the Genome Directory.
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84 # The part after the last '/' and before the first '.'
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85 root_annotations_dirname = src_location.split("/")[-1].split(".")[0]
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86
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87 # We want to make sure that destination is absolute fully specified path.
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88 cannonical_destination = os.path.realpath(destination)
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89 if cannonical_destination.split("/")[-1] != root_annotations_dirname:
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90 cannonical_destination += "/" + root_annotations_dirname
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91 if os.path.exists(cannonical_destination):
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92 if not os.path.isdir(cannonical_destination):
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93 raise ValueError("The destination is not a directory: " + \
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94 "{:s}".format(cannonical_destination))
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95 # else all is good. It is a directory.
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96 else:
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97 # We need to create it.
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98 try:
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99 os.makedirs(cannonical_destination)
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100 except os.error:
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101 print "ERROR: Trying to create the following directory path:"
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102 print "\t{:s}".format(cannonical_destination)
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103 raise
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104
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105 # Make sure the directory now exists and we can write to it.
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106 if not os.path.exists(cannonical_destination):
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107 # It should have been created, but if it doesn't exist at this point
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108 # in the code, something is wrong. Raise an error.
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109 raise OSError("The destination directory could not be created: " + \
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110 "{:s}".format(cannonical_destination))
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111 test_writing_file = "{:s}/{:s}".format(cannonical_destination, _Download_TestFile)
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112 try:
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113 filehandle = open(test_writing_file, "w")
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114 filehandle.write("Testing writing to this file.")
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115 filehandle.close()
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116 os.remove(test_writing_file)
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117 except IOError:
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118 print "The destination directory could not be written into: " + \
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119 "{:s}".format(cannonical_destination)
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120 raise
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121
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122 # Get the list of files in the directory,
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123 # We use it to check for a previous download or extraction among other things.
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124 orig_files_in_destdir = set(os.listdir(cannonical_destination))
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125 # See whether the file has been downloaded already.
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126 download_success_file_path = "{:s}/{:s}".format(cannonical_destination, _DownloadSuccessFile)
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127 if (_DownloadSuccessFile not in orig_files_in_destdir) or force_download:
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128 # Check whether there is enough space on the device for the annotations.
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129 statvfs = os.statvfs(cannonical_destination)
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130 num_avail_bytes = statvfs.f_frsize * statvfs.f_bavail # Number of free bytes that ordinary users
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131 # are allowed to use (excl. reserved space)
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132 if (num_avail_bytes < _NumBytesNeededForAnnotations):
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133 raise OSError("There is insufficient space ({:s} bytes)".format(str(num_avail_bytes)) + \
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134 " on the device of the destination directory: " + \
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135 "{:s}".format(cannonical_destination))
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136
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137
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138 if (_DownloadSuccessFile in orig_files_in_destdir):
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139 # Since we are redoing the download,
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140 # the success file needs to be removed
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141 # until the download has succeeded.
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142 os.remove(download_success_file_path)
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143 # We want to transfer and untar the file without storing the tar file, because that
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144 # adds all that much more space to the needed amount of free space on the disk.
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145 # Use subprocess to pipe the output of curl into tar.
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146 # Make curl silent so progress is not printed to stderr.
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147 command = "curl --silent {:s} | tar -xzf - -C {:s} --strip 1".format(src_location, cannonical_destination)
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148 try: # to send the command that downloads and extracts the file.
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149 command_output = subprocess.check_output(command, shell=True)
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150 # FIX - not sure check_output is what we want to use. If we want to have an error raised on
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151 # any problem, maybe we should not be checking output.
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152 except subprocess.CalledProcessError:
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153 print "ERROR: Trying to run the following command:\n\t{:s}".format(command)
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154 raise
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155 else:
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156 annotations_was_downloaded = True
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157
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158 # Some code to help us if errors occur.
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159 print "\n*******************************\nFinished download and extraction."
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160 if os.path.exists(cannonical_destination) and os.path.isdir(cannonical_destination):
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161 subprocess.check_call("ls -la {:s} 2>&1".format(cannonical_destination), shell=True)
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162
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163 files_in_destdir = set(os.listdir(cannonical_destination))
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164 found_filenames = set()
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165 for filename in files_in_destdir:
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166 # There should be three files, but some OS's might have created
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167 # other files in the directory, or maybe the user did.
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168 # Look for the annotations files.
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169 # The download files' names should start with the root_annotations_dirname
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170 # print "Is root: {:s} in file: {:s}".format(root_annotations_dirname, filename)
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171 if root_annotations_dirname in filename:
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172 found_filenames.add(filename)
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173 # print "The found_filenames are:\n\t{:s}".format(str(found_filenames))
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174 ## Changed from found_filenames
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175 if (len(files_in_destdir) >= 4):
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176 # FIX - we could md5 the files to make sure they are correct.
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177 # Or at least check their sizes, to see if the download completed ok.
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178 # Also we could check the names of the files.
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179 try:
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180 # Create a file to indicate that the download succeeded.
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181 subprocess.check_call("touch {:s}".format(download_success_file_path), shell=True)
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182 except IOError:
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183 print "The download_success file could not be created: " + \
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184 "{:s}".format(download_success_file_path)
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185 raise
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186 else:
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187 print "After download, the potential annotations files found are:\n\t{:s}".format(str(found_filenames))
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188 raise ValueError("ERROR: Could not find the extracted annotations files " + \
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189 "in the destination directory:\n\t{:s}".format(cannonical_destination))
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190
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191 return (cannonical_destination, root_annotations_dirname, annotations_was_downloaded)
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192
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193 def main():
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194 #Parse Command Line
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195 # print "At start before parsing arguments."
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196 parser = argparse.ArgumentParser()
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197 parser.add_argument('-d', '--download_location', default="", \
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198 help='This is the download location of the lncrna annotations.')
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199 parser.add_argument('-n', '--display_name', default="", \
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200 help='Is used as the selector text for the entry of this lncrna annotations in the data table.')
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201 parser.add_argument('-p', '--destination_path', \
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202 help='Full path of the lncrna annotations location or destination, either where it is, or where it will be placed.')
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203 parser.add_argument('-o', '--output_filename', \
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204 help='Name of the output file, where the json dictionary will be written.')
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205 parser.add_argument('-f', '--force_download',
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206 help='Forces download of lncrna annotations, even if previously downloaded. ' + \
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207 'Requires download_location to be set in order to work.', action="store_true")
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208 args = parser.parse_args()
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209
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210 # print "Arguments are parsed."
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211 print "\ndownload_location is {:s}".format(str(args.download_location))
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212 print "display_name is {:s}".format(str(args.display_name))
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213 print "destination_path is {:s}\n".format(str(args.destination_path))
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214 root_annotations_dirname = None
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215 # FIX - Prob don't need annotations_was_downloaded. Not doing anything with it.
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216 # But it indicates success downloading the annotations, so maybe should be checking it.
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217 annotations_was_downloaded = False
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218 if (args.download_location != ""):
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219 annotations_directory, root_annotations_dirname, annotations_was_downloaded = \
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220 download_annotations(src_location=args.download_location, \
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221 destination=args.destination_path, \
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222 force_download=args.force_download)
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223 else:
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224 cannonical_destination = os.path.realpath(args.destination_path)
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225 if not os.path.exists(cannonical_destination):
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226 raise ValueError("Cannot find the Lncrna annotations.\n" + \
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227 "The directory does not exist:\n\t{:s}".format(annotations_directory))
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228 # If args.destination_path is a directory containing
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229 # a subdirectory that contains the annotations files,
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230 # then we need to set the annotations_directory to be that subdirectory.
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231 files_in_destination_path = os.listdir(cannonical_destination)
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232 if (len(files_in_destination_path) == 4):
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233 path_to_file = "{:s}/{:s}".format(cannonical_destination, files_in_destination_path[0])
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234 if os.path.isdir(path_to_file):
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235 annotations_directory = path_to_file
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236 else:
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237 annotations_directory = cannonical_destination
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238 else:
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239 annotations_directory = cannonical_destination
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240 # Get the root_annotations_dirname of the annotations from the annotations_directory name.
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241 root_annotations_dirname = annotations_directory.split("/")[-1].split(".")[0]
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242
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243 # Check if there is an actual Lncrna annotations file in the annotations_directory.
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244 print "\nThe location of the Lncrna annotations is {:s}.\n".format(annotations_directory)
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245 files_in_annotations_directory = set(os.listdir(annotations_directory))
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246 annotations_file_found = False
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247 annotations_file_path_mm9 = annotations_directory+"/mm9"
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248 annotations_file_path_mm10 = annotations_directory+"/mm10"
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249 annotations_file_path_hg19 = annotations_directory+"/hg19"
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250 annotations_file_path_hg38 = annotations_directory+"/hg38"
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251
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252 # Set the display_name
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253 if (args.display_name is None) or (args.display_name == ""):
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254 # Use the root_annotations_dirname.
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255 if (root_annotations_dirname != None) and (root_annotations_dirname != ""):
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256 display_name_hg19 = "hg19"
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257 display_name_hg38 = "hg38"
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258 display_name_mm10 = "mm10"
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259 display_name_mm9 = "mm9"
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260 else:
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261 display_name = _CTAT_lncrna_DisplayNamePrefix + _CTAT_lncrnaDir_Name
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262 print "WARNING: Did not set the display name. Using the default: {:s}".format(display_name_value)
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263 else:
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264 display_name = _CTAT_lncrna_DisplayNamePrefix + args.display_name
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265 # display_name = display_name.replace(" ","_")
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266
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267 # Set the unique_id
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268 datetime_stamp = datetime.now().strftime("_%Y_%m_%d_%H_%M_%S_%f")
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269 if (root_annotations_dirname != None) and (root_annotations_dirname != ""):
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270 hg19_unique_id = "ctat_lncrna_hg19" + datetime_stamp
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271 mm10_unique_id = "ctat_lncrna_mm10" + datetime_stamp
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272 mm9_unique_id = "ctat_lncrna_mm9" + datetime_stamp
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273 hg38_unique_id = "ctat_lncrna_hg38" + datetime_stamp
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274 else:
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275 unique_id = _CTAT_lncrnaDir_Name + datetime_stamp
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276
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277 print "The hg19 Index's display_name will be set to: {:s}\n".format(display_name_hg19)
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278 print "Its hg19 unique_id will be set to: {:s}\n".format(hg19_unique_id)
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279 print "Its hg19 dir_path will be set to: {:s}\n".format(annotations_file_path_hg19)
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280
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281
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282 print "The hg38 Index's display_name will be set to: {:s}\n".format(display_name_hg38)
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283 print "Its hg38 unique_id will be set to: {:s}\n".format(hg38_unique_id)
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284 print "Its hg38 dir_path will be set to: {:s}\n".format(annotations_file_path_hg38)
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285
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286
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287 print "The mm9 Index's display_name will be set to: {:s}\n".format(display_name_mm9)
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288 print "Its mm9 unique_id will be set to: {:s}\n".format(mm9_unique_id)
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289 print "Its mm9 dir_path will be set to: {:s}\n".format(annotations_file_path_mm9)
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290
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291
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292 print "The mm10 Index's display_name will be set to: {:s}\n".format(display_name_mm10)
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293 print "Its mm10 unique_id will be set to: {:s}\n".format(mm10_unique_id)
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294 print "Its mm10 dir_path will be set to: {:s}\n".format(annotations_file_path_mm10)
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295
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296 data_manager_dict = {}
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297 data_manager_dict['data_tables'] = {}
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298 data_manager_dict['data_tables'][_CTAT_lncrnaTableName] = []
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299 data_table_entry_mm9 = dict(value=mm9_unique_id, name=display_name_mm9, path=annotations_file_path_mm9)
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300 data_manager_dict['data_tables'][_CTAT_lncrnaTableName].append(data_table_entry_mm9)
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301
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302 data_table_entry_mm10 = dict(value=mm10_unique_id, name=display_name_mm10, path=annotations_file_path_mm10)
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303 data_manager_dict['data_tables'][_CTAT_lncrnaTableName].append(data_table_entry_mm10)
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304
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305 data_table_entry_hg19 = dict(value=hg19_unique_id, name=display_name_hg19, path=annotations_file_path_hg19)
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306 data_manager_dict['data_tables'][_CTAT_lncrnaTableName].append(data_table_entry_hg19)
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307
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308 data_table_entry_hg38 = dict(value=hg38_unique_id, name=display_name_hg38, path=annotations_file_path_hg38)
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309 data_manager_dict['data_tables'][_CTAT_lncrnaTableName].append(data_table_entry_hg38)
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310
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311 # Temporarily the output file's dictionary is written for debugging:
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312 print "The dictionary for the output file is:\n\t{:s}".format(str(data_manager_dict))
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313 # Save info to json file. This is used to transfer data from the DataManager tool, to the data manager,
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314 # which then puts it into the correct .loc file (I think).
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315 # Remove the following line when testing without galaxy package.
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316 # open(args.output_filename, 'wb').write(to_json_string(data_manager_dict))
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317
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318 if __name__ == "__main__":
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319 main()
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