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1 #!/usr/bin/env python
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2 # encoding: utf-8
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3 '''
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4 Module wrapping the NIST MSSEARCH application for matching
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5 spectra one or more spectra libraries.
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6 '''
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7 import csv
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8 import sys
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9 import fileinput
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10 import urllib2
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11 import time
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12 import utils
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13 import uuid
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14 import os
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15 import subprocess
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16 from report_generator import ReportGenerator
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17
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18 __author__ = "Pieter Lukasse"
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19 __contact__ = "pieterlukasse@gmail.com,pieter.lukasse@wur.nl"
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20 __copyright__ = "Copyright, 2015"
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21 __license__ = "Apache v2"
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22
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23
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24
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7
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25 def _prepare_NIST(uuid_value, nist_home_dir, nist_ini_file, spectrum_file, is_wine, log_file):
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26 '''
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27 executes the following steps:
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28 - copy nist_home_dir folder to nist_home_dir+_uuid
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29 - copy spectrum_file.msp to ~/.wine/drive_c/NIST_uid
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30 - creates nist_home_dir+_uuid/MSSEARCH/AUTOIMP.MSD -> pointing to C:\NIST_uid\MSSEARCH\temp.msd (in case of is_wine) or to nist_home_dir+_uuidM\SSEARCH\temp.msd
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31 - creates nist_home_dir+_uuid/MSSEARCH/temp.msd -> pointing to C:\NIST_uid\spectrum_file.msp (in case of is_wine) or to nist_home_dir+_uuid\spectrum_file.msp
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32 and the text "10 724" in the second row
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33 - copy nistms.INI to nist_home_dir+_uuid/MSSEARCH , overwriting the existing one
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34 - in case of is_wine:
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35 replace all occurrences of C:\NIST with C:\NIST_uid in this new nistms.INI
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36 else:
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37 replace all occurrences of C:\NIST with nist_home_dir+_uuid in this new nistms.INI
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38 '''
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39 if nist_home_dir.endswith("/") or nist_home_dir.endswith("\\"):
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40 nist_home_dir = nist_home_dir[:-1]
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41
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42 # small validation for wine scenario
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43 if is_wine and not nist_home_dir.endswith("drive_c/NIST"):
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44 raise Exception('Error: invalid NIST home. For wine usage NIST home dir must be in the .wine folder and then in drive_c/NIST')
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45
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46 new_nist_home = nist_home_dir+uuid_value
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47 utils.copy_dir(nist_home_dir, new_nist_home)
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48
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49 utils.copy_file(spectrum_file, new_nist_home+"/spectrum_file.msp")
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50
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51 utils.log_message(log_file, "configuring NIST input...")
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52 # remove old file:
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53 os.remove(new_nist_home+"/MSSEARCH/AUTOIMP.MSD")
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54 with open(new_nist_home + "/MSSEARCH/AUTOIMP.MSD", "a") as text_file:
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55 if is_wine:
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56 text_file.write("C:\\NIST" + uuid_value + "\\MSSEARCH\\temp.msd")
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57 else:
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58 text_file.write(new_nist_home + "\\MSSEARCH\\temp.msd")
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59
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60 with open(new_nist_home + "/MSSEARCH/temp.msd", "a") as text_file:
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61 if is_wine:
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62 text_file.write("C:\\NIST" + uuid_value + "\\spectrum_file.msp\n")
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63 else:
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64 text_file.write(new_nist_home + "\\spectrum_file.msp\n")
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65 text_file.write("10 724")
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66
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67 replacement_text = new_nist_home
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68 if is_wine:
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69 replacement_text = "C:\\NIST" + uuid_value
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70
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71 # remove old file
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72 os.remove(new_nist_home+"/MSSEARCH/nistms.INI")
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73 # make new one
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74 utils.log_message(log_file, "configuring NIST ini...")
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75 o = open(new_nist_home+"/MSSEARCH/nistms.INI","a") #open for append
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76 # TODO : this loop/replace below is a bit limited to specific variables...either test different NIST versions or make more generic (harder in case of wine, or we need extra "home in .INI file" parameter):
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77 for line in open(nist_ini_file):
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78 if "Library Directory=" in line:
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79 line = "Library Directory="+ new_nist_home + "\\MSSEARCH\\\n"
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80 if "Dir=" in line:
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81 line = "Dir="+ replacement_text + "\\MSSEARCH\\\n"
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82
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83 o.write(line)
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84 o.close()
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85
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86 return new_nist_home
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87
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88 def _clean_up_NIST(new_nist_home):
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89 '''
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90 remove folder
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91 '''
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92 utils.remove_dir(new_nist_home)
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93
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94 def _run_NIST(new_nist_home, output_file, is_wine, log_file, job_size):
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95 '''
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96 - run : (wine) new_nist_home/MSSEARCH/nistms$.exe /INSTRUMENT /PAR=2
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97 - monitor : new_nist_home/MSSEARCH/SRCREADY.TXT for content = "1"
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98 - when ready:
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99 > copy SRCRESLT.TXT to output_file
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100 > kill nist process
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101 > (optional)remove ~/.wine/drive_c/NIST_uid/
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102 > finish
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103 '''
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104 # to avoid conflicts in the orphan process killing (see end of this method), we will
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105 # only run NIST again after previous nistms.exe process has been killed:
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106 # TODO : solution is currently only for wine (in the windows context the solution is not there yet, but parallel calls are not expected as in windows we only run tests one by one for now)
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107
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108
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109 # remove old file, if it is there:
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110 file_to_monitor = new_nist_home+"/MSSEARCH/SRCREADY.TXT"
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111 if os.path.exists(file_to_monitor):
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112 os.remove(file_to_monitor)
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113
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114 exec_path = new_nist_home + "/MSSEARCH/nistms$.exe"
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115
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116 pro = ""
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117 if is_wine:
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118 utils.log_message(log_file, "calling wine with " + exec_path)
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119 cmd = ["wine "+ exec_path + " /INSTRUMENT /PAR=2"]
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120 # The os.setsid() is passed in the argument preexec_fn so
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121 # it's run after the fork() and before exec() to run the shell.
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122 pro = subprocess.Popen(cmd, stdout=subprocess.PIPE,
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123 shell=True, preexec_fn=os.setsid)
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124 else:
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125 cmd = [
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126 exec_path,
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127 "/INSTRUMENT",
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128 "/PAR=2"]
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129 subprocess.call(cmd)
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130
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131
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132 timeSleeping = 0
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133 startUpTime = 30
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134 # monitor process by checking state file:
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135 utils.log_message(log_file, "monitoring SRCREADY.TXT...")
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136 # TODO2: do the controller part
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137 # TODO3: do the popover part
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138 while True:
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139 # check if SRCREADY.TXT is there already:
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140 if os.path.exists(file_to_monitor):
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141 break
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142 time.sleep(2)
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143 timeSleeping = timeSleeping+2
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144 if timeSleeping > (startUpTime + job_size*2):
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145 # abort with timeout:
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146 utils.log_message(log_file, "No results after " + timeSleeping + " seconds...")
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147 raise Exception('Error: timeout waiting for NIST results.')
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148
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149 # kill process:
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150 #p.terminate() - not needed, nistm$ will terminate...nistms.exe is the one that
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151 #stays open...and orphan..killing it:
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152
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153 if is_wine:
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154 # pid = utils.get_process_pid("nistms.exe")
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155 # os.kill(pid, 9)
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156 os.killpg(pro.pid, 9)
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157 else:
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158 # windows case:
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159 proc_name = "nistms.exe"
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160 os.system("taskkill /f /im " + proc_name)
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161
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162 # copy SRCRESLT.TXT to output_file
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163 result_file = new_nist_home+"/MSSEARCH/SRCRESLT.TXT"
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164 utils.copy_file(result_file, output_file)
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165
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166
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167 def _create_html_report(output_html_report, output_html_report_files_path, hits_dict, spectra_dict):
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168 '''
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169 This report will contain a page that displays essentially the same list as found in the
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170 tabular output file (rendered with datatables jquery plugin), with some extra features:
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171 - when user clicks on an entry, it should display the query spectrum and the hit spectrum
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172 in "head to tail" and "difference" mode (see galaxy/report_example.png)
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173 -> the query spectrum can be generated from the data in the input MSP file
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174 -> the library "online representative" spectrum can be generated from data returned by http://webbook.nist.gov/cgi/cbook.cgi?JCAMP=C537268&Index=0&Type=Mass ,
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175 where C537268 in this case is the CAS ID without the '-' separators
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176 '''
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177 # step 1 : generate HTML via the jinja template engine
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178 # step 1.1: make sure to link the query spectrum data to the corresponding html object for quick rendering when needed
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179
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180 # copy necessary .js files as well:
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181 templates_folder = os.path.dirname(__file__) + '/templates/'
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182 utils.copy_dir(templates_folder, output_html_report_files_path)
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183
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184 html_file = open(output_html_report,'w')
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185 html_render = ReportGenerator(os.path.dirname(__file__), 'templates/main_template.html',hits_dict, spectra_dict)
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186 html_render.render(html_file)
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187
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188 html_file.close()
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189
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190
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191
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192
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193
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194 return None
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195
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196 def _get_extra_info_and_link_cols(data_found, data_type_found, query_link):
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197 '''
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198 This method will go over the data found and will return a
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199 list with the following items:
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200 - Experiment details where hits have been found :
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201 'organism', 'tissue','experiment_name','user_name','column_type'
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202 - Link that executes same query
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203
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204 '''
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205 # set() makes a unique list:
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206 organism_set = []
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207 tissue_set = []
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208 experiment_name_set = []
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209 user_name_set = []
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210 column_type_set = []
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211 cas_nr_set = []
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212
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213 if 'organism' in data_found:
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214 organism_set = set(data_found['organism'])
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215 if 'tissue' in data_found:
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216 tissue_set = set(data_found['tissue'])
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217 if 'experiment_name' in data_found:
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218 experiment_name_set = set(data_found['experiment_name'])
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219 if 'user_name' in data_found:
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220 user_name_set = set(data_found['user_name'])
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221 if 'column_type' in data_found:
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222 column_type_set = set(data_found['column_type'])
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223 if 'CAS' in data_found:
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224 cas_nr_set = set(data_found['CAS'])
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225
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226
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227 result = [data_type_found,
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228
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229 #To let Excel interpret as link, use e.g. =HYPERLINK("http://stackoverflow.com", "friendly name"):
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230 "=HYPERLINK(\""+ query_link + "\", \"Link to entries found in DB \")"]
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231 return result
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232
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233
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234
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235
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236
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237 # alternative: ?
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238 # s = requests.Session()
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239 # s.verify = False
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240 # #s.auth = (token01, token02)
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241 # resp = s.get(url, params={'name': 'anonymous'}, stream=True)
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242 # content = resp.content
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243 # # transform to dictionary:
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244
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245
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246
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247 def _save_data(data_rows, headers, out_csv):
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248 '''
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249 Writes tab-separated data to file
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250 @param data_rows: dictionary containing merged/enriched dataset
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251 @param out_csv: output csv file
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252 '''
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253
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254 # Open output file for writing
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255 outfile_single_handle = open(out_csv, 'wb')
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256 output_single_handle = csv.writer(outfile_single_handle, delimiter="\t")
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257
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258 # Write headers
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259 output_single_handle.writerow(headers)
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260
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261 # Write one line for each row
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262 for data_row in data_rows:
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263 output_single_handle.writerow(data_row)
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264
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265 def _get_metexp_URL(metexp_dblink_file):
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266 '''
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267 Read out and return the URL stored in the given file.
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268 '''
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269 file_input = fileinput.input(metexp_dblink_file)
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270 try:
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271 for line in file_input:
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272 if line[0] != '#':
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273 # just return the first line that is not a comment line:
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274 return line
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275 finally:
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276 file_input.close()
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277
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278
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279 def main():
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280 '''
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281 Wrapper main function
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282
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283 The input expected is:
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284 NIST_HOME dir
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285 nistms.INI
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286 spectrum_file.msp
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287 outputfileName
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288 (optional) htmlReportFile
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289 (optional) htmlReportFile.files_path
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290 '''
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291 seconds_start = int(round(time.time()))
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292
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293 nist_home_dir = sys.argv[1]
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294 nist_ini_file = sys.argv[2]
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295 spectrum_file = sys.argv[3]
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296 nist_output_file = sys.argv[4]
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297 final_output_file = sys.argv[5]
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298 output_log_file = sys.argv[6]
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299 # html report pars:
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300 output_html_report = None
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301 output_html_report_files_path = None
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302 if len(sys.argv) > 7:
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303 output_html_report = sys.argv[7]
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304 output_html_report_files_path = sys.argv[8]
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305
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306 is_wine = False
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307 if "wine" in nist_home_dir:
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308 is_wine = True
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309
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310 uuid_value = str(uuid.uuid4())
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311
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312 # prepare NIST environment for running:
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313 new_nist_home = _prepare_NIST(uuid_value, nist_home_dir, nist_ini_file, spectrum_file, is_wine, output_log_file)
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314
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315 # run NIST search command:
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316 spectra_dict = utils.get_spectra_file_as_dict(spectrum_file)
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317 job_size = len(spectra_dict)
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318 _run_NIST(new_nist_home, nist_output_file, is_wine, output_log_file, job_size)
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319
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320 # clean-up NIST environment:
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321 _clean_up_NIST(new_nist_home)
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322
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323 # write output tabular:
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324 hits_dict = utils.get_nist_out_as_dict(nist_output_file)
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325 utils.save_dict_as_tsv(hits_dict, final_output_file)
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326
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327 # create report:
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328 if len(sys.argv) > 7:
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329 _create_html_report(output_html_report, output_html_report_files_path, hits_dict, spectra_dict)
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330
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331
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332 #_save_data(enriched_data, headers, output_result)
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333
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334 seconds_end = int(round(time.time()))
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335 print "Took " + str(seconds_end - seconds_start) + " seconds"
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336
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337
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338
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339 if __name__ == '__main__':
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340 main()
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