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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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25 def _prepare_NIST(uuid_value, nist_home_dir, nist_ini_file, spectrum_file, is_wine):
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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 # remove old file:
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52 os.remove(new_nist_home+"/MSSEARCH/AUTOIMP.MSD")
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53 with open(new_nist_home + "/MSSEARCH/AUTOIMP.MSD", "a") as text_file:
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54 if is_wine:
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55 text_file.write("C:\\NIST" + uuid_value + "\\MSSEARCH\\temp.msd")
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56 else:
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57 text_file.write(new_nist_home + "\\MSSEARCH\\temp.msd")
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58
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59 with open(new_nist_home + "/MSSEARCH/temp.msd", "a") as text_file:
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60 if is_wine:
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61 text_file.write("C:\\NIST" + uuid_value + "\\spectrum_file.msp\n")
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62 else:
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63 text_file.write(new_nist_home + "\\spectrum_file.msp\n")
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64 text_file.write("10 724")
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65
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66 replacement_text = new_nist_home
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67 if is_wine:
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68 replacement_text = "C:\\NIST" + uuid_value
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69
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70 # remove old file
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71 os.remove(new_nist_home+"/MSSEARCH/nistms.INI")
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72 # make new one
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73 o = open(new_nist_home+"/MSSEARCH/nistms.INI","a") #open for append
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74 # 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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75 for line in open(nist_ini_file):
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76 if "Library Directory=" in line:
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77 line = "Library Directory="+ new_nist_home + "\\MSSEARCH\\\n"
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78 if "Dir=" in line:
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79 line = "Dir="+ replacement_text + "\\MSSEARCH\\\n"
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80
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81 o.write(line)
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82 o.close()
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83
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84 return new_nist_home
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85
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86 def _run_NIST(new_nist_home, output_file, is_wine):
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87 '''
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88 - run : (wine) new_nist_home/MSSEARCH/nistms$.exe /INSTRUMENT /PAR=2
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89 - monitor : new_nist_home/MSSEARCH/SRCREADY.TXT for content = "1"
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90 - when ready:
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91 > copy SRCRESLT.TXT to output_file
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92 > kill nist process
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93 > (optional)remove ~/.wine/drive_c/NIST_uid/
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94 > finish
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95 '''
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96 # to avoid conflicts in the orphan process killing (see end of this method), we will
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97 # only run NIST again after previous nistms.exe process has been killed:
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98 # 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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99 # if is_wine:
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100 # while True:
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101 # # check if process exists. If not, break loop and continue
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102 # pid = utils.get_process_pid("nistms.exe")
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103 # if pid == -1:
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104 # break
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105 # time.sleep(2)
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106
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107
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108 # remove old file, if it is there:
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109 file_to_monitor = new_nist_home+"/MSSEARCH/SRCREADY.TXT"
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110 if os.path.exists(file_to_monitor):
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111 os.remove(file_to_monitor)
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112
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113 exec_path = new_nist_home + "/MSSEARCH/nistms$.exe"
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114
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115 pro = ""
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116 if is_wine:
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117 print "calling wine with " + exec_path
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118 cmd = ["wine "+ exec_path + " /INSTRUMENT /PAR=2"]
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119 # The os.setsid() is passed in the argument preexec_fn so
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120 # it's run after the fork() and before exec() to run the shell.
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121 pro = subprocess.Popen(cmd, stdout=subprocess.PIPE,
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122 shell=True, preexec_fn=os.setsid)
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123 else:
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124 cmd = [
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125 exec_path,
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126 "/INSTRUMENT",
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127 "/PAR=2"]
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128 subprocess.call(cmd)
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129
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130
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131 # monitor process by checking state file:
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132 while True:
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133 # check if SRCREADY.TXT is there already:
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134 if os.path.exists(file_to_monitor):
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135 break
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136 time.sleep(2)
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137
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138 # kill process:
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139 #p.terminate() - not needed, nistm$ will terminate...nistms.exe is the one that
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140 #stays open...and orphan..killing it:
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141
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142 if is_wine:
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143 # pid = utils.get_process_pid("nistms.exe")
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144 # os.kill(pid, 9)
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145 os.killpg(pro.pid, 9)
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146 else:
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147 # windows case:
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148 proc_name = "nistms.exe"
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149 os.system("taskkill /f /im " + proc_name)
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150
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151 # copy SRCRESLT.TXT to output_file
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152 result_file = new_nist_home+"/MSSEARCH/SRCRESLT.TXT"
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153 utils.copy_file(result_file, output_file)
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154
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155
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156 def _create_html_report(output_html_report, output_html_report_files_path, hits_dict, spectra_dict):
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157 '''
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158 This report will contain a page that displays essentially the same list as found in the
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159 tabular output file (rendered with datatables jquery plugin), with some extra features:
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160 - when user clicks on an entry, it should display the query spectrum and the hit spectrum
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161 in "head to tail" and "difference" mode (see galaxy/report_example.png)
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162 -> the query spectrum can be generated from the data in the input MSP file
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163 -> 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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164 where C537268 in this case is the CAS ID without the '-' separators
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165 '''
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166 # step 1 : generate HTML via the jinja template engine
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167 # 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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168
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169 html_file = open(output_html_report,'w')
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170 html_render = ReportGenerator(os.path.dirname(__file__), 'templates/main_template.html',hits_dict, spectra_dict)
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171 html_render.render(html_file)
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172 # copy necessary .js files as well:
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173 templates_folder = os.path.dirname(__file__) + '/templates/'
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174 utils.copy_file(templates_folder + 'spectrum_gen.js', output_html_report_files_path+"/spectrum_gen.js")
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175 utils.copy_dir(templates_folder + 'lib', output_html_report_files_path+'/lib' )
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176 utils.copy_dir(templates_folder + 'images', output_html_report_files_path+'/images' )
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177
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178 html_file.close()
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179
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180
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181
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182
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183
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184 return None
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185
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186 def _get_extra_info_and_link_cols(data_found, data_type_found, query_link):
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187 '''
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188 This method will go over the data found and will return a
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189 list with the following items:
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190 - Experiment details where hits have been found :
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191 'organism', 'tissue','experiment_name','user_name','column_type'
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192 - Link that executes same query
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193
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194 '''
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195 # set() makes a unique list:
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196 organism_set = []
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197 tissue_set = []
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198 experiment_name_set = []
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199 user_name_set = []
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200 column_type_set = []
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201 cas_nr_set = []
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202
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203 if 'organism' in data_found:
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204 organism_set = set(data_found['organism'])
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205 if 'tissue' in data_found:
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206 tissue_set = set(data_found['tissue'])
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207 if 'experiment_name' in data_found:
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208 experiment_name_set = set(data_found['experiment_name'])
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209 if 'user_name' in data_found:
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210 user_name_set = set(data_found['user_name'])
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211 if 'column_type' in data_found:
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212 column_type_set = set(data_found['column_type'])
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213 if 'CAS' in data_found:
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214 cas_nr_set = set(data_found['CAS'])
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215
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216
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217 result = [data_type_found,
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218
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219 #To let Excel interpret as link, use e.g. =HYPERLINK("http://stackoverflow.com", "friendly name"):
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220 "=HYPERLINK(\""+ query_link + "\", \"Link to entries found in DB \")"]
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221 return result
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222
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223
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224
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225
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226
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227 # alternative: ?
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228 # s = requests.Session()
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229 # s.verify = False
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230 # #s.auth = (token01, token02)
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231 # resp = s.get(url, params={'name': 'anonymous'}, stream=True)
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232 # content = resp.content
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233 # # transform to dictionary:
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234
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235
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236
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237 def _save_data(data_rows, headers, out_csv):
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238 '''
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239 Writes tab-separated data to file
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240 @param data_rows: dictionary containing merged/enriched dataset
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241 @param out_csv: output csv file
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242 '''
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243
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244 # Open output file for writing
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245 outfile_single_handle = open(out_csv, 'wb')
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246 output_single_handle = csv.writer(outfile_single_handle, delimiter="\t")
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247
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248 # Write headers
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249 output_single_handle.writerow(headers)
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250
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251 # Write one line for each row
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252 for data_row in data_rows:
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253 output_single_handle.writerow(data_row)
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254
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255 def _get_metexp_URL(metexp_dblink_file):
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256 '''
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257 Read out and return the URL stored in the given file.
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258 '''
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259 file_input = fileinput.input(metexp_dblink_file)
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260 try:
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261 for line in file_input:
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262 if line[0] != '#':
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263 # just return the first line that is not a comment line:
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264 return line
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265 finally:
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266 file_input.close()
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267
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268
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269 def main():
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270 '''
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271 Wrapper main function
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272
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273 The input expected is:
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274 NIST_HOME dir
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275 nistms.INI
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276 spectrum_file.msp
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277 outputfileName
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278 (optional) htmlReportFile
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279 (optional) htmlReportFile.files_path
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280 '''
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281 seconds_start = int(round(time.time()))
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282
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283 nist_home_dir = sys.argv[1]
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284 nist_ini_file = sys.argv[2]
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285 spectrum_file = sys.argv[3]
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286 nist_output_file = sys.argv[4]
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287 final_output_file = sys.argv[5]
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288 # html report pars:
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289 output_html_report = None
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290 output_html_report_files_path = None
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291 if len(sys.argv) > 6:
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292 output_html_report = sys.argv[6]
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293 output_html_report_files_path = sys.argv[7]
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294
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295 is_wine = False
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296 if "wine" in nist_home_dir:
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297 is_wine = True
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298
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299 uuid_value = str(uuid.uuid4())
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300
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301 # prepare NIST environment for running:
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302 new_nist_home = _prepare_NIST(uuid_value, nist_home_dir, nist_ini_file, spectrum_file, is_wine)
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303
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304 # run NIST search command:
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305 _run_NIST(new_nist_home, nist_output_file, is_wine)
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306
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307 # write output tabular:
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308 hits_dict = utils.get_nist_out_as_dict(nist_output_file)
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309 utils.save_dict_as_tsv(hits_dict, final_output_file)
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310
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311 # create report:
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312 if len(sys.argv) > 6:
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313 spectra_dict = utils.get_spectra_file_as_dict(spectrum_file)
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314 _create_html_report(output_html_report, output_html_report_files_path, hits_dict, spectra_dict)
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315
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316
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317 #_save_data(enriched_data, headers, output_result)
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318
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319 seconds_end = int(round(time.time()))
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320 print "Took " + str(seconds_end - seconds_start) + " seconds"
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321
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322
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323
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324 if __name__ == '__main__':
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325 main()
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