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1 from __future__ import print_function
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2 import requests
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3 import json
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4 import time
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5 try:
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6 # Python 3.0+
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7 from urllib.request import urlretrieve
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8 except:
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9 # Python 2.7
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10 from urllib import urlretrieve
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11 import sys
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12 import csv
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13 import argparse
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14
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15 """
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16 Tool's email:
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17 usernmae: cravatgalaxy@gmail.com
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18 password: chicken_quesadilla
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19 """
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20
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21 email = 'cravatgalaxy@gmail.com'
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22
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23 class CravatSubmissionException(Exception):
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24 def __init__(self, message):
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25 super(CravatSubmissionException, self).__init__(message)
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26
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27 class CravatSubmission(object):
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28
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29 def get_cmd_args(self, argv):
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30 parser = argparse.ArgumentParser()
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31 parser.add_argument('path',
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32 help="Path to python module")
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33 parser.add_argument('--input',
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34 '-i',
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35 required = True,
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36 help='Input path to a cravat file for querying',)
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37 parser.add_argument('--output',
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38 '-o',
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39 default = None,
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40 help = 'Output path to write results from query')
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41 parser.add_argument('--analysis',
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42 '-a',
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43 required=True,
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44 help = "Cravat analysis. Should be 'VEST', 'CHASM', 'NONE', or 'VEST;CHASM'")
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45 return parser.parse_args(argv)
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46
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47 def is_valid_analysis(self, analysis):
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48 """: Test if analysis is a recognized value"""
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49 analyses = ["VEST", "CHASM", "VEST;CHASM", ""]
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50 return analysis in analyses
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51
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52 def is_skippable(self, s):
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53 """: Test if a line (str or list/tuple) is skippable, a.k.a. a header or blank line"""
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54 if not isinstance(s, str):
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55 raise CravatSubmissionException("is_skippable accepts a string")
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56 skippable = s == "" \
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57 or s[0] == "#" \
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58 or s.startswith('"#For more information on CRAVAT') \
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59 or s.isspace()
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60 return skippable
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61
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62 def parse(self, s, sep='\t'):
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63 """: Convert string line to an array of values"""
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64 return s.strip().split(sep)
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65
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66 def unparse(self, array, sep='\t', newline='\n'):
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67 """: Convert an array of values to a writable string line"""
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68 return sep.join([str(i) for i in array]) + newline
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69
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70 def get_headers(self, path, pattern='Input line', sep='\t'):
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71 """: Get the headers from a Results/Details file obtained from by a finished Cravat submission"""
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72 with open(path, 'r') as f:
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73 for line in f:
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74 if line.startswith(pattern):
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75 return self.parse(line)
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76 return None
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77
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78 def create_index(self, path, prop='Input line'):
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79 """
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80 : Create an index of seek/tell positions in file associated to a line value. Used to record
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81 : the location of lines betwen two files that are associated with each other without reading entire
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82 : files into memory.
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83 """
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84 headers = self.get_headers(path)
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85 if prop not in headers:
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86 raise CravatSubmissionException("Index retrievel property not found in headers")
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87 prop_loc = headers.index(prop)
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88 index = {}
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89 with open(path, 'r') as f:
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90 pos = 0
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91 line = f.readline()
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92 while line != "":
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93 if not self.is_skippable(line):
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94 parsed = self.parse(line)
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95 if not parsed == headers:
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96 index[parsed[prop_loc]] = pos
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97 pos = f.tell()
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98 line = f.readline()
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99 return index
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100
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101 def get_header_val_dict(self, headers, vals):
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102 """: Associate an array of header keys to an array of values."""
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103 return { header:val for (header, val) in zip(headers, vals) }
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104
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105 def write_results(self, results_path, details_path, out_path, write_headers=True):
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106 """
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107 : Using the paths to the Results and Details file from a Cravat Sumbission,
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108 : write the output file.
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109 """
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110 results_headers = self.get_headers(results_path)
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111 details_headers = self.get_headers(details_path)
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112 if results_headers == None \
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113 or details_headers == None:
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114 raise CravatSubmissionException("Unable to intepret headers in Results or Details submission files")
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115 headers = results_headers
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116 headers.extend(filter(lambda x: x not in headers, details_headers))
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117 results_index = self.create_index(results_path)
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118 details_index = self.create_index(details_path)
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119 with open(results_path, 'r') as results_file, \
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120 open(details_path, 'r') as details_file, \
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121 open(out_path, 'w') as out_file:
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122 if write_headers:
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123 out_file.write(self.unparse(headers))
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124 for line_id, file_pos in results_index.items():
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125 results_file.seek(file_pos)
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126 results_vals = self.parse(results_file.readline())
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127 results_dict = self.get_header_val_dict(results_headers, results_vals)
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128 if line_id in details_index:
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129 details_file.seek(details_index[line_id])
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130 details_vals = self.parse(details_file.readline())
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131 details_dict = self.get_header_val_dict(details_headers, details_vals)
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132 # On a repeated entry, the Details value will overwrite Results value
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133 results_dict.update(details_dict)
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134 line = [ results_dict.get(header, 'None') for header in headers ]
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135 out_file.write(self.unparse(line))
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136
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137 def submit(self, in_path, analysis):
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138 """: Make a POST request to submit a job to production CRAVAT server."""
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139 if not self.is_valid_analysis(analysis):
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140 raise ValueError("Did not get valid analyses.")
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141 # Create post request to submit job to CRAVAT production server
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142 submit = requests.post('http://cravat.us/CRAVAT/rest/service/submit',
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143 files={'inputfile' : open(in_path)},
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144 data={'email' : email,
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145 'analyses' : analysis})
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146 # Check job run status in loop until status is 'Success'
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147 jobid = json.loads(submit.text)['jobid']
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148 while True:
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149 check = requests.get('http://cravat.us/CRAVAT/rest/service/status', params={'jobid': jobid})
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150 status = json.loads(check.text)['status']
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151 #print(status)
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152 if status == 'Success':
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153 break
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154 else:
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155 time.sleep(2)
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156 # Download completed job results to local files
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157 timestamp = time.strftime("%Y-%m-%d_%H-%M-%S_")
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158 results_path = 'Z_Variant_Result' + timestamp + '.tsv'
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159 details_path = 'Z_Additional_Details' + timestamp + '.tsv'
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160 urlretrieve("http://cravat.us/CRAVAT/results/" + jobid + "/" + "Variant.Result.tsv",
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161 filename=results_path)
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162 urlretrieve("http://cravat.us/CRAVAT/results/" + jobid + "/" + "Variant_Additional_Details.Result.tsv",
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163 filename=details_path)
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164 return results_path, details_path
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165
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166 if __name__ == "__main__":
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167 submission = CravatSubmission()
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168 cmd_args = submission.get_cmd_args(sys.argv)
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169 # Galaxy converts semi-colons to X's. Switch it back
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170 analysis = cmd_args.analysis
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171 if analysis == "VESTXCHASM":
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172 analysis = "VEST;CHASM"
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173 results_path, details_path = submission.submit(cmd_args.input, analysis)
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174 #submission.write_results('Results_test.tsv', 'Details_test.tsv', 'Out_test.tsv')
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175 submission.write_results(results_path, details_path, cmd_args.output) |