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1 #!/usr/bin/env python
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2
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3 # https://github.com/ross/requests-futures
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4 # http://docs.python-requests.org/en/master/user/quickstart/#more-complicated-post-requests
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5
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6 import os, uuid
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7 import optparse
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8 import requests
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9 from requests_futures.sessions import FuturesSession
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10
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11 #### UV0 ####
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12 # proxy to uv0
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13 #service_url = "http://deputy.bx.psu.edu/";
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14 # url to query page
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15 #query_url = service_url+"query.php";
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16 # url to echo page: just return 'it works!'
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17 #echo_url = service_url+"echo.php";
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18 #############
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19
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20 #### NN14 ####
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21 service_url = "http://nn14.galaxyproject.org:8080/";
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22 query_url = service_url+"tree/0/query";
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23 ##############
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24
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25 '''
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26 # synchronous
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27 def echo( options, args ):
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28 # create a session
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29 session = requests.Session()
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30 # make a sync get request
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31 resp = session.get(echo_url)
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32 # check for response status code
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33 resp_code = resp.status_code;
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34 if resp_code == requests.codes.ok:
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35 # get output file path
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36 output_file_path = options.output;
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37 # write response on the output file
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38 with open(output_file_path, 'w') as out:
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39 #out.write(resp.data);
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40 out.write(resp.content);
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41 return 0;
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42 else:
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43 return resp_code;
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44 '''
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45
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46 # asynchronous
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47 def async_request( options, args, payload ):
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48 # add additional parameters to the payload
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2
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49 #payload["tree_id"] = str(options.treeid);
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50 payload["search_mode"] = str(options.search);
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51 payload["exact_algorithm"] = int(options.exact);
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52 payload["search_threshold"] = float(options.sthreshold);
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53 # set the content type to application/json
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54 headers = {'Content-type': 'application/json'};
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55 # create a session
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56 session = FuturesSession();
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57 # make an async post request with requests-futures
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58 future_req = session.post(query_url, headers=headers, json=payload);
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59 # wait for the request to complete, if it has not already
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60 resp = future_req.result();
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61 # check for response status code
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62 resp_code = resp.status_code;
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63 # get output file path
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64 output_file_path = options.output;
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65 # write response on the output file
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66 with open(output_file_path, 'w') as out:
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67 #out.write(resp.data);
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68 out.write(str(resp.content));
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69 if resp_code == requests.codes.ok:
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70 return 0;
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71 else:
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72 return resp_code;
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73
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74 def srase_query( options, args ):
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75 multiple_data = {};
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76 comma_sep_file_paths = options.files;
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77 #print("files: "+str(comma_sep_file_paths)+" - "+str(type(comma_sep_file_paths)));
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78 # check if options.files contains at least one file path
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79 if comma_sep_file_paths is not None:
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80 # split file paths
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81 file_paths = comma_sep_file_paths.split(",");
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82 # split file names
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83 comma_sep_file_names = str(options.names);
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84 #print("names: "+str(comma_sep_file_names));
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85 file_names = comma_sep_file_names.split(",");
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86 # populate a dictionary with the files containing the sequences to query
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87 sequences = [];
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88 for idx, file_path in enumerate(file_paths):
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89 #file_name = file_names[idx];
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90 with open(file_path, 'r') as content_file:
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91 content = content_file.read()
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92 sequences.append(content.strip());
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93 #multiple_data[file_name] = content;
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94 #print(file_name+": "+content+"\n");
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95 if len(sequences) > 0:
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96 multiple_data['sequences'] = sequences;
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97 return async_request( options, args, multiple_data );
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98 #return echo( options, args );
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99 else:
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100 return -1;
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101 else:
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102 # try with the sequence in --sequence
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103 text_content = options.sequences;
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104 #print("sequences: "+text_content);
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105 # check if options.sequences contains a list of sequences (one for each row)
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106 if text_content is not None:
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107 text_content = str(text_content);
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108 if text_content.strip():
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109 # populate a dictionary with the files containing the sequences to query
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110 multiple_data['sequences'] = text_content.strip().split("__cn__");
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111 return async_request( options, args, multiple_data );
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112 #return echo( options, args );
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113 else:
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114 return -1;
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115 return -1;
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116
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117 def __main__():
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118 # Parse the command line options
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119 usage = "Usage: search.py --files comma_sep_file_paths --names comma_seq_file_names --sequences sequences_text --search search_mode --exact exact_alg --sthreshold threshold --output output_file_path";
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120 parser = optparse.OptionParser(usage = usage);
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121 parser.add_option("-f", "--files", type="string",
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122 action="store", dest="files", help="comma separated files path");
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123 parser.add_option("-n", "--names", type="string",
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124 action="store", dest="names", help="comma separated names associated to the files specified in --files");
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125 parser.add_option("-s", "--sequences", type="string",
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126 action="store", dest="sequences", help="contains a list of sequences (one for each row)");
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127 parser.add_option("-a", "--fasta", type="string",
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128 action="store", dest="fasta", help="contains the content of a fasta file");
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129 parser.add_option("-x", "--search", type="string", default=0,
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130 action="store", dest="search", help="search mode");
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131 parser.add_option("-e", "--exact", type="int", default=0,
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132 action="store", dest="exact", help="exact algorithm (required if search is 1 only)");
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133 parser.add_option("-t", "--sthreshold", type="float",
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134 action="store", dest="sthreshold", help="threshold applied to the search algrithm");
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135 parser.add_option("-o", "--output", type="string",
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136 action="store", dest="output", help="output file path");
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137 (options, args) = parser.parse_args();
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138 return srase_query( options, args );
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139
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140 if __name__ == "__main__": __main__()
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