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comparison search.py @ 0:00d6e82d74e9 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded 20180122
author fabio
date Mon, 22 Jan 2018 16:41:50 -0500
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children 4291c9d1ff07
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-1:000000000000 0:00d6e82d74e9
1 #!/usr/bin/env python
2
3 # https://github.com/ross/requests-futures
4 # http://docs.python-requests.org/en/master/user/quickstart/#more-complicated-post-requests
5
6 import os, uuid
7 import optparse
8 import requests
9 from requests_futures.sessions import FuturesSession
10
11 #### UV0 ####
12 # proxy to uv0
13 #service_url = "http://deputy.bx.psu.edu/";
14 # url to query page
15 #query_url = service_url+"query.php";
16 # url to echo page: just return 'it works!'
17 #echo_url = service_url+"echo.php";
18 #############
19
20 #### NN14 ####
21 service_url = "http://nn14.galaxyproject.org:8080/";
22 query_url = service_url+"tree/0/query";
23 ##############
24
25 '''
26 # synchronous
27 def echo( options, args ):
28 # create a session
29 session = requests.Session()
30 # make a sync get request
31 resp = session.get(echo_url)
32 # check for response status code
33 resp_code = resp.status_code;
34 if resp_code == requests.codes.ok:
35 # get output file path
36 output_file_path = options.output;
37 # write response on the output file
38 with open(output_file_path, 'w') as out:
39 #out.write(resp.data);
40 out.write(resp.content);
41 return 0;
42 else:
43 return resp_code;
44 '''
45
46 # asynchronous
47 def async_request( options, args, payload ):
48 # add additional parameters to the payload
49 payload["tree_id"] = str(options.treeid);
50 payload["search_mode"] = str(options.search);
51 payload["exact_algorithm"] = str(options.exact);
52 payload["search_threshold"] = str(options.sthreshold);
53 # create a session
54 session = FuturesSession();
55 # make an async post request with requests-futures
56 future_req = session.post(query_url, data=payload);
57 # wait for the request to complete, if it has not already
58 resp = future_req.result();
59 # check for response status code
60 resp_code = resp.status_code;
61 # get output file path
62 output_file_path = options.output;
63 # write response on the output file
64 with open(output_file_path, 'w') as out:
65 #out.write(resp.data);
66 out.write(str(resp_code)+"\n"+str(resp.content));
67 if resp_code == requests.codes.ok:
68 return 0;
69 else:
70 return resp_code;
71
72 def srase_query( options, args ):
73 multiple_files = {};
74 comma_sep_file_paths = options.files;
75 #print("files: "+str(comma_sep_file_paths)+" - "+str(type(comma_sep_file_paths)));
76 # check if options.files contains at least one file path
77 if comma_sep_file_paths is not None:
78 # split file paths
79 file_paths = comma_sep_file_paths.split(",");
80 # split file names
81 comma_sep_file_names = str(options.names);
82 #print("names: "+str(comma_sep_file_names));
83 file_names = comma_sep_file_names.split(",");
84 # populate a dictionary with the files containing the sequences to query
85 for idx, file_path in enumerate(file_paths):
86 file_name = file_names[idx];
87 with open(file_path, 'r') as content_file:
88 content = content_file.read()
89 multiple_files[file_name] = content;
90 #print(file_name+": "+content+"\n");
91 if len(multiple_files) > 0:
92 return async_request( options, args, multiple_files );
93 #return echo( options, args );
94 else:
95 search_mode = str(options.search);
96 text_content = "";
97 if search_mode == "0":
98 # try with the sequence in --sequence
99 text_content = options.sequences;
100 elif search_mode == "1":
101 # try with the fasta content in --fasta
102 text_content = options.fasta;
103 #print("sequences: "+text_content);
104 # check if options.sequences contains a list of sequences (one for each row)
105 if text_content is not None:
106 text_content = str(text_content);
107 if text_content.strip():
108 if search_mode == "0":
109 # populate a dictionary with the files containing the sequences to query
110 seq_counter = 0;
111 sequences_arr = text_content.split("__cn__");
112 for seq in sequences_arr:
113 seq_index = 'sequence'+str(seq_counter);
114 multiple_files[seq_index] = seq;
115 #print(str(seq_counter)+": "+seq);
116 seq_counter += 1;
117 elif search_mode == "1":
118 multiple_files["fasta"] = text_content;
119 return async_request( options, args, multiple_files );
120 #return echo( options, args );
121 else:
122 return -1;
123 return -1;
124
125 def __main__():
126 # Parse the command line options
127 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";
128 parser = optparse.OptionParser(usage = usage);
129 parser.add_option("-i", "--treeid", type="string",
130 action="store", dest="treeid", help="string representing the tree id");
131 parser.add_option("-f", "--files", type="string",
132 action="store", dest="files", help="comma separated files path");
133 parser.add_option("-n", "--names", type="string",
134 action="store", dest="names", help="comma separated names associated to the files specified in --files");
135 parser.add_option("-s", "--sequences", type="string",
136 action="store", dest="sequences", help="contains a list of sequences (one for each row)");
137 parser.add_option("-a", "--fasta", type="string",
138 action="store", dest="fasta", help="contains the content of a fasta file");
139 parser.add_option("-x", "--search", type="int", default=0,
140 action="store", dest="search", help="search mode");
141 parser.add_option("-e", "--exact", type="int", default=0,
142 action="store", dest="exact", help="exact algorithm (required if search is 1 only)");
143 parser.add_option("-t", "--sthreshold", type="string",
144 action="store", dest="sthreshold", help="threshold applied to the search algrithm");
145 parser.add_option("-o", "--output", type="string",
146 action="store", dest="output", help="output file path");
147 parser.add_option("-v", "--version", action="store_true", dest="version",
148 default=False, help="display version and exit");
149 (options, args) = parser.parse_args();
150 if options.version:
151 print __version__;
152 else:
153 srase_query( options, args );
154
155 if __name__ == "__main__": __main__()