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comparison query.py @ 6:97dd57f81d77 draft

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Uploaded 20180131
author fabio
date Wed, 31 Jan 2018 15:58:36 -0500
parents 35593423c2e2
children 256d015d69f9
comparison
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5:5e2877685afc 6:97dd57f81d77
9 #### NN14 #### 9 #### NN14 ####
10 service_url = "http://nn14.galaxyproject.org:8080/"; 10 service_url = "http://nn14.galaxyproject.org:8080/";
11 #service_url = "http://127.0.0.1:8082/"; 11 #service_url = "http://127.0.0.1:8082/";
12 query_url = service_url+"tree/0/query"; 12 query_url = service_url+"tree/0/query";
13 status_url = service_url+"status/<task_id>"; 13 status_url = service_url+"status/<task_id>";
14 ##############
15 # query delay in seconds
16 query_delay = 30;
14 ############## 17 ##############
15 18
16 def query_request( options, args, payload ): 19 def query_request( options, args, payload ):
17 # add additional parameters to the payload 20 # add additional parameters to the payload
18 #payload["tree_id"] = str(options.treeid); 21 #payload["tree_id"] = str(options.treeid);
25 # create a session 28 # create a session
26 session = requests.Session(); 29 session = requests.Session();
27 # make a synchronous post request to the query route 30 # make a synchronous post request to the query route
28 req = session.post(query_url, headers=headers, json=payload); 31 req = session.post(query_url, headers=headers, json=payload);
29 resp_code = req.status_code; 32 resp_code = req.status_code;
30 #print(str(req.content)+"\n\n"); 33 print(str(req.content)+"\n\n");
31 if resp_code == requests.codes.ok: 34 if resp_code == requests.codes.ok:
32 resp_content = str(req.content); 35 resp_content = str(req.content);
33 # convert out to json 36 # convert out to json
34 json_content = json.loads(resp_content); 37 json_content = json.loads(resp_content);
35 # retrieve task id 38 # retrieve task id
43 session = requests.Session(); 46 session = requests.Session();
44 # make a synchronous get request to the status route 47 # make a synchronous get request to the status route
45 status_query_url = status_url.replace("<task_id>", task_id); 48 status_query_url = status_url.replace("<task_id>", task_id);
46 status_req = session.get(status_query_url); 49 status_req = session.get(status_query_url);
47 status_resp_content = str(status_req.content); 50 status_resp_content = str(status_req.content);
48 #print(status_resp_content+"\n\n"); 51 print(status_resp_content+"\n\n");
49 # convert out to json 52 # convert out to json
50 json_status_content = json.loads(status_resp_content); 53 json_status_content = json.loads(status_resp_content);
51 # take a look at the state 54 # take a look at the state
52 # state attribute is always available 55 # state attribute is always available
53 if json_status_content['state'] == 'SUCCESS': 56 if json_status_content['state'] == 'SUCCESS':
54 task_processed = True; 57 task_processed = True;
55 break; 58 break;
56 elif json_status_content['state'] in ['FAILURE', 'REVOKED']: 59 elif json_status_content['state'] in ['FAILURE', 'REVOKED']:
57 return "Task status: "+str(json_status_content['state']); 60 return "Task status: "+str(json_status_content['state']);
58 else: 61 else:
59 time.sleep(60); # in seconds 62 time.sleep(query_delay); # in seconds
60 63
61 # get output dir (collection) path 64 # get output dir (collection) path
62 output_dir_path = options.outputdir; 65 output_dir_path = options.outputdir;
63 if not os.path.exists(output_dir_path): 66 if not os.path.exists(output_dir_path):
64 os.makedirs(output_dir_path); 67 os.makedirs(output_dir_path);
100 seq_text = line_split[1]; 103 seq_text = line_split[1];
101 if seq_id in multiple_data: 104 if seq_id in multiple_data:
102 return "Error: the id '"+seq_id+"' is duplicated"; 105 return "Error: the id '"+seq_id+"' is duplicated";
103 multiple_data[seq_id] = seq_text; 106 multiple_data[seq_id] = seq_text;
104 if len(multiple_data) > 0: 107 if len(multiple_data) > 0:
105 return async_request( options, args, multiple_data ); 108 return query_request( options, args, multiple_data );
106 #return echo( options, args ); 109 #return echo( options, args );
107 else: 110 else:
108 return "An error has occurred. Please be sure that your input files are valid."; 111 return "An error has occurred. Please be sure that your input files are valid.";
109 else: 112 else:
110 # try with the sequence in --sequence 113 # try with the sequence in --sequence
124 seq_text = line_split[1]; 127 seq_text = line_split[1];
125 if seq_id in multiple_data: 128 if seq_id in multiple_data:
126 return "Error: the id '"+seq_id+"' is duplicated"; 129 return "Error: the id '"+seq_id+"' is duplicated";
127 multiple_data[seq_id] = seq_text; 130 multiple_data[seq_id] = seq_text;
128 if len(multiple_data) > 0: 131 if len(multiple_data) > 0:
129 return async_request( options, args, multiple_data ); 132 return query_request( options, args, multiple_data );
130 #return echo( options, args ); 133 #return echo( options, args );
131 else: 134 else:
132 return "An error has occurred. Please be sure that your input files are valid."; 135 return "An error has occurred. Please be sure that your input files are valid.";
133 else: 136 else:
134 return "You have to insert at least one row formatted as a tab delimited <id, sequence> touple"; 137 return "You have to insert at least one row formatted as a tab delimited <id, sequence> touple";
162 #--search 'rrr' 165 #--search 'rrr'
163 #--sthreshold 0.5 166 #--sthreshold 0.5
164 #--exact 0 167 #--exact 0
165 #--sequences 'id0__tc__CAATTAATGATAAATATTTTATAAGGTGCGGAAATAAAGTGAGGAATATCTTTTAAATTCAAGTTCAATTCTGAAAGC' 168 #--sequences 'id0__tc__CAATTAATGATAAATATTTTATAAGGTGCGGAAATAAAGTGAGGAATATCTTTTAAATTCAAGTTCAATTCTGAAAGC'
166 #--outputdir 'collection_content' 169 #--outputdir 'collection_content'
167 #sequences = 'id0__tc__CAATTAATGATAAATATTTTATAAGGTGCGGAAATAAAGTGAGGAATATCTTTTAAATTCAAGTTCAATTCTGAAAGC'; 170 #sequences = 'NM_001169378.2__tc__atttcggatgctttggagggaggaactctagtgctgcattgattggggcgtgtgttaatgatattcccagttcgcatggcgagcatcgattcctggtacgtatgtgggccccttgactcccacttatcgcacttgtcgttcgcaatttgcatgaattccgcttcgtctgaaacgcacttgcgccagacttctccggctggtctgatctggtctgtgatccggtctggtggggcgccagttgcgtttcgagctcatcaccagtcactccgcagtcgcattctgccagaggtctccgatcaagagcgcttctccattcgagattcaaacgcagcgcggtctgacgccgccacatcgagtgaaatccatatcgatggccacattcacacaggacgagatcgacttcctgcgcagccatggcaacgagctgtgtgccaagacctggctgggattgtgggatccgaagcgggctgtgcaccagcaggagcagcgcgaactgatgatggacaagtatgagcggaagcgatactacctggagccggccagtcctcttaagtcgctggccaatgcggtcaacctgaagtcgtctgctccggcgacgaaccacactcagaatggccaccaaaatgggtatgccagcatccatttgacgcctcctgctgcccagcggacctcggccaatggattgcagaaggtggccaactcgtcgagtaactcttctggaaagacctcatcctcgatcagtaggccacactataatcaccagaacaacagccaaaacaacaatcacgatgcctttggcctgggtggcggattgagcagcctgaacagcgccggttccacatccactggagctctttccgacaccagcagttgtgctagcaatggcttcggtgcggactgcgactttgtggctgactttggctcggccaacattttcgacgccacatcggcgcgttccacaggatcgccggcggtgtcgtccgtgtcctcagtgggttccagcaatggctacgccaaggtgcagcccatccgggcagctcatctccagcagcaacagcagttgcagcagcagctgcatcagcagcagctcctcaatggcaatggtcatcagggcactgagaactttgccgacttcgatcacgctcccatctacaatgcagtggctccaccgacttttaacgattggatcagcgactggagcaggcggggcttccacgatcccttcgacgattgcgatgactcgccaccaggtgcccgccctccagcacctgcgccagctcctgctcaagttcccgcagtatcatcaccattgccaaccgtccgagaagaaccagagcttgcgtggaatttttgggaggacgagatgcgaatagaggcgcaggaaaaggagtcccaaactaaacagccggagttgggctactccttttcgattagtactactacgcccctttccccttcgaatcccttcctgccctaccttgtcagtgaggagcagcatcgaaatcatccagagaagccctccttttcgtattcgttgttcagctccatatcaaatagttcgcaagaagatcaggcggatgatcatgagatgaatgttttaaatgccaatttccatgatttctttacgtggagtgctcccttgcagaacggccatacgaccagtccgcccaagggcggaaatgcagcgatggcgcccagtgaggatcgatatgccgctcttaaggatctcgacgagcagctgcgagaactgaaggccagcgaaagcgccacagagacgcccacgcccaccagtggcaatgttcaggccacagatgcctttggtggagccctcaacaacaatccaaatcccttcaagggccagcaacagcagcagctcagcagccatgtggtgaatccattccagcagcagcaacagcagcagcaccagcagaatctctatggccagttgacgctcataccaaatgcctacggcagcagttcccagcagcagatggggcaccatctcctccagcagcagcagcagcaacagcagagcttcttcaacttcaacaacaacgggttcgccatctcgcagggtctgcccaacggctgcggcttcggcagcatgcaacccgctcctgtgatggccaacaatccctttgcagccagcggcgccatgaacaccaacaatccattcttatgagactcaacccgggagaatccgcctcgcgccacctggcagaggcgctgagccagcgaacaaagagcagacgcggaggaaccgaaccgaaattagtccattttactaacaatagcgttaatctatgtatacataatgcacgccggagagcactctttgtgtacatagcccaaatatgtacacccgaaaggctccacgctgacgctagtcctcgcggatggcggaggcggactggggcgttgatatattcttttacatggtaactctactctaacgtttacggatacggatatttgtatttgccgtttgccctagaactctatacttgtactaagcgcccatgaacacttcatccactaacatagctactaatcctcatcctagtggaggatgcagttggtccagacactctgttatttgttttatccatcctcgtacttgtctttgtcccatttagcactttcgttgcggataagaactttgtcagttattgattgtgtggccttaataagattataaaactaaatattataacgtacgactatacatatacggatacagatacagattcagacacagttagtacagatacagatatacatatacgcttttgtacctaatgaattgcttcttgtttccattgctaatcatctgcttttcgtgtgctaattttatacactagtacgtgcgatatcggccgtgcagatagattgctcagctcgcgagtcaagcctcttttggttgcacccacggcagacatttgtacatatactgtctgattgtaagcctcgtgtaatacctccattaacaccactcccccaccacccatccatcgaaccccgaatccatgactcaattcactgctcacatgtccatgcccatgccttaacgtgtcaaacattatcgaagccttaaagttatttaaaactacgaaatttcaataaaaacaaataagaacgctatc';
168 #print(sequences); 171 #print(sequences);
169 #(options, args) = parser.parse_args(['-x', 'rrr', '-t', 0.5, '-s', sequences, '-o', 'collection_content']); 172 #(options, args) = parser.parse_args(['-x', 'rrr', '-t', 0.5, '-s', sequences, '-o', 'collection_content']);
170 173
171 (options, args) = parser.parse_args(); 174 (options, args) = parser.parse_args();
172 return query( options, args ); 175 return query( options, args );