comparison dynamic_utils.py @ 0:078d77023c34 draft default tip

planemo upload for repository https://github.com/lu-brn/gmql-galaxy commit 953ee36ceda5814dc9baa03427bc0eb4ee2e93bd-dirty
author geco-team
date Tue, 26 Jun 2018 08:59:19 -0400
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-1:000000000000 0:078d77023c34
1 #!/usr/bin/env python
2 # --------------------------------------------------------------------------------
3 # Class for the dynamic options in the GMQL tools
4 # --------------------------------------------------------------------------------
5 # Luana Brancato, luana.brancato@mail.polimi.it
6 # --------------------------------------------------------------------------------
7
8 import sys, requests
9
10
11 def validate(request_context, error_map, params, inputs):
12 """Generic validate function, it checks if the user is valid."""
13
14 user = params.get('authToken', '')
15
16 if user:
17 try:
18 validate_user(user.file_name)
19 except:
20 error_msg = 'User has expired'
21 error_map['authToken'] = error_msg
22
23
24 def validate_upload(request_context, error_map, params, inputs):
25 """Validate function for uploading tool. It also checks the chosen ds name does not exists already."""
26
27 validate(request_context, error_map, params, inputs)
28
29 name = params.get('name')
30
31 user = params.get('authToken')
32
33 #This MUST be changed in the future to a parametric solution. Hopefully in the future Galaxy will allow
34 #validation without external scripts
35
36 url = 'http://genomic.elet.polimi.it/gmql-rest/datasets'
37
38 datasets = get(url, user=user.file_name)
39 list_datasets = [x['name'] for x in datasets['datasets']]
40
41 if name in list_datasets:
42 error_msg = 'Dataset already exists. Choose another name.'
43 error_map['name'] = error_msg
44
45
46 def validate_variables(request_context, error_map, params, inputs):
47 """Validate function for gmql_compositor. It checks that all queries input variables
48 have been previously defined. """
49
50 validate(request_context, error_map, params, inputs)
51
52 output_vars = set([])
53
54 # TODO: Include in the check output variables eventually defined previously in another query
55
56 for op in params.get('operations'):
57 op_curr = op.get('operation')
58 if op_curr.get('input', ''):
59 input_var = op_curr.get('input').get('input_var', '')
60 if input_var:
61 if input_var not in output_vars:
62 error_msg = '%s has not been defined yet\n' % (input_var)
63 name = '|'.join(['operations_%d' % (op.get('__index__')), 'operation', 'input', 'input_var'])
64 error_map[name] = error_msg
65 else:
66 for key in op_curr.keys():
67 if key.startswith('input_var'):
68 input_var = op_curr.get(key)
69 if input_var:
70 if input_var not in output_vars:
71 error_msg = '%s has not been defined yet\n' % (input_var)
72 name = '|'.join(['operations_%d' % (op.get('__index__')), 'operation', key])
73 error_map[name] = error_msg
74
75 # Update output_vars with the result of current operation
76 output_vars.add(op_curr.get('output_var'))
77
78
79 def validate_user(user):
80 """Check if the user is a valid one"""
81
82 if user:
83 with open(user, 'r') as f:
84 valid = f.readline().rstrip('\n').split('\t')[2]
85 if valid == 'False':
86 raise Exception, "User has expired"
87
88
89 def get_metadata_attr(user, ds, ds_list):
90 options = []
91
92 try:
93 validate_user(user)
94 if ds_list:
95
96 owner = ''
97
98 with open(ds_list, 'r') as f:
99 for d in f.readlines():
100 if d.split('\t')[0] == ds:
101 owner = d.split('\t')[1].rstrip('\n')
102 f.close()
103
104 attr_list = get_metadata(user, ds, str(owner))
105
106 for i, att in enumerate(attr_list['attributes']):
107 options.append((att.get('key', ' '), att.get('key', ' '), i == 0))
108
109 return options
110
111 else:
112 return options
113 except:
114 return options
115
116
117 def get_metadata_values(user, ds, ds_list, att):
118 options = []
119
120 try:
121 validate_user(user)
122 if ds_list:
123
124 owner = ''
125
126 with open(ds_list, 'r') as f:
127 for d in f.readlines():
128 if d.split('\t')[0] == ds:
129 owner = d.split('\t')[1].rstrip('\n')
130 f.close()
131
132 attr_list = get_metadata(user, ds, str(owner), att)
133
134 # By default first option is '*' i.e. any value
135 options.append(('any value', '*', 0))
136
137 for i, att in enumerate(attr_list['values']):
138 options.append(('%s (%d)' % (att.get('text', ' '), att.get('count', 0)), att.get('text', ' '), i == 0))
139
140 return options
141
142 else:
143 return options
144 except:
145 return options
146
147
148 def get_metadata(user, ds, owner='', att_name=''):
149 """Return the metadata attributes names for the given dataset"""
150
151 url = 'http://genomic.elet.polimi.it/gmql-rest/metadata/{datasetName}/filter'
152
153 # Format url
154 if (owner == 'public'):
155 url = url.format(datasetName='public.' + ds)
156 else:
157 url = url.format(datasetName=ds)
158
159 if att_name:
160 url = '{url}/{att}'.format(url=url, att=att_name)
161
162 content = dict()
163 content.update(attributes=[])
164
165 metadata = post(url, content, user=user)
166
167 return metadata
168
169
170 def read_token(input):
171 """It takes the tabular file with the information over the user
172 name authToken valid_flag
173 It checks if the user is still valid and extract the authToken for the REST calls"""
174
175 with open(input, 'r') as f_in:
176 user = f_in.readline().rstrip('\n').split('\t')
177
178 if user[2]:
179 token = user[1]
180 else:
181 stop_err("This session is no longer valid")
182
183 return token
184
185
186 def get(url, user=None, response_type='json'):
187 """GET Request
188 :param url: url where to fetch the requested resource
189 :param user: for authenticated requests; if not provided make an unauthenticated request (es. for login)
190 :param response_type: type of the fetched response.
191 JSON ( Default )
192 TEXT
193 ZIP
194 FILE
195 """
196
197 # Set request headers
198 headers = dict()
199
200 if user:
201 headers.update({'X-AUTH-TOKEN': read_token(user)})
202
203 if response_type == 'text':
204 headers.update({'Accept': 'text/plain'})
205 elif response_type == 'zip':
206 pass
207 elif response_type == 'file':
208 headers.update({'Accept': 'file'})
209 else:
210 headers.update({'Accept': 'application/json'})
211
212 # Make the request
213 response = requests.get(url, headers=headers)
214
215 # Check returned server status
216 status_code = response.status_code
217
218 # Read result. If Server OK, read according to response_type. Raise an error otherwise.
219 if status_code == requests.codes.ok:
220 if response_type == 'json':
221 return response.json()
222 elif response_type == 'text':
223 return response.text
224 else:
225 return response
226 elif status_code == requests.codes.unauthorized:
227 #expire_user(user)
228 stop_err("You are not authorized to do this. \nPlease login first.")
229 elif status_code == requests.codes.not_found:
230 stop_err("Resource not found for this user.")
231 else:
232 stop_err("Error {code}: {reason}\n{message}".format(code=status_code,
233 reason=response.reason,
234 message=response.content))
235
236 def post(url, payload, user=None, params=None, content_type='json', response_type='json') :
237 """ POST Request
238 :param url: url where to post data
239 :param payload: payload for the post request. Type is specified by content_type.
240 :param user: for authenticated requests; if not provided make an unauthenticated request (es. for registration)
241 :param params: optional query parameters
242 :param content_type
243 :param response_type: Default is json
244 """
245
246
247 # Set request headers
248 headers = dict()
249
250 if user:
251 headers.update({'X-AUTH-TOKEN': read_token(user)})
252
253 headers.update({'Accept': 'application/json'})
254
255 if content_type == 'text' :
256 headers.update({'Content-Type' : 'text/plain'})
257 response = requests.post(url, params=params, headers=headers, data=payload)
258 elif content_type == 'multiform' :
259 response = requests.post(url, params=params, headers=headers, files=payload)
260 else :
261 headers.update({'Content-Type': 'application/json'})
262 response = requests.post(url, params=params, headers=headers, json=payload)
263
264 # Check returned server status
265 status_code = response.status_code
266
267
268 if status_code == requests.codes.ok :
269 return response.json()
270 elif status_code == requests.codes.unauthorized :
271 #expire_user(user)
272 stop_err("You are not authorized to do this. \nPlease login first.")
273 else :
274 stop_err("Error {code}: {reason}\n{message}".format(code=status_code,
275 reason=response.reason,
276 message=response.content))
277
278
279 def stop_err(msg):
280 sys.stderr.write("%s\n" % msg)
281 sys.exit()