t2-server 0.6.1 → 0.9.0
Sign up to get free protection for your applications and to get access to all the features.
- data/.rvmrc +1 -0
- data/CHANGES.rdoc +48 -0
- data/LICENCE.rdoc +2 -2
- data/README.rdoc +245 -10
- data/Rakefile +108 -0
- data/bin/t2-delete-runs +21 -34
- data/bin/t2-get-output +134 -0
- data/bin/t2-run-workflow +121 -109
- data/bin/t2-server-admin +128 -0
- data/bin/t2-server-info +25 -38
- data/lib/t2-server-cli.rb +116 -0
- data/lib/t2-server.rb +16 -27
- data/lib/t2-server/admin.rb +147 -0
- data/lib/t2-server/connection-parameters.rb +144 -0
- data/lib/t2-server/connection.rb +352 -0
- data/lib/t2-server/credentials.rb +84 -0
- data/lib/t2-server/exceptions.rb +42 -21
- data/lib/t2-server/port.rb +472 -0
- data/lib/t2-server/run.rb +822 -227
- data/lib/t2-server/server.rb +313 -317
- data/lib/t2-server/util.rb +71 -0
- data/lib/t2-server/xml/libxml.rb +87 -0
- data/lib/t2-server/xml/nokogiri.rb +85 -0
- data/lib/t2-server/xml/rexml.rb +85 -0
- data/lib/t2-server/xml/xml.rb +111 -0
- data/lib/t2server.rb +4 -1
- data/t2-server.gemspec +112 -0
- data/test/tc_admin.rb +63 -0
- data/test/{tc_paths.rb → tc_params.rb} +11 -25
- data/test/tc_perms.rb +132 -0
- data/test/tc_run.rb +200 -67
- data/test/tc_secure.rb +191 -0
- data/test/tc_server.rb +25 -23
- data/test/tc_util.rb +74 -0
- data/test/ts_t2server.rb +57 -12
- data/test/workflows/always_fail.t2flow +69 -0
- data/test/workflows/list_and_value.t2flow +12 -0
- data/test/workflows/list_with_errors.t2flow +107 -0
- data/test/workflows/secure/basic-http.t2flow +74 -0
- data/test/workflows/secure/basic-https.t2flow +74 -0
- data/test/workflows/secure/client-https.t2flow +162 -0
- data/test/workflows/secure/digest-http.t2flow +129 -0
- data/test/workflows/secure/digest-https.t2flow +107 -0
- data/test/workflows/secure/heater-pk.pem +20 -0
- data/test/workflows/secure/user-cert.p12 +0 -0
- data/test/workflows/secure/ws-http.t2flow +180 -0
- data/test/workflows/secure/ws-https.t2flow +180 -0
- data/test/workflows/strings.txt +10 -0
- data/test/workflows/xml_xpath.t2flow +136 -136
- data/version.yml +4 -0
- metadata +132 -34
- data/lib/t2-server/xml.rb +0 -86
data/lib/t2-server/server.rb
CHANGED
@@ -1,4 +1,4 @@
|
|
1
|
-
# Copyright (c) 2010
|
1
|
+
# Copyright (c) 2010-2012 The University of Manchester, UK.
|
2
2
|
#
|
3
3
|
# All rights reserved.
|
4
4
|
#
|
@@ -14,7 +14,7 @@
|
|
14
14
|
#
|
15
15
|
# * Neither the names of The University of Manchester nor the names of its
|
16
16
|
# contributors may be used to endorse or promote products derived from this
|
17
|
-
# software without specific prior written permission.
|
17
|
+
# software without specific prior written permission.
|
18
18
|
#
|
19
19
|
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
|
20
20
|
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
|
@@ -30,459 +30,455 @@
|
|
30
30
|
#
|
31
31
|
# Author: Robert Haines
|
32
32
|
|
33
|
-
require 'rubygems'
|
34
33
|
require 'base64'
|
35
34
|
require 'uri'
|
36
|
-
require 'net/https'
|
37
|
-
require 'libxml'
|
38
35
|
|
39
36
|
module T2Server
|
40
37
|
|
41
38
|
# An interface for directly communicating with one or more Taverna 2 Server
|
42
39
|
# instances.
|
43
40
|
class Server
|
44
|
-
include
|
41
|
+
include XML::Methods
|
45
42
|
|
46
|
-
|
43
|
+
# The version of the remote Taverna Server instance.
|
44
|
+
attr_reader :version
|
47
45
|
|
48
|
-
# The URI of this server instance.
|
49
|
-
attr_reader :uri
|
50
|
-
|
51
|
-
# The maximum number of runs that this server will allow at any one time.
|
52
|
-
# Runs in any state (+Initialized+, +Running+ and +Finished+) are counted
|
53
|
-
# against this maximum.
|
54
|
-
attr_reader :run_limit
|
55
|
-
|
56
|
-
# list of servers we know about
|
57
|
-
@@servers = []
|
58
|
-
|
59
46
|
# :stopdoc:
|
60
|
-
|
61
|
-
|
62
|
-
|
63
|
-
|
64
|
-
|
65
|
-
|
66
|
-
|
67
|
-
|
68
|
-
|
69
|
-
|
70
|
-
|
71
|
-
|
72
|
-
|
73
|
-
|
74
|
-
|
75
|
-
@password = password
|
76
|
-
|
77
|
-
@http.use_ssl = true
|
78
|
-
@http.verify_mode = OpenSSL::SSL::VERIFY_NONE
|
79
|
-
end
|
80
|
-
|
81
|
-
# add a slash to the end of this address to work around this bug:
|
82
|
-
# http://www.mygrid.org.uk/dev/issues/browse/TAVSERV-113
|
83
|
-
@links = parse_description(get_attribute("#{@rest_path}/"))
|
84
|
-
#@links.each {|key, val| puts "#{key}: #{val}"}
|
85
|
-
|
86
|
-
# get max runs
|
87
|
-
@run_limit = get_attribute(@links[:runlimit]).to_i
|
88
|
-
|
89
|
-
# initialise run list
|
90
|
-
@runs = {}
|
91
|
-
@runs = get_runs
|
92
|
-
end
|
47
|
+
XPaths = {
|
48
|
+
# Server top-level XPath queries
|
49
|
+
:server => XML::Methods.xpath_compile("//nsr:serverDescription"),
|
50
|
+
:policy => XML::Methods.xpath_compile("//nsr:policy"),
|
51
|
+
:run => XML::Methods.xpath_compile("//nsr:run"),
|
52
|
+
:runs => XML::Methods.xpath_compile("//nsr:runs"),
|
53
|
+
|
54
|
+
# Server policy XPath queries
|
55
|
+
:runlimit => XML::Methods.xpath_compile("//nsr:runLimit"),
|
56
|
+
:permwkf => XML::Methods.xpath_compile("//nsr:permittedWorkflows"),
|
57
|
+
:permlstn => XML::Methods.xpath_compile("//nsr:permittedListeners"),
|
58
|
+
:permlstt => XML::Methods.xpath_compile("//nsr:permittedListenerTypes"),
|
59
|
+
:notify =>
|
60
|
+
XML::Methods.xpath_compile("//nsr:enabledNotificationFabrics")
|
61
|
+
}
|
93
62
|
# :startdoc:
|
94
63
|
|
95
64
|
# :call-seq:
|
96
|
-
#
|
65
|
+
# new(uri, connection_parameters = nil) -> Server
|
66
|
+
# new(uri, connection_parameters = nil) {|self| ...}
|
97
67
|
#
|
98
|
-
#
|
99
|
-
#
|
68
|
+
# Create a new Server instance that represents the real server at _uri_.
|
69
|
+
# If _connection_parameters_ are supplied they will be used to set up the
|
70
|
+
# network connection to the server.
|
100
71
|
#
|
101
|
-
#
|
102
|
-
|
103
|
-
def Server.connect(uri, username="", password="")
|
72
|
+
# It will _yield_ itself if a block is given.
|
73
|
+
def initialize(uri, params = nil)
|
104
74
|
# we want to use URIs here but strings can be passed in
|
105
|
-
|
106
|
-
uri = URI.parse(uri
|
75
|
+
unless uri.is_a? URI
|
76
|
+
uri = URI.parse(Util.strip_path_slashes(uri))
|
107
77
|
end
|
108
|
-
|
78
|
+
|
109
79
|
# strip username and password from the URI if present
|
110
|
-
|
111
|
-
|
112
|
-
new_uri = URI::HTTP.new(uri.scheme, nil, uri.host, uri.port, nil,
|
80
|
+
if uri.user != nil
|
81
|
+
uri = URI::HTTP.new(uri.scheme, nil, uri.host, uri.port, nil,
|
113
82
|
uri.path, nil, nil, nil);
|
114
|
-
|
115
|
-
# see if we've already got this server
|
116
|
-
server = @@servers.find {|s| s.uri == new_uri}
|
117
|
-
|
118
|
-
if !server
|
119
|
-
# no, so create new one and return it
|
120
|
-
server = new(new_uri, username, password)
|
121
|
-
@@servers << server
|
122
83
|
end
|
123
|
-
|
124
|
-
|
84
|
+
|
85
|
+
# setup connection
|
86
|
+
@connection = ConnectionFactory.connect(uri, params)
|
87
|
+
|
88
|
+
# add a slash to the end of this address to work around this bug:
|
89
|
+
# http://www.mygrid.org.uk/dev/issues/browse/TAVSERV-113
|
90
|
+
server_description = xml_document(get_attribute("#{uri.path}/rest/",
|
91
|
+
"application/xml"))
|
92
|
+
@version = get_version(server_description)
|
93
|
+
@links = get_description(server_description)
|
94
|
+
@links[:admin] = "#{uri.path}/admin"
|
95
|
+
|
96
|
+
# initialize run object cache
|
97
|
+
@runs = {}
|
98
|
+
|
99
|
+
yield(self) if block_given?
|
100
|
+
end
|
101
|
+
|
102
|
+
# :stopdoc:
|
103
|
+
def Server.connect(uri, username="", password="")
|
104
|
+
warn "[DEPRECATION] 'Server#connect' is deprecated and will be " +
|
105
|
+
"removed in 1.0."
|
106
|
+
new(uri)
|
107
|
+
end
|
108
|
+
# :startdoc:
|
109
|
+
|
110
|
+
# :call-seq:
|
111
|
+
# administrator(credentials = nil) -> Administrator
|
112
|
+
# administrator(credentials = nil) {|admin| ...}
|
113
|
+
#
|
114
|
+
# Return an instance of the Taverna Server administrator interface. This
|
115
|
+
# method will _yield_ the newly created administrator if a block is given.
|
116
|
+
def administrator(credentials = nil)
|
117
|
+
admin = Administrator.new(self, credentials)
|
118
|
+
|
119
|
+
yield(admin) if block_given?
|
120
|
+
admin
|
125
121
|
end
|
126
122
|
|
127
123
|
# :call-seq:
|
128
|
-
#
|
124
|
+
# create_run(workflow, credentials = nil) -> run
|
125
|
+
# create_run(workflow, credentials = nil) {|run| ...}
|
129
126
|
#
|
130
127
|
# Create a run on this server using the specified _workflow_.
|
131
|
-
|
132
|
-
|
133
|
-
|
128
|
+
# This method will _yield_ the newly created Run if a block is given.
|
129
|
+
def create_run(workflow, credentials = nil)
|
130
|
+
id = initialize_run(workflow, credentials)
|
131
|
+
run = Run.create(self, "", credentials, id)
|
132
|
+
|
133
|
+
# cache newly created run object - this must be done per user
|
134
|
+
user = credentials.nil? ? :all : credentials.username
|
135
|
+
@runs[user] = {} unless @runs[user]
|
136
|
+
@runs[user][id] = run
|
137
|
+
|
138
|
+
yield(run) if block_given?
|
139
|
+
run
|
134
140
|
end
|
135
141
|
|
136
142
|
# :call-seq:
|
137
|
-
#
|
143
|
+
# initialize_run(workflow, credentials = nil) -> string
|
138
144
|
#
|
139
145
|
# Create a run on this server using the specified _workflow_ but do not
|
140
|
-
# return it as a Run instance. Return its
|
141
|
-
def initialize_run(workflow)
|
142
|
-
|
143
|
-
|
144
|
-
|
145
|
-
|
146
|
-
|
147
|
-
|
148
|
-
response = @http.request(request, Fragments::WORKFLOW % workflow)
|
149
|
-
rescue InternalHTTPError => e
|
150
|
-
raise ConnectionError.new(e)
|
151
|
-
end
|
152
|
-
|
153
|
-
case response
|
154
|
-
when Net::HTTPCreated
|
155
|
-
# return the uuid of the newly created run
|
156
|
-
epr = URI.parse(response['location'])
|
157
|
-
epr.path[-36..-1]
|
158
|
-
when Net::HTTPForbidden
|
159
|
-
raise ServerAtCapacityError.new(@run_limit)
|
160
|
-
when Net::HTTPUnauthorized
|
161
|
-
raise AuthorizationError.new(@username)
|
162
|
-
else
|
163
|
-
raise UnexpectedServerResponse.new(response)
|
164
|
-
end
|
146
|
+
# return it as a Run instance. Return its identifier instead.
|
147
|
+
def initialize_run(workflow, credentials = nil)
|
148
|
+
# set up the run object cache - this must be done per user
|
149
|
+
user = credentials.nil? ? :all : credentials.username
|
150
|
+
@runs[user] = {} unless @runs[user]
|
151
|
+
|
152
|
+
@connection.POST_run("#{@links[:runs]}",
|
153
|
+
XML::Fragments::WORKFLOW % workflow, credentials)
|
165
154
|
end
|
166
155
|
|
167
156
|
# :call-seq:
|
168
|
-
#
|
157
|
+
# uri -> URI
|
169
158
|
#
|
170
|
-
#
|
171
|
-
def
|
172
|
-
@
|
159
|
+
# The URI of the connection to the remote Taverna Server.
|
160
|
+
def uri
|
161
|
+
@connection.uri
|
173
162
|
end
|
174
163
|
|
175
164
|
# :call-seq:
|
176
|
-
#
|
165
|
+
# run_limit(credentials = nil) -> num
|
166
|
+
#
|
167
|
+
# The maximum number of runs that this server will allow at any one time.
|
168
|
+
# Runs in any state (+Initialized+, +Running+ and +Finished+) are counted
|
169
|
+
# against this maximum.
|
170
|
+
def run_limit(credentials = nil)
|
171
|
+
get_attribute(@links[:runlimit], "text/plain", credentials).to_i
|
172
|
+
end
|
173
|
+
|
174
|
+
# :call-seq:
|
175
|
+
# runs(credentials = nil) -> [runs]
|
177
176
|
#
|
178
177
|
# Return the set of runs on this server.
|
179
|
-
def runs
|
180
|
-
get_runs.values
|
178
|
+
def runs(credentials = nil)
|
179
|
+
get_runs(credentials).values
|
181
180
|
end
|
182
181
|
|
183
182
|
# :call-seq:
|
184
|
-
#
|
183
|
+
# run(identifier, credentials = nil) -> run
|
185
184
|
#
|
186
185
|
# Return the specified run.
|
187
|
-
def run(
|
188
|
-
get_runs[
|
186
|
+
def run(identifier, credentials = nil)
|
187
|
+
get_runs(credentials)[identifier]
|
189
188
|
end
|
190
189
|
|
191
190
|
# :call-seq:
|
192
|
-
#
|
191
|
+
# delete_run(run, credentials = nil) -> bool
|
193
192
|
#
|
194
193
|
# Delete the specified run from the server, discarding all of its state.
|
195
|
-
# _run_ can be either a Run instance or a
|
196
|
-
def delete_run(run)
|
197
|
-
# get the
|
194
|
+
# _run_ can be either a Run instance or a identifier.
|
195
|
+
def delete_run(run, credentials = nil)
|
196
|
+
# get the identifier from the run if that is what is passed in
|
198
197
|
if run.instance_of? Run
|
199
|
-
run = run.
|
198
|
+
run = run.identifier
|
200
199
|
end
|
201
200
|
|
202
|
-
|
203
|
-
|
204
|
-
|
205
|
-
|
206
|
-
begin
|
207
|
-
response = @http.request(request)
|
208
|
-
rescue InternalHTTPError => e
|
209
|
-
raise ConnectionError.new(e)
|
210
|
-
end
|
211
|
-
|
212
|
-
case response
|
213
|
-
when Net::HTTPNoContent
|
214
|
-
# Success, carry on...
|
215
|
-
@runs.delete(run)
|
201
|
+
if delete_attribute("#{@links[:runs]}/#{run}", credentials)
|
202
|
+
# delete cached run object - this must be done per user
|
203
|
+
user = credentials.nil? ? :all : credentials.username
|
204
|
+
@runs[user].delete(run) if @runs[user]
|
216
205
|
true
|
217
|
-
when Net::HTTPNotFound
|
218
|
-
raise RunNotFoundError.new(run)
|
219
|
-
when Net::HTTPForbidden
|
220
|
-
raise AccessForbiddenError.new("run #{run}")
|
221
|
-
when Net::HTTPUnauthorized
|
222
|
-
raise AuthorizationError.new(@username)
|
223
|
-
else
|
224
|
-
raise UnexpectedServerResponse.new(response)
|
225
206
|
end
|
226
207
|
end
|
227
208
|
|
228
209
|
# :call-seq:
|
229
|
-
#
|
210
|
+
# delete_all_runs(credentials = nil)
|
230
211
|
#
|
231
212
|
# Delete all runs on this server, discarding all of their state.
|
232
|
-
def delete_all_runs
|
213
|
+
def delete_all_runs(credentials = nil)
|
233
214
|
# first refresh run list
|
234
|
-
runs.each {|run| run.delete}
|
215
|
+
runs(credentials).each {|run| run.delete}
|
235
216
|
end
|
236
217
|
|
237
|
-
# :
|
238
|
-
|
239
|
-
|
240
|
-
|
241
|
-
|
242
|
-
|
243
|
-
|
218
|
+
# :stopdoc:
|
219
|
+
def set_run_input(run, input, value, credentials = nil)
|
220
|
+
warn "[DEPRECATION] 'Server#set_run_input' is deprecated and will be " +
|
221
|
+
"removed in 1.0. Input ports are set directly instead. The most " +
|
222
|
+
"direct replacement for this method is: " +
|
223
|
+
"'Run#input_port(input).value = value'"
|
224
|
+
|
225
|
+
# get the run from the identifier if that is what is passed in
|
244
226
|
if not run.instance_of? Run
|
245
|
-
run = run(run)
|
227
|
+
run = run(run, credentials)
|
246
228
|
end
|
247
229
|
|
248
|
-
|
249
|
-
path = "#{@links[:runs]}/#{run.uuid}/#{run.inputs}/input/#{input}"
|
250
|
-
set_attribute(path, Fragments::RUNINPUTVALUE % xml_value, "application/xml")
|
251
|
-
rescue AttributeNotFoundError => e
|
252
|
-
if get_runs.has_key? run.uuid
|
253
|
-
raise e
|
254
|
-
else
|
255
|
-
raise RunNotFoundError.new(run.uuid)
|
256
|
-
end
|
230
|
+
run.input_port(input).value = value
|
257
231
|
end
|
258
232
|
|
259
|
-
|
260
|
-
|
261
|
-
|
262
|
-
|
263
|
-
|
264
|
-
|
265
|
-
# get the run from the
|
233
|
+
def set_run_input_file(run, input, filename, credentials = nil)
|
234
|
+
warn "[DEPRECATION] 'Server#set_run_input_file' is deprecated and " +
|
235
|
+
"will be removed in 1.0. Input ports are set directly instead. The " +
|
236
|
+
"most direct replacement for this method is: " +
|
237
|
+
"'Run#input_port(input).remote_file = filename'"
|
238
|
+
|
239
|
+
# get the run from the identifier if that is what is passed in
|
266
240
|
if not run.instance_of? Run
|
267
|
-
run = run(run)
|
241
|
+
run = run(run, credentials)
|
268
242
|
end
|
269
243
|
|
270
|
-
|
271
|
-
path = "#{@links[:runs]}/#{run.uuid}/#{run.inputs}/input/#{input}"
|
272
|
-
set_attribute(path, Fragments::RUNINPUTFILE % xml_value, "application/xml")
|
273
|
-
rescue AttributeNotFoundError => e
|
274
|
-
if get_runs.has_key? run.uuid
|
275
|
-
raise e
|
276
|
-
else
|
277
|
-
raise RunNotFoundError.new(run.uuid)
|
278
|
-
end
|
244
|
+
run.input_port(input).remote_file = filename
|
279
245
|
end
|
280
246
|
|
281
|
-
|
282
|
-
|
283
|
-
#
|
284
|
-
# Create a directory _dir_ within the directory _root_ on _run_. _run_ can
|
285
|
-
# be either a Run instance or a UUID. This is mainly for use by Run#mkdir.
|
286
|
-
def make_run_dir(run, root, dir)
|
287
|
-
# get the uuid from the run if that is what is passed in
|
247
|
+
def create_dir(run, root, dir, credentials = nil)
|
248
|
+
# get the identifier from the run if that is what is passed in
|
288
249
|
if run.instance_of? Run
|
289
|
-
run = run.
|
250
|
+
run = run.identifier
|
290
251
|
end
|
291
252
|
|
292
253
|
raise AccessForbiddenError.new("subdirectories (#{dir})") if dir.include? ?/
|
293
|
-
|
294
|
-
|
295
|
-
|
296
|
-
|
297
|
-
|
298
|
-
|
299
|
-
|
300
|
-
|
301
|
-
|
254
|
+
@connection.POST_dir("#{@links[:runs]}/#{run}/#{root}",
|
255
|
+
XML::Fragments::MKDIR % dir, run, dir, credentials)
|
256
|
+
end
|
257
|
+
|
258
|
+
def make_run_dir(run, root, dir, credentials = nil)
|
259
|
+
warn "[DEPRECATION] 'Server#make_run_dir' is deprecated and will be " +
|
260
|
+
"removed in 1.0. Please use 'Run#mkdir' instead."
|
261
|
+
|
262
|
+
create_dir(run, root, dir, credentials)
|
263
|
+
end
|
264
|
+
|
265
|
+
def upload_file(run, filename, location, rename, credentials = nil)
|
266
|
+
contents = IO.read(filename)
|
267
|
+
rename = filename.split('/')[-1] if rename == ""
|
268
|
+
|
269
|
+
if upload_data(run, contents, rename, location, credentials)
|
270
|
+
rename
|
302
271
|
end
|
272
|
+
end
|
303
273
|
|
304
|
-
|
305
|
-
|
306
|
-
|
307
|
-
|
308
|
-
when Net::HTTPNotFound
|
309
|
-
raise RunNotFoundError.new(run)
|
310
|
-
when Net::HTTPForbidden
|
311
|
-
raise AccessForbiddenError.new("#{dir} on run #{run}")
|
312
|
-
when Net::HTTPUnauthorized
|
313
|
-
raise AuthorizationError.new(@username)
|
314
|
-
else
|
315
|
-
raise UnexpectedServerResponse.new(response)
|
274
|
+
def upload_data(run, data, remote_name, location, credentials = nil)
|
275
|
+
# get the identifier from the run if that is what is passed in
|
276
|
+
if run.instance_of? Run
|
277
|
+
run = run.identifier
|
316
278
|
end
|
279
|
+
|
280
|
+
contents = Base64.encode64(data)
|
281
|
+
|
282
|
+
@connection.POST_file("#{@links[:runs]}/#{run}/#{location}",
|
283
|
+
XML::Fragments::UPLOAD % [remote_name, contents], run, credentials)
|
317
284
|
end
|
318
285
|
|
319
|
-
|
320
|
-
|
321
|
-
|
322
|
-
|
323
|
-
|
324
|
-
|
325
|
-
|
286
|
+
def upload_run_file(run, filename, location, rename, credentials = nil)
|
287
|
+
warn "[DEPRECATION] 'Server#upload_run_file' is deprecated and will " +
|
288
|
+
"be removed in 1.0. Please use 'Run#upload_file' or " +
|
289
|
+
"'Run#input_port(input).file = filename' instead."
|
290
|
+
|
291
|
+
upload_file(run, filename, location, rename, credentials)
|
292
|
+
end
|
293
|
+
|
294
|
+
def create_run_attribute(run, path, value, type, credentials = nil)
|
295
|
+
# get the identifier from the run if that is what is passed in
|
326
296
|
if run.instance_of? Run
|
327
|
-
run = run.
|
297
|
+
run = run.identifier
|
328
298
|
end
|
329
299
|
|
330
|
-
|
331
|
-
|
332
|
-
|
333
|
-
|
334
|
-
|
335
|
-
|
300
|
+
create_attribute("#{@links[:runs]}/#{run}/#{path}", value, type,
|
301
|
+
credentials)
|
302
|
+
rescue AttributeNotFoundError => e
|
303
|
+
if get_runs(credentials).has_key? run
|
304
|
+
raise e
|
305
|
+
else
|
306
|
+
raise RunNotFoundError.new(run)
|
336
307
|
end
|
337
|
-
|
338
|
-
|
339
|
-
|
340
|
-
|
308
|
+
end
|
309
|
+
|
310
|
+
def get_run_attribute(run, path, type, credentials = nil)
|
311
|
+
# get the identifier from the run if that is what is passed in
|
312
|
+
if run.instance_of? Run
|
313
|
+
run = run.identifier
|
341
314
|
end
|
342
315
|
|
343
|
-
|
344
|
-
|
345
|
-
|
346
|
-
|
347
|
-
when Net::HTTPNotFound
|
348
|
-
raise RunNotFoundError.new(run)
|
349
|
-
when Net::HTTPForbidden
|
350
|
-
raise AccessForbiddenError.new("run #{run}")
|
351
|
-
when Net::HTTPUnauthorized
|
352
|
-
raise AuthorizationError.new(@username)
|
316
|
+
get_attribute("#{@links[:runs]}/#{run}/#{path}", type, credentials)
|
317
|
+
rescue AttributeNotFoundError => e
|
318
|
+
if get_runs(credentials).has_key? run
|
319
|
+
raise e
|
353
320
|
else
|
354
|
-
raise
|
321
|
+
raise RunNotFoundError.new(run)
|
355
322
|
end
|
356
323
|
end
|
357
324
|
|
358
|
-
|
359
|
-
|
360
|
-
#
|
361
|
-
# Get the attribute at _path_ in _run_. _run_ can be either a Run instance
|
362
|
-
# or a UUID.
|
363
|
-
def get_run_attribute(run, path)
|
364
|
-
# get the uuid from the run if that is what is passed in
|
325
|
+
def set_run_attribute(run, path, value, type, credentials = nil)
|
326
|
+
# get the identifier from the run if that is what is passed in
|
365
327
|
if run.instance_of? Run
|
366
|
-
run = run.
|
328
|
+
run = run.identifier
|
367
329
|
end
|
368
330
|
|
369
|
-
|
331
|
+
set_attribute("#{@links[:runs]}/#{run}/#{path}", value, type,
|
332
|
+
credentials)
|
370
333
|
rescue AttributeNotFoundError => e
|
371
|
-
if get_runs.has_key? run
|
334
|
+
if get_runs(credentials).has_key? run
|
372
335
|
raise e
|
373
336
|
else
|
374
337
|
raise RunNotFoundError.new(run)
|
375
338
|
end
|
376
339
|
end
|
377
340
|
|
378
|
-
|
379
|
-
|
380
|
-
#
|
381
|
-
# Set the attribute at _path_ in _run_ to _value_. _run_ can be either a
|
382
|
-
# Run instance or a UUID.
|
383
|
-
def set_run_attribute(run, path, value)
|
384
|
-
# get the uuid from the run if that is what is passed in
|
341
|
+
def delete_run_attribute(run, path, credentials = nil)
|
342
|
+
# get the identifier from the run if that is what is passed in
|
385
343
|
if run.instance_of? Run
|
386
|
-
run = run.
|
344
|
+
run = run.identifier
|
387
345
|
end
|
388
346
|
|
389
|
-
|
347
|
+
delete_attribute("#{@links[:runs]}/#{run}/#{path}", credentials)
|
390
348
|
rescue AttributeNotFoundError => e
|
391
|
-
if get_runs.has_key? run
|
349
|
+
if get_runs(credentials).has_key? run
|
392
350
|
raise e
|
393
351
|
else
|
394
352
|
raise RunNotFoundError.new(run)
|
395
353
|
end
|
396
354
|
end
|
397
355
|
|
398
|
-
|
399
|
-
|
400
|
-
|
401
|
-
|
402
|
-
request.basic_auth @username, @password
|
403
|
-
end
|
404
|
-
begin
|
405
|
-
response = @http.request(request)
|
406
|
-
rescue InternalHTTPError => e
|
407
|
-
raise ConnectionError.new(e)
|
356
|
+
def download_run_file(run, path, range, credentials = nil)
|
357
|
+
# get the identifier from the run if that is what is passed in
|
358
|
+
if run.instance_of? Run
|
359
|
+
run = run.identifier
|
408
360
|
end
|
409
361
|
|
410
|
-
|
411
|
-
|
412
|
-
|
413
|
-
|
414
|
-
raise
|
415
|
-
when Net::HTTPForbidden
|
416
|
-
raise AccessForbiddenError.new("attribute #{path}")
|
417
|
-
when Net::HTTPUnauthorized
|
418
|
-
raise AuthorizationError.new(@username)
|
362
|
+
get_attribute("#{@links[:runs]}/#{run}/#{path}",
|
363
|
+
"application/octet-stream", range, credentials)
|
364
|
+
rescue AttributeNotFoundError => e
|
365
|
+
if get_runs(credentials).has_key? run
|
366
|
+
raise e
|
419
367
|
else
|
420
|
-
raise
|
368
|
+
raise RunNotFoundError.new(run)
|
421
369
|
end
|
422
370
|
end
|
423
371
|
|
424
|
-
def
|
425
|
-
|
426
|
-
|
427
|
-
|
428
|
-
|
372
|
+
def get_admin_attribute(path, credentials = nil)
|
373
|
+
get_attribute("#{@links[:admin]}/#{path}", "*/*", credentials)
|
374
|
+
end
|
375
|
+
|
376
|
+
def set_admin_attribute(path, value, credentials = nil)
|
377
|
+
set_attribute("#{@links[:admin]}/#{path}", value, "text/plain",
|
378
|
+
credentials)
|
379
|
+
end
|
380
|
+
|
381
|
+
def admin_resource_writable?(path, credentials = nil)
|
382
|
+
headers = @connection.OPTIONS("#{@links[:admin]}/#{path}", credentials)
|
383
|
+
headers["allow"][0].split(",").include? "PUT"
|
384
|
+
end
|
385
|
+
# :startdoc:
|
386
|
+
|
387
|
+
private
|
388
|
+
def create_attribute(path, value, type, credentials = nil)
|
389
|
+
@connection.POST(path, value, type, credentials)
|
390
|
+
end
|
391
|
+
|
392
|
+
def get_attribute(path, type, *rest)
|
393
|
+
credentials = nil
|
394
|
+
range = nil
|
395
|
+
|
396
|
+
rest.each do |param|
|
397
|
+
case param
|
398
|
+
when HttpCredentials
|
399
|
+
credentials = param
|
400
|
+
when Range
|
401
|
+
range = param
|
402
|
+
when Array
|
403
|
+
range = param[0]..param[1]
|
404
|
+
end
|
429
405
|
end
|
406
|
+
|
430
407
|
begin
|
431
|
-
|
432
|
-
rescue
|
433
|
-
|
408
|
+
@connection.GET(path, type, range, credentials)
|
409
|
+
rescue ConnectionRedirectError => cre
|
410
|
+
@connection = cre.redirect
|
411
|
+
retry
|
434
412
|
end
|
413
|
+
end
|
435
414
|
|
436
|
-
|
437
|
-
|
438
|
-
|
439
|
-
|
440
|
-
|
441
|
-
|
442
|
-
|
443
|
-
|
444
|
-
|
445
|
-
|
415
|
+
def set_attribute(path, value, type, credentials = nil)
|
416
|
+
@connection.PUT(path, value, type, credentials)
|
417
|
+
end
|
418
|
+
|
419
|
+
def delete_attribute(path, credentials = nil)
|
420
|
+
@connection.DELETE(path, credentials)
|
421
|
+
end
|
422
|
+
|
423
|
+
def get_version(doc)
|
424
|
+
version = xpath_attr(doc, XPaths[:server], "serverVersion")
|
425
|
+
if version == nil
|
426
|
+
raise RuntimeError.new("Taverna Servers prior to version 2.3 " +
|
427
|
+
"are no longer supported.")
|
446
428
|
else
|
447
|
-
|
429
|
+
return version.to_f
|
448
430
|
end
|
449
431
|
end
|
450
432
|
|
451
|
-
def
|
452
|
-
|
453
|
-
|
454
|
-
|
455
|
-
|
456
|
-
|
457
|
-
|
458
|
-
|
459
|
-
|
433
|
+
def get_description(doc)
|
434
|
+
links = {}
|
435
|
+
links[:runs] = URI.parse(xpath_attr(doc, XPaths[:runs], "href")).path
|
436
|
+
|
437
|
+
links[:policy] = URI.parse(xpath_attr(doc, XPaths[:policy], "href")).path
|
438
|
+
doc = xml_document(get_attribute(links[:policy], "application/xml"))
|
439
|
+
|
440
|
+
links[:permlisteners] =
|
441
|
+
URI.parse(xpath_attr(doc, XPaths[:permlstt], "href")).path
|
442
|
+
links[:notifications] =
|
443
|
+
URI.parse(xpath_attr(doc, XPaths[:notify], "href")).path
|
444
|
+
|
445
|
+
links[:runlimit] =
|
446
|
+
URI.parse(xpath_attr(doc, XPaths[:runlimit], "href")).path
|
447
|
+
links[:permworkflows] =
|
448
|
+
URI.parse(xpath_attr(doc, XPaths[:permwkf], "href")).path
|
449
|
+
|
450
|
+
links
|
460
451
|
end
|
461
452
|
|
462
|
-
def get_runs
|
463
|
-
run_list = get_attribute("#{@links[:runs]}"
|
453
|
+
def get_runs(credentials = nil)
|
454
|
+
run_list = get_attribute("#{@links[:runs]}", "application/xml",
|
455
|
+
credentials)
|
464
456
|
|
465
|
-
doc =
|
457
|
+
doc = xml_document(run_list)
|
466
458
|
|
467
|
-
# get list of run
|
468
|
-
|
469
|
-
doc
|
470
|
-
|
459
|
+
# get list of run identifiers
|
460
|
+
ids = []
|
461
|
+
xpath_find(doc, XPaths[:run]).each do |run|
|
462
|
+
ids << xml_node_attribute(run, "href").split('/')[-1]
|
471
463
|
end
|
472
464
|
|
465
|
+
# cache run objects - this must be done per user
|
466
|
+
user = credentials.nil? ? :all : credentials.username
|
467
|
+
@runs[user] = {} unless @runs[user]
|
468
|
+
|
473
469
|
# add new runs
|
474
|
-
|
475
|
-
if !@runs.has_key?
|
476
|
-
@runs[
|
470
|
+
ids.each do |id|
|
471
|
+
if !@runs[user].has_key? id
|
472
|
+
@runs[user][id] = Run.create(self, "", credentials, id)
|
477
473
|
end
|
478
474
|
end
|
479
475
|
|
480
476
|
# clear out the expired runs
|
481
|
-
if @runs.length >
|
482
|
-
@runs.delete_if {|key, val| !
|
477
|
+
if @runs[user].length > ids.length
|
478
|
+
@runs[user].delete_if {|key, val| !ids.member? key}
|
483
479
|
end
|
484
480
|
|
485
|
-
@runs
|
481
|
+
@runs[user]
|
486
482
|
end
|
487
|
-
end
|
483
|
+
end
|
488
484
|
end
|