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1 : disz 1.1
2 :     package ACHserver;
3 :    
4 : olson 1.4 #
5 :     # This is a SAS Component
6 :     #
7 : parrello 1.7 use strict;
8 :     use LWP::UserAgent;
9 :     use YAML;
10 :     use ErrorMessage;
11 :     no warnings qw(once);
12 : disz 1.1
13 : parrello 1.6 =head1 Annotation Clearinghouse Server Helper Object
14 :    
15 :     =head2 Description
16 :    
17 :     This module is used to call the Annotation Clearinghouse Server, which is a
18 :     special-purpose server for assertion data from the Sapling database. Each
19 :     Annotation Clearinghouse Server function corresponds to a method of this object.
20 :    
21 :     This package deliberately uses no internal SEED packages or scripts, only common
22 :     PERL modules.
23 :    
24 :     The fields in this object are as follows.
25 :    
26 :     =over 4
27 :    
28 :     =item server_url
29 :    
30 :     The URL used to request data from the subsystem server.
31 :    
32 :     =item ua
33 :    
34 :     The user agent for communication with the server.
35 :    
36 :     =item singleton
37 :    
38 :     Indicates whether or not results are to be returned in singleton mode. In
39 :     singleton mode, if the return document is a hash reference with only one
40 :     entry, the entry value is returned rather than the hash.
41 :    
42 :     =back
43 :    
44 :     =cut
45 :    
46 :     =head3 new
47 :    
48 : parrello 1.7 my $ss = ACHserver->new(%options);
49 : parrello 1.6
50 : parrello 1.7 Construct a new server object. The
51 :     following options are supported.
52 : parrello 1.6
53 :     =over 4
54 :    
55 :     =item url
56 : disz 1.1
57 : parrello 1.7 URL for the server. This option is required.
58 : disz 1.5
59 : parrello 1.7 =item singleton (optional)
60 : disz 1.5
61 : parrello 1.6 If TRUE, results from methods will be returned in singleton mode. In singleton
62 :     mode, if a single result comes back, it will come back as a scalar rather than
63 :     as a hash value accessible via an incoming ID.
64 : disz 1.1
65 : parrello 1.6 =back
66 : olson 1.3
67 : parrello 1.6 =cut
68 : disz 1.1
69 : parrello 1.6 sub new {
70 :     # Get the parameters.
71 :     my ($class, %options) = @_;
72 : parrello 1.7 # Turn off YAML compression, which causes problems with our hash keys.
73 :     $YAML::CompressSeries = 0;
74 : parrello 1.6 # Get the options.
75 : parrello 1.8 my $url = $options{url} || "http://servers.nmpdr.org/ach/server.cgi";
76 : parrello 1.6 my $singleton = $options{singleton} || 0;
77 : parrello 1.7 # Create the fields of the object. Note that if we're in localhost mode,
78 :     # the user agent is actually a SAP object.
79 : parrello 1.6 my $server_url = $url;
80 : parrello 1.7 my $ua;
81 :     if ($server_url ne 'localhost') {
82 :     require LWP::UserAgent;
83 :     $ua = LWP::UserAgent->new();
84 : olson 1.9 $ua->timeout(20 * 60);
85 : parrello 1.7 } else {
86 :     require "ACH.pm";
87 :     $ua = ACH->new();
88 :     }
89 :     # Create the server object.
90 : parrello 1.6 my $retVal = {
91 :     server_url => $server_url,
92 :     ua => $ua,
93 :     singleton => $singleton,
94 :     };
95 : parrello 1.7 # Bless it.
96 : parrello 1.6 bless $retVal, $class;
97 : parrello 1.7 # Get the list of permitted methods from the server.
98 :     my $methodList = $retVal->_call_method(methods => []);
99 :     # Convert it to a hash and store it in this object.
100 :     $retVal->{methodHash} = { map { $_ => 1 } @$methodList };
101 :     # Return the object.
102 : parrello 1.6 return $retVal;
103 : disz 1.1 }
104 :    
105 : parrello 1.6 =head3 AUTOLOAD
106 : disz 1.1
107 : parrello 1.7 my $result = $server->method(%args);
108 : disz 1.1
109 : parrello 1.6 Call a function on the server. Any method call on this object (other than
110 :     the constructor) is translated into a request against the server. This
111 :     enables us to add new server functions without requiring an update to this
112 : parrello 1.7 object or its parent. The parameters are usually specified as a hash, and the
113 :     result is a scalar or object reference. In some cases the parameters are a list.
114 :     To deistinguish between the two cases, all hash keys must begin with hyphens.
115 :    
116 :     If an error occurs, we will throw an exception.
117 : parrello 1.6
118 :     =cut
119 :    
120 :     # This variable will contain the method name.
121 :     our $AUTOLOAD;
122 :    
123 :     sub AUTOLOAD {
124 :     # Get the parameters. We do some fancy dancing to allow the user to pass
125 : parrello 1.7 # in a hash, a list, a list reference, or a hash reference.
126 : parrello 1.6 my $self = shift @_;
127 :     my $args = $_[0];
128 :     if (defined $args) {
129 :     if (scalar @_ gt 1) {
130 :     # Here we have multiple arguments. We check the first one for a
131 :     # leading hyphen.
132 :     if ($args =~ /^-/) {
133 :     # This means we have hash-form parameters.
134 :     my %args = @_;
135 :     $args = \%args;
136 :     } else {
137 :     # This means we have list-form parameters.
138 :     my @args = @_;
139 :     $args = \@args;
140 :     }
141 :     } else {
142 :     # Here we have a single argument. If it's a scalar, we convert it
143 :     # to a singleton list.
144 :     if (! ref $args) {
145 :     $args = [$args];
146 : disz 1.5 }
147 : parrello 1.6 }
148 :     }
149 :     # Declare the return variable.
150 :     my $retVal;
151 :     # Get the method name.
152 :     my $function = $AUTOLOAD;
153 :     # Strip off the stuff before the method name.
154 :     $function =~ s/.+:://;
155 : parrello 1.7 # Validate the method name.
156 :     if (! $self->{methodHash}{$function}) {
157 :     die "Method \"$function\" not supported.";
158 : parrello 1.6 } else {
159 : parrello 1.7 # Call the method.
160 :     $retVal = $self->_call_method($function, $args);
161 :     # We have our result. Adjust for singleton mode.
162 :     if ($self->{singleton} && ref $retVal eq 'HASH' && scalar(keys %$retVal) <= 1) {
163 :     # Here we're in singleton mode and we got a single result,
164 :     # so we dereference a bit to make it easier for the user
165 :     # to access it.
166 :     ($retVal) = values %$retVal;
167 : parrello 1.6 }
168 :     }
169 :     # Return the result.
170 :     return $retVal;
171 : disz 1.5 }
172 :    
173 : parrello 1.6 =head3 DESTROY
174 :    
175 :     $ss->DESTROY();
176 : disz 1.1
177 : parrello 1.6 This method has no function. It's purpose is to keep the destructor from
178 :     being caught by the autoload processing.
179 : disz 1.1
180 : parrello 1.6 =cut
181 : disz 1.1
182 : parrello 1.6 sub DESTROY { }
183 : disz 1.1
184 : parrello 1.7 =head2 Utility Methods
185 :    
186 :     =head3 _call_method
187 :    
188 :     my $result = $server->_call_method($method, $args);
189 :    
190 :     Call the specified method on the server with the specified arguments and
191 :     return the result. The arguments must already be packaged as a hash or
192 :     list reference. This method is the heart of the AUTOLOAD method, and is
193 :     provided as a utility for specialized methods that can't use the AUTOLOAD
194 :     facility.
195 :    
196 :     =over 4
197 :    
198 :     =item method
199 :    
200 :     Name of the server function being invoked.
201 :    
202 :     =item args
203 :    
204 :     Argument object to pass to the function.
205 :    
206 :     =item RETURN
207 :    
208 :     Returns a hash or list reference with the function results.
209 :    
210 :     =back
211 :    
212 :     =cut
213 :    
214 :     sub _call_method {
215 :     # Get the parameters.
216 :     my ($self, $method, $args) = @_;
217 :     # Declare the return variable.
218 :     my $retVal;
219 :     # Get our user agent.
220 :     my $ua = $self->{ua};
221 :     # Determine the type.
222 :     if (ref $ua eq 'LWP::UserAgent') {
223 :     # Here we're going to a server. Compute the argument document.
224 :     my $argString = YAML::Dump($args);
225 :     # Request the function from the server.
226 :     my $content = $self->_send_request(function => $method, args => $argString,
227 :     source => __PACKAGE__);
228 :     $retVal = YAML::Load($content);
229 :     } else {
230 :     # Here we're calling a local method.
231 :     $retVal = eval("\$ua->$method(\$args)");
232 :     # Check for an error.
233 :     if ($@) {
234 :     die "Package error: $@";
235 :     }
236 :     }
237 :     # Return the result.
238 :     return $retVal;
239 :     }
240 :    
241 :     =head3 _send_request
242 :    
243 :     my $result = $server->_send_request(%parms);
244 :    
245 :     Send a request to the server. This method must not be called in localhost
246 :     mode. If an error occurs, this method will die; otherwise, the content of
247 :     the response will be passed back as the result.
248 :    
249 :     =over 4
250 :    
251 :     =item parms
252 :    
253 :     Hash of CGI parameters to send to the server.
254 :    
255 :     =item RETURN
256 :    
257 :     Returns the string returned by the server in response to the request.
258 :    
259 :     =back
260 :    
261 :     =cut
262 :    
263 :     sub _send_request {
264 :     # Get the parameters.
265 :     my ($self, %parms) = @_;
266 :     # Get the user agent.
267 :     my $ua = $self->{ua};
268 :     # Request the function from the server. Note that the hash is actually passed
269 :     # as a list reference.
270 : olson 1.10
271 :     #
272 :     # retries is the set of retry wait times in seconds we should use. when
273 :     # we run out the call will fail.
274 :     #
275 :    
276 :     my @retries = (1, 2, 5, 10, 20, 60, 60, 60, 60, 60, 60);
277 :     my %codes_to_retry = map { $_ => 1 } qw(110 408 502 503 504 200) ;
278 :    
279 :     while (1)
280 :     {
281 :     my $response = $ua->post($self->{server_url}, [ %parms ]);
282 :    
283 :     if ($response->is_success)
284 :     {
285 :     my $retVal = $response->content;
286 :     return $retVal;
287 :     }
288 :    
289 :     #
290 :     # If this is not one of the error codes we retry for, or if we
291 :     # are out of retries, fail immediately
292 :     #
293 :     my $code = $response->code;
294 :     if (!$codes_to_retry{$code} || @retries == 0)
295 :     {
296 :     die ErrorMessage->new($response->content, $response->status_line);
297 :     }
298 :    
299 :     #
300 :     # otherwise, sleep & loop.
301 :     #
302 :     my $retry_time = shift(@retries);
303 :     print STDERR "Request failed with code=$code, sleeping $retry_time and retrying\n";
304 :     sleep($retry_time);
305 :    
306 : parrello 1.7 }
307 : olson 1.10
308 :     #
309 :     # Should never get here.
310 :     #
311 : parrello 1.7 }
312 :    
313 : disz 1.1
314 : parrello 1.6 1;

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