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comparison lib/golm_ws_api.pm @ 0:e3d43b8c987b draft

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Init repository with last tool-bank-golm-lib_search master version
author fgiacomoni
date Mon, 05 Dec 2016 08:32:04 -0500
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children 11779b6402bc
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-1:000000000000 0:e3d43b8c987b
1 package lib::golm_ws_api ;
2
3 use strict;
4 use warnings ;
5 use Exporter ;
6 use Carp ;
7
8 use Data::Dumper ;
9 #use SOAP::Lite +trace => [qw (debug)];
10 use SOAP::Lite ;
11 use JSON ;
12
13 use vars qw($VERSION @ISA @EXPORT %EXPORT_TAGS);
14
15 our $VERSION = "1.0";
16 our @ISA = qw(Exporter);
17 our @EXPORT = qw( connectWSlibrarySearchGolm LibrarySearch test_query_golm filter_scores_golm_results filter_replica_results);
18 our %EXPORT_TAGS = ( ALL => [qw( connectWSlibrarySearchGolm LibrarySearch test_query_golm filter_scores_golm_results filter_replica_results)] );
19
20 =head1 NAME
21
22 My::Module - An example module
23
24 =head1 SYNOPSIS
25
26 use My::Module;
27 my $object = My::Module->new();
28 print $object->as_string;
29
30 =head1 DESCRIPTION
31
32 This module does not really exist, it
33 was made for the sole purpose of
34 demonstrating how POD works.
35
36 =head1 METHODS
37
38 Methods are :
39
40 =head2 METHOD new
41
42 ## Description : new
43 ## Input : $self
44 ## Ouput : bless $self ;
45 ## Usage : new() ;
46
47 =cut
48
49 sub new {
50 ## Variables
51 my $self={};
52 bless($self) ;
53 return $self ;
54 }
55 ### END of SUB
56
57 =head2 METHOD connectWSlibrarySearchGolm
58
59 ## Description : create a soap object throught the webservice LibrarySearch of Golm.
60 ## Input : $ws_url, $ws_proxy
61 ## Ouput : $soap ;
62 ## Usage : my $soap = connectWSlibrarySearchGolm($ws_url, $ws_proxy) ;
63
64 =cut
65
66 sub connectWSlibrarySearchGolm() {
67 ## Retrieve Values
68 my $self = shift ;
69 my ($ws_url, $ws_proxy) = @_ ;
70
71 my $osoap = SOAP::Lite
72 -> soapversion('1.2')
73 -> envprefix('soap12')
74 -> readable(1)
75 -> uri( $ws_url )
76 -> proxy( $ws_proxy."/" )
77 -> on_fault(sub { my($soap, $res) = @_;
78 eval { die ref $res ? $res->faultstring : $soap->transport->status, "\n"};
79 return ref $res ? $res : new SOAP::SOM ;
80 });
81
82 return ($osoap);
83 }
84 ### END of SUB
85
86
87
88
89
90 =head2 METHOD test_query_golm
91
92 ## Description : send a test request (default given on ws website) to golm database.
93 ## Input : $ws_url, $ws_proxy
94 ## Ouput : $soap ;
95 ## Usage : my $soap = test_query_golm($ws_url, $ws_proxy) ;
96
97 =cut
98
99 sub test_query_golm() {
100 ## Retrieve Values
101 my $self = shift ;
102 my ($ws_url, $ws_proxy) = @_ ;
103
104 my $soap = SOAP::Lite
105 -> uri($ws_url)
106 -> on_action( sub { join '/', $ws_proxy, $_[1] } )
107 -> proxy($ws_proxy, timeout => 500);
108
109 # Setting Content-Type myself
110 my $http_request = $soap
111 ->{'_transport'}
112 ->{'_proxy'}
113 ->{'_http_request'};
114 $http_request->content_type("text/xml; charset=utf-8");
115
116 my $method = SOAP::Data->name('LibrarySearch')
117 ->attr({xmlns => $ws_proxy."/"});
118
119 my @params = (
120 SOAP::Data->name('ri' => 1898),
121 SOAP::Data->name('riWindow' => 5),
122 SOAP::Data->name('AlkaneRetentionIndexGcColumnComposition' => 'VAR5'),
123 SOAP::Data->name('spectrum' => "70 3 71 3 72 16 73 999 74 87 75 78 76 4 77 5 81 1 82 6 83 13 84 4 85 3 86 4 87 5 88 4 89 52 90 4 91 2 97 2 98 1 99 4 100 12 101 16 102 9 103 116 104 11 105 26 106 2 107 1 111 1 112 1 113 4 114 11 115 7 116 5 117 93 118 9 119 8 126 1 127 3 128 3 129 101 130 19 131 25 132 4 133 60 134 8 135 4 140 1 141 1 142 4 143 13 144 2 145 6 146 1 147 276 148 44 149 27 150 3 151 1 156 1 157 70 158 12 159 5 160 148 161 26 162 7 163 8 164 1 168 1 169 2 170 1 172 3 173 4 174 1 175 4 177 4 186 2 187 1 189 28 190 7 191 13 192 2 193 1 201 5 202 1 203 3 204 23 205 162 206 31 207 16 208 2 210 2 214 1 215 2 216 8 217 88 218 18 219 8 220 1 221 6 222 1 229 23 230 6 231 11 232 3 233 4 234 3 235 1 243 1 244 2 245 1 246 2 247 1 256 1 262 3 263 1 269 2 270 1 274 4 275 1 277 4 278 1 291 7 292 2 293 1 300 1 305 4 306 1 307 4 308 1 318 1 319 122 320 37 321 17 322 3 323 1 343 1 364 2 365 1" ) );
124
125 my $som = $soap->call($method => @params);
126 die $som->faultstring if ($som->fault);
127
128 ## Get the hits + status of the query
129 my $results = $som->result->{Results} ;
130 my $status = $som->result->{Status} ;
131
132 if ($status eq 'success' && $results ne '') {
133 print "\n\n\nThe test request succeeded - Golm Service available.\n\n\n" ;
134 return 1 ;
135 }
136 else { croak "\n\n\nSomething went wrong with the test request. Status delivered by Golm = ".$status."\n\n" ; }
137 }
138 ### END of SUB
139
140
141
142 =head2 METHOD LibrarySearch
143
144 ## Description : Matches a single user submitted GC-EI mass spectrum against the Golm Metabolome Database (GMD).
145 ##  A limited amount of hits can be kept according to the maxHits value and after them being filtered by $filter value
146 ## Input : $osoap, $ri, $riWindow, $gcColumn, $spectrum, $maxHits
147 ## Ouput : \@limited_hits, \@json_res
148 ## Usage : ($limited_hits,$json_res) = LibrarySearch($osoap, $ri, $riWindow, $gcColumn, $spectrum, $maxHits) ;
149
150 =cut
151
152 sub LibrarySearch() {
153 ## Retrieve Values
154 my $self = shift ;
155 my ($ri, $riWindow, $gcColumn, $spectrum, $maxHits,$JaccardDistanceThreshold,$s12GowerLegendreDistanceThreshold,$DotproductDistanceThreshold,
156 $HammingDistanceThreshold,$EuclideanDistanceThreshold, $ws_url, $ws_proxy, $default_ri, $default_ri_window, $default_gc_column) = @_ ;
157
158 #init in case :
159 $ri = $default_ri if ( !defined $ri ) ;
160 $riWindow = $default_ri_window if ( !defined $riWindow ) ;
161 $gcColumn = $default_gc_column if ( !defined $gcColumn ) ;
162
163
164 my $result ;
165 my @filtered_limited_res = () ;
166 my @json_res ;
167
168 if ( defined $spectrum ){
169
170 if ( $spectrum ne '' ) {
171
172 my $soap = SOAP::Lite
173 -> uri($ws_url)
174 -> on_action( sub { join '/', $ws_proxy, $_[1] } )
175 -> proxy($ws_proxy);
176
177 # Setting Content-Type myself
178 my $http_request = $soap
179 ->{'_transport'}
180 ->{'_proxy'}
181 ->{'_http_request'};
182 $http_request->content_type("text/xml; charset=utf-8");
183
184 my $method = SOAP::Data->name('LibrarySearch')
185 ->attr({xmlns => $ws_proxy."/"});
186
187 my @params = (
188 SOAP::Data->name('ri' => $ri),
189 SOAP::Data->name('riWindow' => $riWindow),
190 SOAP::Data->name('AlkaneRetentionIndexGcColumnComposition' => $gcColumn),
191 SOAP::Data->name('spectrum' => $spectrum) ) ;
192
193 my $som = $soap->call($method => @params);
194 die $som->faultstring if ($som->fault);
195
196 ## Get the hits + status of the query
197 my $results = $som->result->{Results} ;
198 my $status = $som->result->{Status} ;
199
200 ## Limitate number of hits returned according to user's $maxHit
201 ## and filter hits on specific values with thresholds
202 my @results = @$results ;
203
204 ### Return all hits
205 my $oapi = lib::golm_ws_api->new() ;
206 if ($maxHits == 100 && $status eq 'success') {
207
208 my $filtered_res = $oapi->filter_scores_golm_results(\@results,$JaccardDistanceThreshold,$s12GowerLegendreDistanceThreshold,
209 $DotproductDistanceThreshold,$HammingDistanceThreshold,$EuclideanDistanceThreshold) ;
210
211 if(!@$filtered_res){ push (@$filtered_res , "no results") ; }
212
213 return ($filtered_res) ;
214 }
215 elsif ($maxHits < 100 && $maxHits > 0 && $status eq 'success'){
216
217 my $filtered_res_before_hits_limited = $oapi->filter_scores_golm_results(\@results,$JaccardDistanceThreshold,$s12GowerLegendreDistanceThreshold,
218 $DotproductDistanceThreshold,$HammingDistanceThreshold,$EuclideanDistanceThreshold) ;
219 if (@$filtered_res_before_hits_limited) {
220
221 for (my $i=0 ; $i<$maxHits ; $i++) {
222
223 push (@filtered_limited_res , @$filtered_res_before_hits_limited[$i]) ;
224 }
225 }
226 else {
227
228 if(!@$filtered_res_before_hits_limited){ push (@filtered_limited_res , "no results") ; }
229 }
230 return (\@filtered_limited_res) ;
231 }
232 else { carp "No match returned from Golm for the query.\n" }
233 }
234 else { carp "The spectrum for query is empty, Golm soap will stop.\n" ; }
235 }
236 else { carp "The spectrum for query is undef, Golm soap will stop.\n" ; }
237
238 return \@filtered_limited_res ;
239 }
240 ### END of SUB
241
242
243
244
245 =head2 METHOD filter_scores_golm_results
246 ## Description : filter golm's hits by distance scores
247 ## Input : $results,$JaccardDistanceThreshold,$s12GowerLegendreDistanceThreshold,
248 ## $DotproductDistanceThreshold,$HammingDistanceThreshold,$EuclideanDistanceThreshold
249 ## Ouput : \@filtered_res ;
250 ## Usage : my ($filtered_res) = filter_scores_golm_results($results,$JaccardDistanceThreshold,$s12GowerLegendreDistanceThreshold,
251 ## $DotproductDistanceThreshold,$HammingDistanceThreshold,$EuclideanDistanceThreshold) ;
252
253 =cut
254
255 sub filter_scores_golm_results() {
256 ## Retrieve Values
257 my $self = shift ;
258 my ($results,$JaccardDistanceThreshold,$s12GowerLegendreDistanceThreshold,
259 $DotproductDistanceThreshold,$HammingDistanceThreshold,$EuclideanDistanceThreshold) = @_ ;
260
261 my @results = @$results ;
262 my @filtered_res = () ;
263
264 foreach my $res (@results){
265
266 if ($res->{'JaccardDistance'} <= $JaccardDistanceThreshold && $res->{'s12GowerLegendreDistance'} <= $s12GowerLegendreDistanceThreshold
267 && $res->{'DotproductDistance' } <= $DotproductDistanceThreshold && $res->{'HammingDistance'} <= $HammingDistanceThreshold &&
268 $res->{'EuclideanDistance' } <= $EuclideanDistanceThreshold) {
269
270 push (@filtered_res , $res) ;
271 }
272 }
273
274 my $oapi = lib::golm_ws_api->new() ;
275 my $sorted_analytes = $oapi->filter_replica_results(\@filtered_res) ;
276
277 return $sorted_analytes ;
278 }
279
280
281
282 =head2 METHOD _filter_replica_results
283 ## Description : remove replicated hits, keep the ones with the lowest dot product distance
284 ## Input : $results
285 ## Ouput : \@clean_res ;
286 ## Usage : my ($clean_res) = filter_replica_results($results) ;
287
288 =cut
289
290 sub filter_replica_results() {
291 ## Retrieve Values
292 my $self = shift ;
293 my ($results) = @_ ;
294 my %seen ;
295 my @sortAnalytes = grep { !$seen{$_->{'analyteName'}}++ } sort { $a->{'DotproductDistance'} <=> $b->{'DotproductDistance'} } @$results ;
296
297 return \@sortAnalytes ;
298 }
299
300
301
302
303
304 1 ;
305
306
307 __END__
308
309 =head1 SUPPORT
310
311 You can find documentation for this module with the perldoc command.
312
313 perldoc golm_ws_api.pm
314
315 =head1 Exports
316
317 =over 4
318
319 =item :ALL is connectWSlibrarySearchGolm LibrarySearch test_query_golm filter_scores_golm_results filter_replica_results
320
321 =back
322
323 =head1 AUTHOR
324
325 Franck Giacomoni E<lt>franck.giacomoni@clermont.inra.frE<gt>
326 Gabriel Cretin E<lt>gabriel.cretin@clermont.inra.frE<gt>
327
328 =head1 LICENSE
329
330 This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
331
332 =head1 VERSION
333
334 version 1 : 03 / 06 / 2016
335
336 version 2 : 24 / 06 / 2016
337
338 =cut