1 /**
2 * \file appendAnnotation.cpp
3 * \brief adds annotation strings to a model and a species
4 * \author Akiya Jouraku
5 *
6 * <!--------------------------------------------------------------------------
7 * This sample program is distributed under a different license than the rest
8 * of libSBML. This program uses the open-source MIT license, as follows:
9 *
10 * Copyright (c) 2013-2018 by the California Institute of Technology
11 * (California, USA), the European Bioinformatics Institute (EMBL-EBI, UK)
12 * and the University of Heidelberg (Germany), with support from the National
13 * Institutes of Health (USA) under grant R01GM070923. All rights reserved.
14 *
15 * Permission is hereby granted, free of charge, to any person obtaining a
16 * copy of this software and associated documentation files (the "Software"),
17 * to deal in the Software without restriction, including without limitation
18 * the rights to use, copy, modify, merge, publish, distribute, sublicense,
19 * and/or sell copies of the Software, and to permit persons to whom the
20 * Software is furnished to do so, subject to the following conditions:
21 *
22 * The above copyright notice and this permission notice shall be included in
23 * all copies or substantial portions of the Software.
24 *
25 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
26 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
27 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
28 * THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
29 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
30 * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
31 * DEALINGS IN THE SOFTWARE.
32 *
33 * Neither the name of the California Institute of Technology (Caltech), nor
34 * of the European Bioinformatics Institute (EMBL-EBI), nor of the University
35 * of Heidelberg, nor the names of any contributors, may be used to endorse
36 * or promote products derived from this software without specific prior
37 * written permission.
38 * ------------------------------------------------------------------------ -->
39 */
40
41 #include <iostream>
42 #include <sbml/SBMLTypes.h>
43
44 #include <sbml/xml/XMLNode.h>
45 #include <sbml/annotation/CVTerm.h>
46 #include <sbml/annotation/ModelHistory.h>
47 using namespace std;
48 LIBSBML_CPP_NAMESPACE_USE
49
50 int
main(int argc,char * argv[])51 main (int argc, char *argv[])
52 {
53
54 SBMLDocument* d;
55 unsigned int errors;
56
57 if (argc != 3)
58 {
59 cout << endl
60 << " usage: appendAnnotation <input-filename> <output-filename>" << endl
61 << endl;
62 return 2;
63 }
64
65
66 d = readSBML(argv[1]);
67 errors = d->getNumErrors();
68
69 if (errors > 0)
70 {
71 cout << "Read Error(s):" << endl;
72 d->printErrors(cout);
73
74 cout << "Correct the above and re-run." << endl;
75 }
76 else
77 {
78 int n;
79 Species_t* s;
80
81 const string model_history_annotation =
82 "<annotation>\n"
83 " <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n"
84 " <rdf:Description rdf:about=\"#\">\n"
85 " <dc:creator rdf:parseType=\"Resource\">\n"
86 " <rdf:Bag>\n"
87 " <rdf:li rdf:parseType=\"Resource\">\n"
88 " <vCard:N rdf:parseType=\"Resource\">\n"
89 " <vCard:Family>Keating</vCard:Family>\n"
90 " <vCard:Given>Sarah</vCard:Given>\n"
91 " </vCard:N>\n"
92 " <vCard:EMAIL>sbml-team@caltech.edu</vCard:EMAIL>\n"
93 " <vCard:ORG>\n"
94 " <vCard:Orgname>University of Hertfordshire</vCard:Orgname>\n"
95 " </vCard:ORG>\n"
96 " </rdf:li>\n"
97 " </rdf:Bag>\n"
98 " </dc:creator>\n"
99 " <dcterms:created rdf:parseType=\"Resource\">\n"
100 " <dcterms:W3CDTF>1999-11-13T06:54:32Z</dcterms:W3CDTF>\n"
101 " </dcterms:created>\n"
102 " <dcterms:modified rdf:parseType=\"Resource\">\n"
103 " <dcterms:W3CDTF>2007-11-31T06:54:00-02:00</dcterms:W3CDTF>\n"
104 " </dcterms:modified>\n"
105 " </rdf:Description>\n"
106 " </rdf:RDF>\n"
107 "</annotation>\n";
108
109 d->getModel()->appendAnnotation(model_history_annotation);
110
111 /*
112 * The above code can be replaced by the following code.
113 *
114
115 ModelHistory * h = new ModelHistory();
116
117 ModelCreator *c = new ModelCreator();
118 c->setFamilyName("Keating");
119 c->setGivenName("Sarah");
120 c->setEmail("sbml-team@caltech.edu");
121 c->setOrganisation("University of Hertfordshire");
122
123 h->addCreator(c);
124
125 Date * date = new Date("1999-11-13T06:54:32");
126 Date * date2 = new Date("2007-11-31T06:54:00-02:00");
127
128 h->setCreatedDate(date);
129 h->setModifiedDate(date2);
130
131 d->getModel()->setModelHistory(h);
132
133 *
134 */
135
136
137 n = d->getModel()->getNumSpecies();
138
139 if (n > 0)
140 {
141 s = d->getModel()->getSpecies(0);
142
143 const string cvterms_annotation =
144 "<annotation>\n"
145 " <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n"
146 " <rdf:Description rdf:about=\"#\">\n"
147 " <bqbiol:isVersionOf>\n"
148 " <rdf:Bag>\n"
149 " <rdf:li rdf:resource=\"http://www.geneontology.org/#GO:0005892\"/>\n"
150 " <rdf:li rdf:resource=\"http://www.ebi.ac.uk/interpro/#IPR002394\"/>\n"
151 " </rdf:Bag>\n"
152 " </bqbiol:isVersionOf>\n"
153 " <bqbiol:is>\n"
154 " <rdf:Bag>\n"
155 " <rdf:li rdf:resource=\"http://www.geneontology.org/#GO:0005895\"/>\n"
156 " </rdf:Bag>\n"
157 " </bqbiol:is>\n"
158 " </rdf:Description>\n"
159 " </rdf:RDF>\n"
160 "</annotation>\n";
161
162 s->appendAnnotation(cvterms_annotation);
163
164 /*
165 * The above code can be replaced by the following code.
166 *
167
168 CVTerm *cv = new CVTerm();
169 cv->setQualifierType(BIOLOGICAL_QUALIFIER);
170 cv->setBiologicalQualifierType(BQB_IS_VERSION_OF);
171 cv->addResource("http://www.geneontology.org/#GO:0005892");
172
173 CVTerm *cv2 = new CVTerm();
174 cv2->setQualifierType(BIOLOGICAL_QUALIFIER);
175 cv2->setBiologicalQualifierType(BQB_IS);
176 cv2->addResource("http://www.geneontology.org/#GO:0005895");
177
178 CVTerm *cv1 = new CVTerm();
179 cv1->setQualifierType(BIOLOGICAL_QUALIFIER);
180 cv1->setBiologicalQualifierType(BQB_IS_VERSION_OF);
181 cv1->addResource("http://www.ebi.ac.uk/interpro/#IPR002394");
182
183 s->addCVTerm(cv);
184 s->addCVTerm(cv2);
185 s->addCVTerm(cv1);
186
187 *
188 */
189 }
190
191 writeSBML(d, argv[2]);
192 }
193
194 delete d;
195 return errors;
196 }
197
198
199