Examples of Reaction

Examples of it.freedomotic.reactions.Reaction

88
89
90
91
92
93
94
95
96
97
98
99
     */
    public Reaction resolve(Reaction r) {
        this.reaction = r;

        if ((context != null) && (reaction != null)) {
            Reaction clone =
                    new Reaction(reaction.getTrigger(),
                    performSubstitutionInCommands(reaction.getCommands()));

            return clone;
        }

View Full Code Here

Examples of it.freedomotic.reactions.Reaction

185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
                //Searching for reactions using this trigger
                boolean found = false;

                while (it.hasNext()) {
                    Reaction reaction = it.next();
                    Trigger reactionTrigger = reaction.getTrigger();

                    //found a related reaction. This must be executed
                    if (trigger.equals(reactionTrigger) && !reaction.getCommands().isEmpty()) {
                        if (!checkAdditionalConditions(reaction)) {
                            LOG.log(Level.INFO,
                                    "Additional conditions test failed in reaction {0}", reaction.toString());
                            return;
                        }
                        reactionTrigger.setExecuted();
                        found = true;
                        LOG.log(Level.FINE, "Try to execute reaction {0}", reaction.toString());

                        try {
                            //executes the commands in sequence (only the first sequence is used)
                            //if more then one sequence is needed it can be done with two reactions with the same trigger
                            Resolver commandResolver = new Resolver();
                            event.getPayload().addStatement("description",
                                    trigger.getDescription()); //embedd the trigger description to the event payload
                            commandResolver.addContext("event.",
                                    event.getPayload());

                            for (final Command command : reaction.getCommands()) {
                                if (command == null) {
                                    continue; //skip this loop
                                }

                                if (command.getReceiver()
                                        .equalsIgnoreCase(BehaviorManager.getMessagingChannel())) {
                                    //this command is for an object so it needs only to know only about event parameters
                                    Command resolvedCommand = commandResolver.resolve(command);
                                    //doing so we bypass messaging system gaining better performances
                                    BehaviorManager.parseCommand(resolvedCommand);
                                } else {
                                    //if the event has a target object we include also object info
                                    EnvObjectLogic targetObject =
                                            EnvObjectPersistence.getObjectByName(event.getProperty("object.name"));

                                    if (targetObject != null) {
                                        commandResolver.addContext("current.",
                                                targetObject.getExposedProperties());
                                        commandResolver.addContext("current.",
                                                targetObject.getExposedBehaviors());
                                    }

                                    final Command resolvedCommand = commandResolver.resolve(command);

                                    //it's not a user level command for objects (eg: turn it on), it is for another kind of actuator
                                    Command reply = busService.send(resolvedCommand); //blocking wait until executed

                                    if (reply == null) {
                                        LOG.log(Level.WARNING,
                                                "Unreceived reply within given time ({0}ms) for command {1}",
                                                new Object[]{command.getReplyTimeout(), command.getName()});
                                    } else {
                                        if (reply.isExecuted()) {
                                            LOG.log(Level.FINE, "Executed succesfully {0}", command.getName());
                                        } else {
                                            LOG.log(Level.WARNING, "Unable to execute command{0}", command.getName());
                                        }
                                    }
                                }
                            }
                        } catch (Exception e) {
                            LOG.severe("Exception while merging event parameters into reaction.\n");
                            LOG.severe(Freedomotic.getStackTraceInfo(e));

                            return;
                        }

                        String info =
                                "Executing automation '" + reaction.toString() + "' takes "
                                + (System.currentTimeMillis() - event.getCreation()) + "ms.";
                        LOG.info(info);

                        MessageEvent message = new MessageEvent(null, info);
                        message.setType("callout"); //display as callout on frontends
View Full Code Here

Examples of it.freedomotic.reactions.Reaction

49
50
51
52
53
54
55
56
    }

    public ReactionEditor(I18n i18n) {
        this.I18n = i18n;
        initComponents();
        this.reaction = new Reaction();
        init();
    }
View Full Code Here

Examples of it.freedomotic.reactions.Reaction

78
79
80
81
82
83
84
85
86
87
88
                }

                if (!found) { //add an empty reaction if none
                    pos = panel.getComponentCount();

                    ReactionEditor editor = new ReactionEditor(I18n, new Reaction(trigger),
                            this);
                    panel.add(editor, pos++);
                }

                panel.add(new JSeparator(),
View Full Code Here

Examples of it.freedomotic.reactions.Reaction

127
128
129
130
131
132
133
134
135
136
137
                        }
                    }

                    if (!alreadyStored) { //add an empty reaction if none

                        ReactionEditor editor = new ReactionEditor(I18n, new Reaction(trigger),
                                this);
                        panel.add(editor);
                    }
                }
            }
View Full Code Here

Examples of it.freedomotic.reactions.Reaction

140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
    }

    private String manageMessage(String mess) {
        Command c;
        Trigger t = null;
        Reaction r;
        NaturalLanguageProcessor nlp2 = new NaturalLanguageProcessor();
        //  String sentenceMess[] = nlp.getSentenceDetector().sentDetect(mess);
        String tokenMess[] = mess.split(" "); //nlp.getTokenizer().tokenize(sentenceMess[0]);
        String triggername = "";
        int conditionSep = 0;
        if (tokenMess[0].equalsIgnoreCase(HELP)) {
            return help(tokenMess);
        }
        if (tokenMess[0].equalsIgnoreCase(LIST)) {
            return list(tokenMess);
        }

        if (tokenMess[0].equalsIgnoreCase(IF) || tokenMess[0].equalsIgnoreCase(WHEN)) {
            for (int i = 1; i < tokenMess.length; i++) {
                if (tokenMess[i].equalsIgnoreCase(THEN)) {
                    triggername = unsplit(tokenMess, 1, i - 1, " ");
                    conditionSep = i + 1;
                    break;
                }
            }
            t = TriggerPersistence.getTrigger(triggername);
        }

        String commandName = unsplit(tokenMess, conditionSep, tokenMess.length - conditionSep, " ");
        List<NaturalLanguageProcessor.Rank> mostSimilar = nlp2.getMostSimilarCommand(commandName, 10);
        // user is asking for help
        if (commandName.contains("*")) {
            String response = "";
            for (NaturalLanguageProcessor.Rank nlpr : mostSimilar) {
                response += "? " + nlpr.getCommand().getName() + "\n";
            }
            return response;
        }
        if (!mostSimilar.isEmpty() && mostSimilar.get(0).getSimilarity() > 0) {
            c = mostSimilar.get(0).getCommand();
        } else {
            return "No available commands similar to: " + commandName;
        }
        if (tokenMess[0].equalsIgnoreCase(IF)) {
            Trigger NEWt = t.clone();
            NEWt.setNumberOfExecutions(1);
            r = new Reaction(NEWt, c);
            ReactionPersistence.add(r);
        } else if (tokenMess[0].equalsIgnoreCase(WHEN)) {
            // do something
            r = new Reaction(t, c);
            ReactionPersistence.add(r);
        } else {
            send(c);
            return c.getName() + "\n DONE.";
        }
View Full Code Here

Examples of org.sbml.jsbml.Reaction

65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
    Species s1 = m.createSpecies("s1", "species1", c);
    Species s2 = m.createSpecies("s2", "species2", c);
    Species s3 = m.createSpecies("s3", "species3", c);
    Species s4 = m.createSpecies("s4", "species4", c);
   
    Reaction r1 = m.createReaction("r1");
    r1.setName("reaction1");
    r1.setCompartment(c);
    SpeciesReference sr1 = r1.createReactant("sr1", s1);
    sr1.setName("reactant1");
    sr1.setStoichiometry(1d);
    SpeciesReference sr2 = r1.createProduct("sr2", s2);
    sr2.setName("product1");
    sr2.setStoichiometry(1d);
    ModifierSpeciesReference msr1 = r1.createModifier("msr1", s3);
    msr1.setName("modifier");
   
    Reaction r2 = m.createReaction("r2");
    r2.setName("reaction2");
    r2.setCompartment(c);
    SpeciesReference sr3 = r2.createReactant("sr3", s1);
    sr3.setName("reactant2");
    sr3.setStoichiometry(2d);
    SpeciesReference sr4 = r2.createProduct("sr4", s4);
    sr4.setName("product2");
    sr4.setStoichiometry(1d);
    ModifierSpeciesReference msr2 = r2.createModifier("msr2", s3);
    msr2.setName("modifier");
   
    SBMLWriter.write(doc, System.out, ' ', (short) 2);
    System.out.println('\n');
  }
View Full Code Here

Examples of org.sbml.jsbml.Reaction

125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
    Model m = doc.getModel();
    List<TreeNode> list = new LinkedList<TreeNode>();
    list.add(doc);
    list.add(m);
    list.add(m.getListOfReactions());
    Reaction r1 = m.getReaction(0);
    list.add(r1);
    list.add(r1.getListOfModifiers());
    list.add(r1.getModifier(0));
    Reaction r2 = m.getReaction(1);
    list.add(r2);
    list.add(r2.getListOfModifiers());
    list.add(r2.getModifier(0));
    List<? extends TreeNode> result = doc.filter(filter, true);
    System.out.println("filter result retain internals without pruning:\n  " + result);
    assertTrue(result.equals(list));
  }
View Full Code Here

Examples of org.sbml.jsbml.Reaction

148
149
150
151
152
153
154
155
156
157
158
159
160
    Model m = doc.getModel();
    List<TreeNode> list = new LinkedList<TreeNode>();
    list.add(doc);
    list.add(m);
    list.add(m.getListOfReactions());
    Reaction r1 = m.getReaction(0);
    list.add(r1);
    list.add(r1.getListOfModifiers());
    list.add(r1.getModifier(0));
    List<? extends TreeNode> result = doc.filter(filter, true, true);
    System.out.println("filter result retain internals with pruning:\n  " + result);
    assertTrue(result.equals(list));
  }
View Full Code Here

Examples of org.sbml.jsbml.Reaction

83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
    SBMLDocument d;
    Model m;
    Compartment c;
    KineticLaw kl;
    LocalParameter p;
    Reaction r;
    Species s;
    SpeciesReference sr;
    UnitDefinition ud;
    String filename = DATA_FOLDER + "/libsbml-test-data/l1v1-branch.xml";
    d = new SBMLReader().readSBML(filename);
    if (d == null)
      ;
    {
    }
    assertTrue(d.getLevel() == 1);
    assertTrue(d.getVersion() == 1);
    m = d.getModel();
    assertTrue(m.getName().equals("Branch"));
    assertTrue(m.getCompartmentCount() == 1);
    c = m.getCompartment(0);
    assertTrue(c.getName().equals("compartmentOne"));
    assertTrue(c.getVolume() == 1);
    ud = c.getDerivedUnitDefinition();
    assertTrue(ud.getUnitCount() == 1);

    // assertTrue(ud.getUnit(0).getKind() == Unit.Kind.LITRE); // getDerivedUnitDefinition not working properly
    assertTrue(m.getSpeciesCount() == 4);
    s = m.getSpecies(0);
    assertTrue(s.getName().equals("S1"));
    assertTrue(s.getCompartment().equals("compartmentOne"));
    assertTrue(s.getInitialAmount() == 0);
    assertTrue(s.getBoundaryCondition() == false);

    //    ud = s.getDerivedUnitDefinition(); // getDerivedUnitDefinition not working properly
//    assertTrue(ud.getUnitCount() == 2);
//    assertTrue(ud.getUnit(0).getKind() == Unit.Kind.MOLE);
//    assertTrue(ud.getUnit(0).getExponent() == 1);
//    assertTrue(ud.getUnit(1).getKind() == Unit.Kind.LITRE);
//    assertTrue(ud.getUnit(1).getExponent() == -1);
   
    s = m.getSpecies(1);
    assertTrue(s.getName().equals("X0"));
    assertTrue(s.getCompartment().equals("compartmentOne"));
    assertTrue(s.getInitialAmount() == 0);
    assertTrue(s.getBoundaryCondition() == true);
    s = m.getSpecies(2);
    assertTrue(s.getName().equals("X1"));
    assertTrue(s.getCompartment().equals("compartmentOne"));
    assertTrue(s.getInitialAmount() == 0);
    assertTrue(s.getBoundaryCondition() == true);
    s = m.getSpecies(3);
    assertTrue(s.getName().equals("X2"));
    assertTrue(s.getCompartment().equals("compartmentOne"));
    assertTrue(s.getInitialAmount() == 0);
    assertTrue(s.getBoundaryCondition() == true);
    assertTrue(m.getReactionCount() == 3);
    r = m.getReaction(0);
    assertTrue(r.getName().equals("reaction_1"));
    assertTrue(r.getReversible() == false);
    assertTrue(r.getFast() == false);
    ud = r.getKineticLaw().getDerivedUnitDefinition();

    //    assertTrue(ud.getUnitCount() == 2);
//    assertTrue(ud.getUnit(0).getKind() == Unit.Kind.MOLE);
//    assertTrue(ud.getUnit(0).getExponent() == 1);
//    assertTrue(ud.getUnit(1).getKind() == Unit.Kind.LITRE);
//    assertTrue(ud.getUnit(1).getExponent() == -1);
   
    assertTrue(r.getKineticLaw().containsUndeclaredUnits() == true);
    r = m.getReaction(1);
    assertTrue(r.getName().equals("reaction_2"));
    assertTrue(r.getReversible() == false);
    assertTrue(r.getFast() == false);
    r = m.getReaction(2);
    assertTrue(r.getName().equals("reaction_3"));
    assertTrue(r.getReversible() == false);
    assertTrue(r.getFast() == false);
    r = m.getReaction(0);
    assertTrue(r.getReactantCount() == 1);
    assertTrue(r.getProductCount() == 1);
    sr = r.getReactant(0);
    assertTrue(sr.getSpecies().equals("X0"));
    assertTrue(sr.getStoichiometry() == 1);
    assertTrue(sr.getDenominator() == 1);
    sr = r.getProduct(0);
    assertTrue(sr.getSpecies().equals("S1"));
    assertTrue(sr.getStoichiometry() == 1);
    assertTrue(sr.getDenominator() == 1);
    kl = r.getKineticLaw();
    assertTrue(kl.getFormula().equals("k1*X0")); // We are not putting the same space in the formula
    assertTrue(kl.getLocalParameterCount() == 1);
    p = kl.getParameter(0);
    assertTrue(p.getName().equals("k1"));
    assertTrue(p.getValue() == 0);
    r = m.getReaction(1);
    assertTrue(r.getReactantCount() == 1);
    assertTrue(r.getProductCount() == 1);
    sr = r.getReactant(0);
    assertTrue(sr.getSpecies().equals("S1"));
    assertTrue(sr.getStoichiometry() == 1);
    assertTrue(sr.getDenominator() == 1);
    sr = r.getProduct(0);
    assertTrue(sr.getSpecies().equals("X1"));
    assertTrue(sr.getStoichiometry() == 1);
    assertTrue(sr.getDenominator() == 1);
    kl = r.getKineticLaw();
    assertTrue(kl.getFormula().equals("k2*S1")); // equals("k2 * S1")
    assertTrue(kl.getLocalParameterCount() == 1);
    p = kl.getParameter(0);
    assertTrue(p.getName().equals("k2"));
    assertTrue(p.getValue() == 0);
    r = m.getReaction(2);
    assertTrue(r.getReactantCount() == 1);
    assertTrue(r.getProductCount() == 1);
    sr = r.getReactant(0);
    assertTrue(sr.getSpecies().equals("S1"));
    assertTrue(sr.getStoichiometry() == 1);
    assertTrue(sr.getDenominator() == 1);
    sr = r.getProduct(0);
    assertTrue(sr.getSpecies().equals("X2"));
    assertTrue(sr.getStoichiometry() == 1);
    assertTrue(sr.getDenominator() == 1);
    kl = r.getKineticLaw();
    assertTrue(kl.getFormula().equals("k3*S1")); // equals("k3 * S1")
    assertTrue(kl.getLocalParameterCount() == 1);
    p = kl.getParameter(0);
    assertTrue(p.getName().equals("k3"));
    assertTrue(p.getValue() == 0);
View Full Code Here
TOP
Copyright © 2018 www.massapi.com. All rights reserved.
All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.