Changeset 3491

Timestamp:

09/09/10 16:45:43 (17 months ago)

Author:

erikroos

Message:

• Corrected date parsing error in loader
• Began work on report 5

Location:

molgenis_projects/molgenis4phenotype/handwritten/java/plugin

Files:

• fillanimaldb/LoadAnimalDB.java (modified) (1 diff)
• yearlyreportplugin/VWAReport4.java (modified) (4 diffs)
• yearlyreportplugin/VWAReport5.java (modified) (3 diffs)

molgenis_projects/molgenis4phenotype/handwritten/java/plugin/fillanimaldb/LoadAnimalDB.java

@@ -583 +583 @@
                                 ct.MarkGroup(invid, decappid, actorid, now, "DecApplication");
                                 
-                                SimpleDateFormat sdf = new SimpleDateFormat("d-M-yyyy", Locale.US);
+                                SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd", Locale.US);
                                 //applicationstartdate -> time
                                 String appStartDateString = tuple.getString("applicationstartdate");

molgenis_projects/molgenis4phenotype/handwritten/java/plugin/yearlyreportplugin/VWAReport4.java

@@ -218 +218 @@
                                                 if (endstatus.equals("B. Gedood na beeindiging van de proef") || endstatus.equals("C. Na einde proef in leven gelaten")) col13 = true;
                                         }
+                                        
+                                        // TODO: handle 'afgevoerde' animals! (col 14-17)
                                 }
                                 
@@ -442 +444 @@
                 for (int col = 1; col <= nrCol; col++) {
                         output += "<th";
-                        if (col == 10 || col == 17) output += " style='border-right-width:2'";
+                        if (col == 2 || col == 10 || col == 17) output += " style='border-right-width:2'";
                         output += (">" + col + "</th>");
                 }
@@ -448 +450 @@
                 output += "<tr>";
                 output += "<td>Codenummer/diersoort en/of naam</td>";
-                output += "<td>aanwezig op 1 jan. " + year + "</td>";
+                output += "<td style='border-right-width:2'>aanwezig op 1 jan. " + year + "</td>";
                 output += "<td>eigen fok</td>";
                 output += "<td>organisatorische eenheid RuG</td>";
@@ -470 +472 @@
                         for (int col = 1; col <= nrCol; col++) {
                                 output += "<td";
-                                if (col == 10 || col == 17) output += " style='border-right-width:2'";
+                                if (col == 2 || col == 10 || col == 17) output += " style='border-right-width:2'";
                                 output += (">" + matrix[idx][col - 1] + "</td>");
                         }

molgenis_projects/molgenis4phenotype/handwritten/java/plugin/yearlyreportplugin/VWAReport5.java

@@ -1 +1 @@
 package plugin.yearlyreportplugin;
 
+import java.text.SimpleDateFormat;
+import java.util.ArrayList;
+import java.util.Date;
 import java.util.List;
+import java.util.Locale;
 
 import org.molgenis.framework.db.Database;
+import org.molgenis.framework.db.Query;
+import org.molgenis.framework.db.QueryRule;
+import org.molgenis.framework.db.QueryRule.Operator;
 
 import commontasks.CommonTasks;
 
 import pheno.target.ObservationTarget;
+import pheno.value.ObservedValue;
 
 public class VWAReport5 extends AnimalDBReport {
+        
+        private int nrCol = 17;
+        private List<String[]> matrix = new ArrayList<String[]>();
+        List<String> expSpecList = new ArrayList<String>();
+        private int year;
         
         public VWAReport5(Database db) {
@@ -20 +33 @@
         public void makeReport(int year, String type) {
                 try {
-                        //
+                        this.year = year;
+                        SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd", Locale.US);
+                        Date startOfYear = sdf.parse(year + "-01-01");
+                        Date endOfYear = sdf.parse((year + 1) + "-01-01");
+                        
+                        List<ObservationTarget> decappList = ct.GetAllMarkedGroups("DecApplication");
+                        for (ObservationTarget d : decappList) {
+                                // Check if the DEC application was (partly) in this year
+                                int featid = ct.GetObservableFeatureId("DecNr");
+                                Query q = db.query(ObservedValue.class);
+                                q.addRules(new QueryRule("observationTarget", Operator.EQUALS, d.getId()));
+                                q.addRules(new QueryRule("observableFeature", Operator.EQUALS, featid));
+                                List<ObservedValue> valueList = q.find();
+                                if (valueList.size() > 0) {
+                                        String decNr = valueList.get(0).getValue();
+                                        Date startOfDec = valueList.get(0).getTime();
+                                        Date endOfDec = valueList.get(0).getEndtime();
+                                        if (startOfDec.after(endOfYear) || endOfDec.before(startOfYear)) {
+                                                continue;
+                                        }
+                                        // Find the experiments belonging to this DEC
+                                        featid = ct.GetObservableFeatureId("DecApplication");
+                                        q = db.query(ObservedValue.class);
+                                        q.addRules(new QueryRule("relatedObservationTarget", Operator.EQUALS, d.getId()));
+                                        q.addRules(new QueryRule("observableFeature", Operator.EQUALS, featid));
+                                        valueList = q.find();
+                                        for (ObservedValue v : valueList) {
+                                                int expid = v.getObservationTarget();
+                                                ObservationTarget exp = ct.GetObservationTargetById(expid);
+                                                
+                                                // Get the experiment subcode
+                                                String expCode = "";
+                                                featid = ct.GetObservableFeatureId("ExperimentNr");
+                                                q = db.query(ObservedValue.class);
+                                                q.addRules(new QueryRule("observationTarget", Operator.EQUALS, expid));
+                                                q.addRules(new QueryRule("observableFeature", Operator.EQUALS, featid));
+                                                valueList = q.find();
+                                                if (valueList.size() > 0) {
+                                                        expCode = valueList.get(0).getValue();
+                                                }
+                                                
+                                                // Get the animals that are/were in the experiment
+                                                featid = ct.GetObservableFeatureId("Experiment");
+                                                q = db.query(ObservedValue.class);
+                                                q.addRules(new QueryRule("relatedObservationTarget", Operator.EQUALS, expid));
+                                                q.addRules(new QueryRule("observableFeature", Operator.EQUALS, featid));
+                                                valueList = q.find();
+                                                for (ObservedValue v2 : valueList) {
+                                                        Date entryDate = v2.getTime();
+                                                        Date exitDate = v2.getEndtime();
+                                                        // Check dates
+                                                        if (entryDate.after(endOfYear) || exitDate.before(startOfYear)) {
+                                                                continue;
+                                                        }
+                                                        // Get the data about the animal in the experiment
+                                                        // TODO: find out prot.app.ID so we find the right values
+                                                        // Bijzonderheid dier (animal's AnimalType)
+                                                        // Diersoort (animal's Species)
+                                                        // Herkomst en hergebruik (animal's Source, except for reuse!)
+                                                        // Aantal dieren (count later on!)
+                                                        // Doel vd proef (experiment's Goal)
+                                                        // Belang van de proef (experiment's Concern)
+                                                        // Wettelijke bepalingen (experiment's LawDef)
+                                                        // Toxicologisch / veiligheidsonderzoek (experiment's ToxRes)
+                                                        // Technieken byzondere (experiment's SpecialTechn)
+                                                        // Anesthesie (animal's Anaesthesia)
+                                                        // Pijnbestrijding, postoperatief (animal's PainManagement)
+                                                        // Ongerief (animal's ActualDiscomfort)
+                                                        // Toestand dier na beeindiging proef (animal's ActualAnimalEndStatus)
+                                                        
+                                                        // TODO: if the above values are exactly the same as an earlier row, aggregate them
+                                                        
+                                                        String[] newRow = new String[nrCol];
+                                                        newRow[0] = decNr + expCode + " - " + d.getName();
+                                                        newRow[1] = endOfDec.toString();
+                                                        newRow[15] = decNr + expCode;
+                                                        matrix.add(newRow);
+                                                }
+                                        }
+                                }
+                        }
                 } catch (Exception e) {
                         e.printStackTrace();
@@ -28 +121 @@
         @Override
         public String toString() {
-                return "<br /><br /><strong>VWAReport5</strong>";
+                String output = "<br /><p><strong>JAARSTAAT DIERPROEVEN registratiejaar " + year + " - Registratieformulier 5</strong></p>";
+                output += "<br /><table border='1' cellpadding='5' cellspacing='5'>";
+                output += "<tr>";
+                output += "<th></th>";
+                output += "<th></th>";
+                for (int col = 1; col < 15; col++) {
+                        output += ("<th>" + col + "</th>");
+                }
+                output += "<th></th>";
+                output += "</tr>";
+                output += "<tr>";
+                output += "<td>DEC-nr.</td>";
+                output += "<td>DEC verlopen op</td>";
+                output += "<td>Bijzonderheid dier</td>";
+                output += "<td>Diersoort</td>";
+                output += "<td>Herkomst en hergebruik</td>";
+                output += "<td>Aantal dieren</td>";
+                output += "<td>Doel vd proef</td>";
+                output += "<td>Belang van de proef</td>";
+                output += "<td>Wettelijke bepalingen</td>";
+                output += "<td>Toxicologisch / veiligheidsonderzoek</td>";
+                output += "<td>Bijzondere technieken</td>";
+                output += "<td>Anesthesie</td>";
+                output += "<td>Pijnbestrijding, postoperatief</td>";
+                output += "<td>Ongerief</td>";
+                output += "<td>Toestand dier na beeindiging proef</td>";
+                output += "<td>DEC-nummer / Onderzoeksprotocol</td>";
+                output += "<td>Naam (wetenschappelijke naam)</td>";
+                output += "</tr>";
+                for (String [] currentRow : matrix) {
+                        output += "<tr>";
+                        for (int col = 0; col < nrCol; col++) {
+                                output += ("<td>" + currentRow[col] + "</td>");
+                        }
+                        output += "</tr>";
+                }
+                output += "</table>";
+                return output;
         }
 }