Merge branch 'servlets'

Conflicts:
	datadb/compbio/cassandra/StructureProteinPrediction.java
	server/compbio/statistic/CassandraRequester.java

diff --git a/WEB-INF/web.xml b/WEB-INF/web.xml
index 3f4654f..1c53caf 100644 (file)
--- a/WEB-INF/web.xml
+++ b/WEB-INF/web.xml
@@ -47,11 +47,33 @@
                <servlet-name>ServletDeleteRecord</servlet-name>\r
                <servlet-class>compbio.listeners.ServletDeleteRecord</servlet-class>\r
        </servlet>\r
+       <servlet>\r
+               <description>\r
+               </description>\r
+               <display-name>ServletByJobSequence</display-name>\r
+               <servlet-name>ServletByJobSequence</servlet-name>\r
+               <servlet-class>compbio.listeners.ServletByJobSequence</servlet-class>\r
+       </servlet>\r
+       <servlet>\r
+               <description>\r
+               </description>\r
+               <display-name>ServletJobsByDay</display-name>\r
+               <servlet-name>ServletJobsByDay</servlet-name>\r
+               <servlet-class>compbio.listeners.ServletJobsByDay</servlet-class>\r
+       </servlet>\r
 \r
        <servlet-mapping>\r
                <servlet-name>ServletDeleteRecord</servlet-name>\r
                <url-pattern>/ServletDeleteRecord</url-pattern>\r
        </servlet-mapping>\r
+       <servlet-mapping>\r
+               <servlet-name>ServletByJobSequence</servlet-name>\r
+               <url-pattern>/ServletByJobSequence</url-pattern>\r
+       </servlet-mapping>\r
+       <servlet-mapping>\r
+               <servlet-name>ServletJobsByDay</servlet-name>\r
+               <url-pattern>/ServletJobsByDay</url-pattern>\r
+       </servlet-mapping>\r
 \r
 \r
 \r

diff --git a/conf/Proteocache.properties b/conf/Proteocache.properties
index a376e8c..5ab8858 100644 (file)
--- a/conf/Proteocache.properties
+++ b/conf/Proteocache.properties
@@ -3,7 +3,7 @@
 # test server is 10.0.115.190
 #cassandra.host=localhost
 #cassandra.host=10.31.0.97
-cassandra.host=gjb-www-1.cluster.lifesci.dundee.ac.uk
+cassandra.host=localhost
 
 cassandra.newtables.update=false
 

diff --git a/datadb/compbio/cassandra/CassandraReader.java b/datadb/compbio/cassandra/CassandraReader.java
index 28641db..6e3587b 100644 (file)
--- a/datadb/compbio/cassandra/CassandraReader.java
+++ b/datadb/compbio/cassandra/CassandraReader.java
@@ -51,6 +51,30 @@ public class CassandraReader {
        }
 
        /*
+        * getting data from the db
+        */
+       public List<Pair<String, String>> ReadProteinData(long day) {
+               final long startTime = System.currentTimeMillis();
+               String com = "SELECT JobID, Protein FROM ProteinData WHERE jobtime = " + day + ";";
+               System.out.println("Command: " + com);
+               ResultSet results = session.execute(com);
+               if (results.isExhausted())
+                       return null;
+               final long queryTime = System.currentTimeMillis();
+               List<Row> rows = results.all();
+               System.out.println("Query time is " + (queryTime - startTime) + " msec");
+               List<Pair<String, String>> res = new ArrayList<Pair<String, String>>();
+               int c = 0;
+               for (Row r : rows) {
+                       Pair<String, String> pair = new Pair<String, String>(r.getString("JobID"), r.getString("Protein"));
+                       res.add(pair);
+                       ++c;
+               }
+               final long endTime = System.currentTimeMillis();
+               System.out.println(c + " rows analysed, execution time is " + (endTime - startTime) + " msec");
+               return res;
+       }
+       /*
         * getting data from the db JobDateInfo
         */
        public List<Long> ReadDateTable(long queryDate) {
@@ -89,6 +113,10 @@ public class CassandraReader {
                for (Row r : rows) {
                        AnnotatedProteinSequenceBean structure = new AnnotatedProteinSequenceBean(queryProtein, r.getString("JobID"), r.getMap(
                                        "Predictions", String.class, String.class));
+                       if (structure.getPrediction().containsKey("jnetpred"))
+                               structure.setJnetpred(structure.getPrediction().get("jnetpred"));
+                       else
+                               structure.setJnetpred("");
                        res.add(structure);
                        ++c;
                }
@@ -157,7 +185,7 @@ public class CassandraReader {
        }
 
        /*
-        * getting protein sequences by counter
+        * getting log info for jobid
         */
        public StructureJobLog ReadJobLog(String jobid) {
                final long startTime = System.currentTimeMillis();

diff --git a/datadb/compbio/cassandra/StructureProteinPrediction.java b/datadb/compbio/cassandra/StructureProteinPrediction.java
new file mode 100644 (file)
index 0000000..0e392bf
--- /dev/null
+++ b/datadb/compbio/cassandra/StructureProteinPrediction.java
@@ -0,0 +1,38 @@
+package compbio.cassandra;
+
+import java.util.Map;
+
+public class StructureProteinPrediction {
+       private String sequence;
+       private String jobid;
+       private String jnetpred;
+       private Map<String,String> prediction;
+       
+       public StructureProteinPrediction (String seq, String id, Map<String,String> pred) {
+               this.sequence = seq;
+               this.jobid = id;
+               this.prediction = pred;
+       }
+       
+       
+       public void setJnetpred (String jnetpred) {
+               this.jnetpred = jnetpred;
+       }
+       
+       public String getJnetpred () {
+               return jnetpred;
+       }
+       
+       public String getSequence () {
+               return sequence;
+       }
+       
+       public String getJobid () {
+               return jobid;
+       }
+       
+       public Map<String,String> getPrediction () {
+               return prediction;
+       }
+
+}

diff --git a/server/compbio/statistic/CassandraRequester.java b/server/compbio/statistic/CassandraRequester.java
index 214bf6f..410a722 100755 (executable)
--- a/server/compbio/statistic/CassandraRequester.java
+++ b/server/compbio/statistic/CassandraRequester.java
@@ -21,6 +21,8 @@ public class CassandraRequester {
        private ArrayList<DataBase> query;
        private static long currentDate = 0;
        private static long earlestDate = 0;
+       private final static SimpleDateFormat formatYYMMDD = new SimpleDateFormat("yyyy/MM/dd");
+       private final static SimpleDateFormat formatDDMMYY = new SimpleDateFormat("dd/MM/yyyy");
 
        /*
         * query: execution time for the period from date1 till date2
@@ -32,14 +34,14 @@ public class CassandraRequester {
                if (null == date2) {
                        date1 = "2100/1/1";
                }
-               if (!isThisDateValid(date1) || !isThisDateValid(date2)) {
+               if (!isThisDateValid(date1,formatYYMMDD) || !isThisDateValid(date2,formatYYMMDD)) {
                        System.out.println("Wrong date: point 3");
                        return null;
                }
                SetDateRange();
                int nbins = 5;
-               long dateStart = DateParsing(date1);
-               long dateEnd = DateParsing(date2);
+               long dateStart = DateParsing(date1, formatYYMMDD);
+               long dateEnd = DateParsing(date2, formatYYMMDD);
                if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd)
                        return null;
                if (dateStart < earlestDate)
@@ -121,13 +123,13 @@ public class CassandraRequester {
                if (null == date2) {
                        date1 = "2100/1/1";
                }
-               if (!isThisDateValid(date1) || !isThisDateValid(date2)) {
+               if (!isThisDateValid(date1, formatYYMMDD) || !isThisDateValid(date2, formatYYMMDD)) {
                        System.out.println("Wrong date: point 3");
                        return null;
                }
                SetDateRange();
-               long dateStart = DateParsing(date1);
-               long dateEnd = DateParsing(date2);
+               long dateStart = DateParsing(date1, formatYYMMDD);
+               long dateEnd = DateParsing(date2, formatYYMMDD);
                if (dateEnd < earlestDate || dateStart > currentDate || dateStart > dateEnd)
                        return null;
                if (dateStart < earlestDate)
@@ -161,12 +163,15 @@ public class CassandraRequester {
         * query: protein sequence
         * */
        public List<DataBase> readProteins(String protIn, String flag) {
+               if (protIn == null)
+                       return null;
+               System.out.println(protIn.length());
                query = new ArrayList<DataBase>();
                List<AnnotatedProteinSequenceBean> res;
                if (flag.equals("whole")) 
                        res = db.ReadWholeSequence(protIn);
                 else 
-                       res = db.ReadPartOfSequence(protIn);
+                        res = (protIn.length() > 0) ? db.ReadPartOfSequence(protIn) : null;
                if (res == null)
                        return null;
                for (AnnotatedProteinSequenceBean entry : res) {
@@ -203,13 +208,16 @@ public class CassandraRequester {
         * query jobs log info
         */
        public DataBase readJobLog(String jobid) {
-       //      query = new ArrayList<DataBase>();
+               if (jobid == null)
+                       return null;
                StructureJobLog res = db.ReadJobLog(jobid);
+               if (res == null)
+                       return null;
                DataBase query = new DataBase();
                query.setLogInfo(res);
-       //      query.setres);
                return query;
        }
+       
        /*
         * create list of parts of protein sequence;
         */
@@ -230,12 +238,12 @@ public class CassandraRequester {
        /*
         * convert String date into long date (miliseconds since the epoch start)
         */
-       private static long DateParsing(String datInput) {
+       private static long DateParsing(String datInput, SimpleDateFormat formatter) {
                if (datInput == null) {
                        return 0;
                }
                long dateWorkSt = 0;
-               SimpleDateFormat formatter = new SimpleDateFormat("yyyy/MM/dd");
+               
                try {
                        dateWorkSt = formatter.parse(datInput).getTime();
                } catch (ParseException e) {
@@ -256,7 +264,7 @@ public class CassandraRequester {
         */
        private static void SetDateRange() {
                Calendar cal = Calendar.getInstance();
-               currentDate = DateParsing(cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DAY_OF_MONTH));
+               currentDate = DateParsing(cal.get(Calendar.YEAR) + "/" + (cal.get(Calendar.MONTH) + 1) + "/" + cal.get(Calendar.DAY_OF_MONTH), formatYYMMDD);
                if (0 == earlestDate) {
                        CassandraRequester cr = new CassandraRequester();
                        earlestDate = cr.earliestDate();
@@ -264,12 +272,11 @@ public class CassandraRequester {
                }
        }
 
-       public boolean isThisDateValid(String dateToValidate) {
+       public boolean isThisDateValid(String dateToValidate, SimpleDateFormat sdf) {
                if (dateToValidate == null || dateToValidate.equals("")) {
                        System.out.println("Undefined date");
                        return false;
                }
-               SimpleDateFormat sdf = new SimpleDateFormat("yyyy/MM/dd");
                try {
                        // if not valid, this will throw ParseException
                        sdf.setLenient(false);

diff --git a/website/ReportJobsByDate.jsp b/website/ReportJobsByDate.jsp
index f531446..8ced12c 100644 (file)
--- a/website/ReportJobsByDate.jsp
+++ b/website/ReportJobsByDate.jsp
@@ -69,10 +69,10 @@
                </tr>
 
                <c:forEach items="${result}" var="res">
-                       <tr>
+                       <tr>    
                                <td>${res.date}</td>
                                <td style="text-align: right">${res.total}</td>
-                               <td style="text-align: right">${res.totalOK}</td>
+                               <td style="text-align: right"><a href="ServletJobsByDay?date=${res.date}">${res.totalOK}</a></td>
                                <td style="text-align: right">${res.totalStopped}</td>
                                <td style="text-align: right">${res.totalError}</td>
                                <td style="text-align: right">${res.totalTimeOut}</td>