SE-140 Result database model changed. Allow registration of data sets directly at experiments.

SVN: 12718

rtd_phosphonetx/etc/service.properties

-# Unique code of this Data Store Server. Not more than 40 characters.
+testtt# Unique code of this Data Store Server. Not more than 40 characters.
 data-store-server-code = DSS1
 
 # The root directory of the data store
@@ -111,6 +111,7 @@ main-thread.data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetI
 main-thread.data-set-info-extractor.strip-file-extension = true
 main-thread.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator}
 main-thread.data-set-info-extractor.group-code = TEST
+main-thread.data-set-info-extractor.index-of-experiment-identifier = 0
 # Location of file containing data set properties 
 #main-thread.data-set-info-extractor.data-set-properties-file-name = data-set.properties
 

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploader.java

@@ -46,6 +46,7 @@ import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinSummaryDataFilt
 import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Sample;
 import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Sequence;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Group;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
 import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
 
 /**
@@ -82,16 +83,30 @@ class ResultDataSetUploader extends AbstractHandler
             Experiment experiment = getOrCreateExperiment(dataSetInfo.tryToGetExperiment().getPermId());
             ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample dataSetInfoSample =
                     dataSetInfo.tryToGetSample();
-            if (dataSetInfoSample == null)
+            Sample sample = null;
+            GroupIdentifier groupIdentifier = null;
+            if (dataSetInfoSample != null)
             {
-                throw new UserFailureException("Missing sample in " + dataSetInfo);
+                sample = getOrCreateSample(experiment, dataSetInfoSample.getPermId());
+                Group group = dataSetInfoSample.getGroup();
+                groupIdentifier = new GroupIdentifier(group.getInstance().getCode(), group.getCode());
+            } else
+            {
+                ExperimentIdentifier experimentIdentifier = dataSetInfo.getExperimentIdentifier();
+                if (experimentIdentifier == null)
+                {
+                    throw new UserFailureException(
+                            "Neither sample nor experiment identifier specified: " + dataSetInfo);
+                }
+                groupIdentifier =
+                        new GroupIdentifier(experimentIdentifier.getDatabaseInstanceCode(),
+                                experimentIdentifier.getGroupCode());
             }
-            Sample sample = getOrCreateSample(experiment, dataSetInfoSample.getPermId());
             String referenceDatabase = summary.getSummaryHeader().getReferenceDatabase();
             Database database = getOrGreateDatabase(referenceDatabase);
             DataSet ds =
                     getOrCreateDataSet(experiment, sample, database, dataSetInfo.getDataSetCode());
-            addToDatabase(ds, experiment, dataSetInfoSample.getGroup(), summary);
+            addToDatabase(ds, experiment, groupIdentifier, summary);
             if (errorMessages.length() == 0)
             {
                 connection.commit();
@@ -136,7 +151,7 @@ class ResultDataSetUploader extends AbstractHandler
         return database;
     }
 
-    private DataSet getOrCreateDataSet(Experiment experiment, Sample sample, Database database,
+    private DataSet getOrCreateDataSet(Experiment experiment, Sample sampleOrNull, Database database,
             String dataSetPermID)
     {
         DataSet dataSet = dao.tryToGetDataSetByPermID(dataSetPermID);
@@ -146,8 +161,12 @@ class ResultDataSetUploader extends AbstractHandler
             dataSet.setPermID(dataSetPermID);
             long experimentID = experiment.getId();
             dataSet.setExperimentID(experimentID);
-            long sampleID = sample.getId();
-            dataSet.setSampleID(sampleID);
+            Long sampleID = null;
+            if (sampleOrNull != null)
+            {
+                sampleID = sampleOrNull.getId();
+                dataSet.setSampleID(sampleID);
+            }
             long databaseID = database.getId();
             dataSet.setDatabaseID(databaseID);
             dataSet.setId(dao.createDataSet(experimentID, sampleID, dataSetPermID, databaseID));
@@ -167,13 +186,11 @@ class ResultDataSetUploader extends AbstractHandler
         return experiment;
     }
 
-    private void addToDatabase(DataSet dataSet, Experiment experiment, Group group,
+    private void addToDatabase(DataSet dataSet, Experiment experiment, GroupIdentifier groupIdentifier,
             ProteinSummary summary)
     {
         long dataSetID = dataSet.getId();
         Long databaseID = dataSet.getDatabaseID();
-        GroupIdentifier groupIdentifier =
-                new GroupIdentifier(group.getInstance().getCode(), group.getCode());
         AbundanceHandler abundanceHandler =
                 new AbundanceHandler(openbisService, dao, groupIdentifier, experiment);
         createProbabilityToFDRMapping(dataSetID, summary);
@@ -339,5 +356,5 @@ class ResultDataSetUploader extends AbstractHandler
         }
         throw new UserFailureException("Missing Protein Prophet details.");
     }
-
 }
+

rtd_phosphonetx/source/sql/postgresql/001/schema-001.sql

@@ -5,8 +5,8 @@
 /* Project name:                                                          */
 /* Author:                                                                */
 /* Script type:           Database creation script                        */
-/* Created on:            2009-08-27 11:01                                */
-/* Model version:         Version 2009-08-27                              */
+/* Created on:            2009-09-28 08:43                                */
+/* Model version:         Version 2009-09-28                              */
 /* ---------------------------------------------------------------------- */
 
 
@@ -34,6 +34,8 @@ CREATE DOMAIN SHORT_SEQUENCE AS CHARACTER VARYING(1000);
 
 CREATE DOMAIN ACCESSION_NUMBER AS CHARACTER VARYING(256);
 
+CREATE DOMAIN SPECTRUM_REFERENCE AS CHARACTER VARYING(100);
+
 /* ---------------------------------------------------------------------- */
 /* Tables                                                                 */
 /* ---------------------------------------------------------------------- */
@@ -56,7 +58,7 @@ CREATE TABLE EXPERIMENTS (
 CREATE TABLE DATA_SETS (
     ID BIGSERIAL  NOT NULL,
     EXPE_ID TECH_ID  NOT NULL,
-    SAMP_ID TECH_ID  NOT NULL,
+    SAMP_ID TECH_ID,
     DB_ID TECH_ID  NOT NULL,
     PERM_ID CODE  NOT NULL,
     CONSTRAINT PK_DATA_SETS PRIMARY KEY (ID),
@@ -203,6 +205,29 @@ CREATE TABLE MODIFIED_PEPTIDES (
     CONSTRAINT PK_MODIFIED_PEPTIDES PRIMARY KEY (ID)
 );
 
+/* ---------------------------------------------------------------------- */
+/* Add table "SPECTRUM_REFERENCES"                                        */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE SPECTRUM_REFERENCES (
+    ID BIGSERIAL  NOT NULL,
+    PEPT_ID TECH_ID  NOT NULL,
+    REFERENCE SPECTRUM_REFERENCE  NOT NULL,
+    CONSTRAINT PK_SPECTRUM_REFERENCES PRIMARY KEY (ID)
+);
+
+/* ---------------------------------------------------------------------- */
+/* Add table "MODIFICATION_FRACTIONS"                                     */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE MODIFICATION_FRACTIONS (
+    ID BIGSERIAL  NOT NULL,
+    MODI_ID TECH_ID  NOT NULL,
+    SAMP_ID TECH_ID,
+    FRACTION REAL_NUMBER  NOT NULL,
+    CONSTRAINT PK_MODIFICATION_FRACTIONS PRIMARY KEY (ID)
+);
+
 /* ---------------------------------------------------------------------- */
 /* Foreign key constraints                                                */
 /* ---------------------------------------------------------------------- */
@@ -248,3 +273,12 @@ ALTER TABLE PROBABILITY_FDR_MAPPINGS ADD CONSTRAINT DATA_SETS_PROBABILITY_FDR_MA
 
 ALTER TABLE MODIFIED_PEPTIDES ADD CONSTRAINT PEPTIDES_MODIFIED_PEPTIDES 
     FOREIGN KEY (PEPT_ID) REFERENCES PEPTIDES (ID);
+
+ALTER TABLE SPECTRUM_REFERENCES ADD CONSTRAINT PEPTIDES_SPECTRUM_REFERENCES 
+    FOREIGN KEY (PEPT_ID) REFERENCES PEPTIDES (ID);
+
+ALTER TABLE MODIFICATION_FRACTIONS ADD CONSTRAINT MODIFICATIONS_MODIFICATION_FRACTIONS 
+    FOREIGN KEY (MODI_ID) REFERENCES MODIFICATIONS (ID);
+
+ALTER TABLE MODIFICATION_FRACTIONS ADD CONSTRAINT SAMPLES_MODIFICATION_FRACTIONS 
+    FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID);