diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/IProtDAO.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/IProtDAO.java
index c71eb911ada3526fb2cfe86230bbf8244a9fb24f..058bc2417a1ab0b9a88e8d6e95e9b8a8958312b5 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/IProtDAO.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/IProtDAO.java
@@ -93,8 +93,8 @@ public interface IProtDAO extends BaseQuery
+ "returning id")
public long createSequence(Sequence sequence);
- @Update("insert into identified_proteins (prot_id, sequ_id, coverage) values (?{1}, ?{2}, ?{3})")
- public void createIdentifiedProtein(long proteinID, long sequenceID, double coverage);
+ @Update("insert into identified_proteins (prot_id, sequ_id, coverage, is_primary) values (?{1}, ?{2}, ?{3}, ?{4})")
+ public void createIdentifiedProtein(long proteinID, long sequenceID, double coverage, boolean primary);
@Update("insert into abundances (prot_id, samp_id, value) values (?{1}, ?{2}, ?{3})")
public void createAbundance(long proteinID, long sampleID, double value);
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploader.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploader.java
index 440b23de9aafc7a13bdcbe5396d7fea6e54a714e..4e8344d7b901036b0345f7370ed83b134b6a8bbe 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploader.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploader.java
@@ -259,10 +259,10 @@ class ResultDataSetUploader extends AbstractHandler
logException(e, "peptide", peptide.getSequence().toString());
}
}
- createIdentifiedProtein(proteinID, peptideSequences, databaseID, protein.getAnnotation());
+ createIdentifiedProtein(proteinID, peptideSequences, databaseID, protein.getAnnotation(), true);
for (AnnotatedProtein annotatedProtein : protein.getIndistinguishableProteins())
{
- createIdentifiedProtein(proteinID, peptideSequences, databaseID, annotatedProtein.getAnnotation());
+ createIdentifiedProtein(proteinID, peptideSequences, databaseID, annotatedProtein.getAnnotation(), false);
}
}
@@ -299,7 +299,7 @@ class ResultDataSetUploader extends AbstractHandler
}
private void createIdentifiedProtein(long proteinID, Set<String> peptideSequences,
- Long databaseID, ProteinAnnotation annotation)
+ Long databaseID, ProteinAnnotation annotation, boolean primary)
{
ProteinDescription protDesc = new ProteinDescription(annotation.getDescription());
String accessionNumber = protDesc.getAccessionNumber();
@@ -323,7 +323,7 @@ class ResultDataSetUploader extends AbstractHandler
sequence.setId(dao.createSequence(sequence));
}
double coverage = calculateCoverage(sequence.getSequence(), peptideSequences);
- dao.createIdentifiedProtein(proteinID, sequence.getId(), coverage);
+ dao.createIdentifiedProtein(proteinID, sequence.getId(), coverage, primary);
}
private double calculateCoverage(String aminoAcidSequence, Set<String> peptideSequences)
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/db/PhosphoNetXDAOFactory.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/db/PhosphoNetXDAOFactory.java
index 07e82ccd48ec6c7d6770af1a9771778c01fb66fb..2f39bb9956dcbaa4ce4c984f912937a5e70cde9a 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/db/PhosphoNetXDAOFactory.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/dataaccess/db/PhosphoNetXDAOFactory.java
@@ -37,7 +37,7 @@ import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.IProteinQue
public class PhosphoNetXDAOFactory implements IPhosphoNetXDAOFactory
{
/** Current version of the database. */
- public static final String DATABASE_VERSION = "003";
+ public static final String DATABASE_VERSION = "004";
private static final Logger operationLog =
LogFactory.getLogger(LogCategory.OPERATION, PhosphoNetXDAOFactory.class);
diff --git a/rtd_phosphonetx/source/sql/postgresql/004/grant-004.sql b/rtd_phosphonetx/source/sql/postgresql/004/grant-004.sql
new file mode 100644
index 0000000000000000000000000000000000000000..2e85f4fb1f6fcbb7f072005f9d1ab5ad9e1fe713
--- /dev/null
+++ b/rtd_phosphonetx/source/sql/postgresql/004/grant-004.sql
@@ -0,0 +1,18 @@
+-- Granting SELECT privilege to group PHOSPHONETX_READONLY
+
+GRANT SELECT ON TABLE EXPERIMENTS TO GROUP PHOSPHONETX_READONLY;
+GRANT SELECT ON TABLE DATA_SETS TO GROUP PHOSPHONETX_READONLY;
+GRANT SELECT ON TABLE MODIFICATIONS TO GROUP PHOSPHONETX_READONLY;
+GRANT SELECT ON TABLE PEPTIDES TO GROUP PHOSPHONETX_READONLY;
+GRANT SELECT ON TABLE PROTEINS TO GROUP PHOSPHONETX_READONLY;
+GRANT SELECT ON TABLE SAMPLES TO GROUP PHOSPHONETX_READONLY;
+GRANT SELECT ON TABLE SEQUENCES TO GROUP PHOSPHONETX_READONLY;
+GRANT SELECT ON TABLE IDENTIFIED_PROTEINS TO GROUP PHOSPHONETX_READONLY;
+GRANT SELECT ON TABLE ABUNDANCES TO GROUP PHOSPHONETX_READONLY;
+GRANT SELECT ON TABLE PROBABILITY_FDR_MAPPINGS TO GROUP PHOSPHONETX_READONLY;
+GRANT SELECT ON TABLE PROTEIN_REFERENCES TO GROUP PHOSPHONETX_READONLY;
+GRANT SELECT ON TABLE DATABASES TO GROUP PHOSPHONETX_READONLY;
+GRANT SELECT ON TABLE MODIFIED_PEPTIDES TO GROUP PHOSPHONETX_READONLY;
+GRANT SELECT ON TABLE SPECTRUM_REFERENCES TO GROUP PHOSPHONETX_READONLY;
+GRANT SELECT ON TABLE MODIFICATION_FRACTIONS TO GROUP PHOSPHONETX_READONLY;
+GRANT SELECT ON TABLE EVENTS TO GROUP PHOSPHONETX_READONLY;
diff --git a/rtd_phosphonetx/source/sql/postgresql/004/schema-004.png b/rtd_phosphonetx/source/sql/postgresql/004/schema-004.png
new file mode 100755
index 0000000000000000000000000000000000000000..fceffeedd9cb97b93e06432546eb207feba07418
Binary files /dev/null and b/rtd_phosphonetx/source/sql/postgresql/004/schema-004.png differ
diff --git a/rtd_phosphonetx/source/sql/postgresql/004/schema-004.sql b/rtd_phosphonetx/source/sql/postgresql/004/schema-004.sql
new file mode 100755
index 0000000000000000000000000000000000000000..824269ff55a707aa7124dbd2b18b3e0f6c4f6a4a
--- /dev/null
+++ b/rtd_phosphonetx/source/sql/postgresql/004/schema-004.sql
@@ -0,0 +1,296 @@
+/* ---------------------------------------------------------------------- */
+/* Script generated with: DeZign for Databases v5.2.3 */
+/* Target DBMS: PostgreSQL 8 */
+/* Project file: schema.dez */
+/* Project name: */
+/* Author: */
+/* Script type: Database creation script */
+/* Created on: 2010-05-27 14:26 */
+/* Model version: Version 2010-05-27 */
+/* ---------------------------------------------------------------------- */
+
+
+/* ---------------------------------------------------------------------- */
+/* Domains */
+/* ---------------------------------------------------------------------- */
+
+CREATE DOMAIN CHECKSUM AS CHARACTER VARYING(8);
+
+CREATE DOMAIN CODE AS CHARACTER VARYING(40);
+
+CREATE DOMAIN DESCRIPTION AS CHARACTER VARYING(2000);
+
+CREATE DOMAIN INTEGER_NUMBER AS INTEGER;
+
+CREATE DOMAIN REAL_NUMBER AS DOUBLE PRECISION;
+
+CREATE DOMAIN LONG_SEQUENCE AS TEXT;
+
+CREATE DOMAIN SHORT_DESCRIPTION AS CHARACTER VARYING(200);
+
+CREATE DOMAIN TECH_ID AS BIGINT;
+
+CREATE DOMAIN SHORT_SEQUENCE AS CHARACTER VARYING(1000);
+
+CREATE DOMAIN ACCESSION_NUMBER AS CHARACTER VARYING(256);
+
+CREATE DOMAIN SPECTRUM_REFERENCE AS CHARACTER VARYING(100);
+
+CREATE DOMAIN BOOLEAN_CHAR AS BOOLEAN DEFAULT FALSE;
+
+/* ---------------------------------------------------------------------- */
+/* Tables */
+/* ---------------------------------------------------------------------- */
+
+/* ---------------------------------------------------------------------- */
+/* Add table "EXPERIMENTS" */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE EXPERIMENTS (
+ ID BIGSERIAL NOT NULL,
+ PERM_ID CODE NOT NULL,
+ CONSTRAINT PK_EXPERIMENTS PRIMARY KEY (ID),
+ CONSTRAINT TUC_EXPERIMENTS_1 UNIQUE (PERM_ID)
+);
+
+/* ---------------------------------------------------------------------- */
+/* Add table "DATA_SETS" */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE DATA_SETS (
+ ID BIGSERIAL NOT NULL,
+ EXPE_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),
+ CONSTRAINT TUC_DATA_SETS_1 UNIQUE (PERM_ID)
+);
+
+CREATE INDEX IX_FK_DATA_SETS_EXPERIMENTS ON DATA_SETS (EXPE_ID);
+
+CREATE INDEX IX_FK_DATA_SETS_SAMPLES ON DATA_SETS (SAMP_ID);
+
+/* ---------------------------------------------------------------------- */
+/* Add table "MODIFICATIONS" */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE MODIFICATIONS (
+ ID BIGSERIAL NOT NULL,
+ MOPE_ID TECH_ID NOT NULL,
+ POS INTEGER_NUMBER NOT NULL,
+ MASS REAL_NUMBER NOT NULL,
+ CONSTRAINT PK_MODIFICATIONS PRIMARY KEY (ID)
+);
+
+/* ---------------------------------------------------------------------- */
+/* Add table "PEPTIDES" */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE PEPTIDES (
+ ID BIGSERIAL NOT NULL,
+ PROT_ID TECH_ID NOT NULL,
+ SEQUENCE SHORT_SEQUENCE NOT NULL,
+ CHARGE INTEGER_NUMBER NOT NULL,
+ CONSTRAINT PK_PEPTIDES PRIMARY KEY (ID)
+);
+
+CREATE INDEX IX_FK_PEPTIDES_PROTEINS ON PEPTIDES (PROT_ID);
+
+/* ---------------------------------------------------------------------- */
+/* Add table "PROTEINS" */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE PROTEINS (
+ ID BIGSERIAL NOT NULL,
+ DASE_ID TECH_ID NOT NULL,
+ PROBABILITY REAL_NUMBER NOT NULL,
+ CONSTRAINT PK_PROTEINS PRIMARY KEY (ID)
+);
+
+CREATE INDEX IDX_PROTEINS_1 ON PROTEINS (DASE_ID);
+
+/* ---------------------------------------------------------------------- */
+/* Add table "SAMPLES" */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE SAMPLES (
+ ID BIGSERIAL NOT NULL,
+ PERM_ID CODE NOT NULL,
+ EXPE_ID TECH_ID NOT NULL,
+ CONSTRAINT PK_SAMPLES PRIMARY KEY (ID),
+ CONSTRAINT TUC_SAMPLES_1 UNIQUE (PERM_ID)
+);
+
+/* ---------------------------------------------------------------------- */
+/* Add table "SEQUENCES" */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE SEQUENCES (
+ ID BIGSERIAL NOT NULL,
+ DB_ID TECH_ID NOT NULL,
+ PRRE_ID TECH_ID NOT NULL,
+ AMINO_ACID_SEQUENCE LONG_SEQUENCE NOT NULL,
+ CHECKSUM CHECKSUM NOT NULL,
+ CONSTRAINT PK_SEQUENCES PRIMARY KEY (ID)
+);
+
+/* ---------------------------------------------------------------------- */
+/* Add table "IDENTIFIED_PROTEINS" */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE IDENTIFIED_PROTEINS (
+ ID BIGSERIAL NOT NULL,
+ PROT_ID TECH_ID NOT NULL,
+ SEQU_ID TECH_ID NOT NULL,
+ COVERAGE REAL_NUMBER,
+ IS_PRIMARY BOOLEAN_CHAR NOT NULL,
+ CONSTRAINT PK_IDENTIFIED_PROTEINS PRIMARY KEY (ID)
+);
+
+/* ---------------------------------------------------------------------- */
+/* Add table "ABUNDANCES" */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE ABUNDANCES (
+ ID BIGSERIAL NOT NULL,
+ PROT_ID TECH_ID NOT NULL,
+ SAMP_ID TECH_ID NOT NULL,
+ VALUE REAL_NUMBER NOT NULL,
+ CONSTRAINT PK_ABUNDANCES PRIMARY KEY (ID)
+);
+
+/* ---------------------------------------------------------------------- */
+/* Add table "PROBABILITY_FDR_MAPPINGS" */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE PROBABILITY_FDR_MAPPINGS (
+ ID BIGSERIAL NOT NULL,
+ DASE_ID TECH_ID NOT NULL,
+ PROBABILITY REAL_NUMBER NOT NULL,
+ FALSE_DISCOVERY_RATE REAL_NUMBER NOT NULL,
+ CONSTRAINT PK_PROBABILITY_FDR_MAPPINGS PRIMARY KEY (ID)
+);
+
+/* ---------------------------------------------------------------------- */
+/* Add table "PROTEIN_REFERENCES" */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE PROTEIN_REFERENCES (
+ ID BIGSERIAL NOT NULL,
+ ACCESSION_NUMBER ACCESSION_NUMBER NOT NULL,
+ DESCRIPTION DESCRIPTION,
+ CONSTRAINT PK_PROTEIN_REFERENCES PRIMARY KEY (ID),
+ CONSTRAINT TUC_PROTEIN_REFERENCES_1 UNIQUE (ACCESSION_NUMBER)
+);
+
+CREATE INDEX IDX_PROTEIN_REFERENCES_1 ON PROTEIN_REFERENCES (ACCESSION_NUMBER);
+
+/* ---------------------------------------------------------------------- */
+/* Add table "DATABASES" */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE DATABASES (
+ ID BIGSERIAL NOT NULL,
+ NAME_AND_VERSION SHORT_DESCRIPTION NOT NULL,
+ CONSTRAINT PK_DATABASES PRIMARY KEY (ID),
+ CONSTRAINT TUC_DATABASES_1 UNIQUE (NAME_AND_VERSION)
+);
+
+/* ---------------------------------------------------------------------- */
+/* Add table "MODIFIED_PEPTIDES" */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE MODIFIED_PEPTIDES (
+ ID BIGSERIAL NOT NULL,
+ PEPT_ID TECH_ID NOT NULL,
+ NTERM_MASS REAL_NUMBER NOT NULL,
+ CTERM_MASS REAL_NUMBER NOT NULL,
+ 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)
+);
+
+/* ---------------------------------------------------------------------- */
+/* Add table "EVENTS" */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE EVENTS (
+ LAST_SEEN_DELETION_EVENT_ID TECH_ID NOT NULL
+);
+
+/* ---------------------------------------------------------------------- */
+/* Foreign key constraints */
+/* ---------------------------------------------------------------------- */
+
+ALTER TABLE DATA_SETS ADD CONSTRAINT DA_EX_FK
+ FOREIGN KEY (EXPE_ID) REFERENCES EXPERIMENTS (ID);
+
+ALTER TABLE DATA_SETS ADD CONSTRAINT DA_SA_FK
+ FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID);
+
+ALTER TABLE DATA_SETS ADD CONSTRAINT DATABASES_DATA_SETS
+ FOREIGN KEY (DB_ID) REFERENCES DATABASES (ID);
+
+ALTER TABLE MODIFICATIONS ADD CONSTRAINT MODIFIED_PEPTIDES_MODIFICATIONS
+ FOREIGN KEY (MOPE_ID) REFERENCES MODIFIED_PEPTIDES (ID) ON DELETE CASCADE;
+
+ALTER TABLE PEPTIDES ADD CONSTRAINT PE_PR_FK
+ FOREIGN KEY (PROT_ID) REFERENCES PROTEINS (ID) ON DELETE CASCADE;
+
+ALTER TABLE PROTEINS ADD CONSTRAINT DATA_SETS_PROTEINS
+ FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE;
+
+ALTER TABLE SEQUENCES ADD CONSTRAINT DATABASES_SEQUENCES
+ FOREIGN KEY (DB_ID) REFERENCES DATABASES (ID);
+
+ALTER TABLE SEQUENCES ADD CONSTRAINT PROTEIN_REFERENCES_SEQUENCES
+ FOREIGN KEY (PRRE_ID) REFERENCES PROTEIN_REFERENCES (ID);
+
+ALTER TABLE IDENTIFIED_PROTEINS ADD CONSTRAINT PROTEINS_IDENTIFIED_PROTEINS
+ FOREIGN KEY (PROT_ID) REFERENCES PROTEINS (ID) ON DELETE CASCADE;
+
+ALTER TABLE IDENTIFIED_PROTEINS ADD CONSTRAINT SEQUENCES_IDENTIFIED_PROTEINS
+ FOREIGN KEY (SEQU_ID) REFERENCES SEQUENCES (ID);
+
+ALTER TABLE ABUNDANCES ADD CONSTRAINT SAMPLES_ABUNDANCES
+ FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID);
+
+ALTER TABLE ABUNDANCES ADD CONSTRAINT PROTEINS_ABUNDANCES
+ FOREIGN KEY (PROT_ID) REFERENCES PROTEINS (ID) ON DELETE CASCADE;
+
+ALTER TABLE PROBABILITY_FDR_MAPPINGS ADD CONSTRAINT DATA_SETS_PROBABILITY_FDR_MAPPINGS
+ FOREIGN KEY (DASE_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE;
+
+ALTER TABLE MODIFIED_PEPTIDES ADD CONSTRAINT PEPTIDES_MODIFIED_PEPTIDES
+ FOREIGN KEY (PEPT_ID) REFERENCES PEPTIDES (ID) ON DELETE CASCADE;
+
+ALTER TABLE SPECTRUM_REFERENCES ADD CONSTRAINT PEPTIDES_SPECTRUM_REFERENCES
+ FOREIGN KEY (PEPT_ID) REFERENCES PEPTIDES (ID) ON DELETE CASCADE;
+
+ALTER TABLE MODIFICATION_FRACTIONS ADD CONSTRAINT MODIFICATIONS_MODIFICATION_FRACTIONS
+ FOREIGN KEY (MODI_ID) REFERENCES MODIFICATIONS (ID) ON DELETE CASCADE;
+
+ALTER TABLE MODIFICATION_FRACTIONS ADD CONSTRAINT SAMPLES_MODIFICATION_FRACTIONS
+ FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID);
diff --git a/rtd_phosphonetx/source/sql/postgresql/migration/migration-003-004.sql b/rtd_phosphonetx/source/sql/postgresql/migration/migration-003-004.sql
new file mode 100644
index 0000000000000000000000000000000000000000..84d3d8a841b803eab39cba657d98ffd029532b8d
--- /dev/null
+++ b/rtd_phosphonetx/source/sql/postgresql/migration/migration-003-004.sql
@@ -0,0 +1,5 @@
+CREATE DOMAIN BOOLEAN_CHAR AS BOOLEAN DEFAULT FALSE;
+
+ALTER TABLE IDENTIFIED_PROTEINS ADD COLUMN IS_PRIMARY BOOLEAN_CHAR NOT NULL;
+
+UPDATE IDENTIFIED_PROTEINS SET IS_PRIMARY = 'T' WHERE ID = ANY(SELECT MIN(ID) FROM IDENTIFIED_PROTEINS GROUP BY PROT_ID);
diff --git a/rtd_phosphonetx/source/sql/postgresql/schema.dez b/rtd_phosphonetx/source/sql/postgresql/schema.dez
index f7c4d30fd3339b751c32db2d62671e1fa0e16fad..b63ef2293f4b087e5763bda67e8e60e05e61521b 100755
--- a/rtd_phosphonetx/source/sql/postgresql/schema.dez
+++ b/rtd_phosphonetx/source/sql/postgresql/schema.dez
@@ -4,14 +4,14 @@
<VERSION>
<PROJECTSETTINGS>
<PROJECTFILENAME>D:\User\felmer\dev-workspace\rtd_phosphonetx\source\sql\postgresql\phosphonetx.dez</PROJECTFILENAME>
-<MODIFIED>2010-03-31</MODIFIED>
+<MODIFIED>2010-05-27</MODIFIED>
<CREATED>2009-06-29</CREATED>
<CREATED2></CREATED2>
<PROJECTNAME></PROJECTNAME>
<DESCRIPTION></DESCRIPTION>
<AUTHOR></AUTHOR>
<COPYRIGHT></COPYRIGHT>
-<LASTGENERATEDFILES>N:\group\cisd\phosphonetx\datamodel\schema.sql;N:\group\cisd\phosphonetx\datamodel\drop.sql;\\d.ethz.ch\dfs\groups\bsse\users\cisd\felmer\Documents\CreateDBLog_201003311.txt</LASTGENERATEDFILES>
+<LASTGENERATEDFILES>N:\group\cisd\phosphonetx\datamodel\schema.sql;N:\group\cisd\phosphonetx\datamodel\drop.sql;\\d.ethz.ch\dfs\groups\bsse\users\cisd\felmer\Documents\CreateDBLog_201005274.txt</LASTGENERATEDFILES>
</PROJECTSETTINGS>
<CONNECTIONSETTINGS>
<SQLFILE>D:\User\felmer\dev-workspace\rtd_phosphonetx\source\sql\postgresql\001\schema-001.sql</SQLFILE>
@@ -20,7 +20,7 @@
</CONNECTIONSETTINGS>
<DATADICT>
<DBID>postgresql8</DBID>
-<LASTID>176</LASTID>
+<LASTID>236</LASTID>
<DDSETTINGS>
<PKCONNAMETEMPLATE>PK_%table%</PKCONNAMETEMPLATE>
<FKCONNAMETEMPLATE>%relname%</FKCONNAMETEMPLATE>
@@ -200,6 +200,30 @@
<INC>1</INC>
</DT>
</DOMAIN>
+<DOMAIN>
+<NAME>BOOLEAN_CHAR</NAME>
+<ID>188</ID>
+<POSNR>0</POSNR>
+<SCHEMA></SCHEMA>
+<DESC></DESC>
+<DT>
+<DTLISTNAME>BOOLEAN</DTLISTNAME>
+<SD>0</SD>
+<INC>1</INC>
+</DT>
+<DEFCON>
+<NAME></NAME>
+<ID>1</ID>
+<POSNR>0</POSNR>
+<SCHEMA></SCHEMA>
+<DESC></DESC>
+<VALUE>FALSE</VALUE>
+<CONLEVEL>0</CONLEVEL>
+<CONTYPE>6</CONTYPE>
+<ATTRIBUTEIDS>
+</ATTRIBUTEIDS>
+</DEFCON>
+</DOMAIN>
</DOMAINS>
<ENTITIES>
<ENT>
@@ -1209,7 +1233,7 @@
<POSNR>0</POSNR>
<SCHEMA></SCHEMA>
<DESC></DESC>
-<ATTRLASTID>6</ATTRLASTID>
+<ATTRLASTID>7</ATTRLASTID>
<IDXLASTID>1</IDXLASTID>
<TRGLASTID>1</TRGLASTID>
<CONLASTID>1</CONLASTID>
@@ -1322,6 +1346,47 @@
<INC>1</INC>
</DT>
</ATTR>
+<ATTR>
+<NAME>IS_PRIMARY</NAME>
+<ID>7</ID>
+<POSNR>0</POSNR>
+<SCHEMA></SCHEMA>
+<DESC></DESC>
+<DOMAINID>188</DOMAINID>
+<DT>
+<DTLISTNAME>BOOLEAN</DTLISTNAME>
+<SD>0</SD>
+<INC>1</INC>
+</DT>
+<NNCON>
+<NAME></NAME>
+<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
+<ID>1</ID>
+<POSNR>0</POSNR>
+<SCHEMA></SCHEMA>
+<DESC></DESC>
+<VALUE>1</VALUE>
+<CONLEVEL>1</CONLEVEL>
+<CONTYPE>5</CONTYPE>
+<ATTRIBUTEIDS>
+<ATTRIBUTEID>7</ATTRIBUTEID>
+</ATTRIBUTEIDS>
+</NNCON>
+<DEFCON>
+<NAME></NAME>
+<NAMETEMPLATE>DEF_%table%_%column%</NAMETEMPLATE>
+<ID>2</ID>
+<POSNR>0</POSNR>
+<SCHEMA></SCHEMA>
+<DESC></DESC>
+<VALUE>FALSE</VALUE>
+<CONLEVEL>1</CONLEVEL>
+<CONTYPE>6</CONTYPE>
+<ATTRIBUTEIDS>
+<ATTRIBUTEID>7</ATTRIBUTEID>
+</ATTRIBUTEIDS>
+</DEFCON>
+</ATTR>
</ATTRIBUTES>
</ENT>
<ENT>
@@ -3065,7 +3130,7 @@
<DIAGRAMID>1</DIAGRAMID>
<W>250</W>
<H>108</H>
-<L>736</L>
+<L>754</L>
<T>328</T>
<BRUSH>0,16777215</BRUSH>
<PEN>0,1,4,0</PEN>
@@ -3076,8 +3141,8 @@
<ENTC>
<ID>47</ID>
<DIAGRAMID>1</DIAGRAMID>
-<W>167</W>
-<H>93</H>
+<W>184</W>
+<H>108</H>
<L>518</L>
<T>328</T>
<BRUSH>0,16777215</BRUSH>
@@ -3117,7 +3182,7 @@
<DIAGRAMID>1</DIAGRAMID>
<W>252</W>
<H>78</H>
-<L>734</L>
+<L>752</L>
<T>480</T>
<BRUSH>0,16777215</BRUSH>
<PEN>0,1,4,0</PEN>
@@ -3130,7 +3195,7 @@
<DIAGRAMID>1</DIAGRAMID>
<W>252</W>
<H>63</H>
-<L>734</L>
+<L>752</L>
<T>91</T>
<BRUSH>0,16777215</BRUSH>
<PEN>0,1,4,0</PEN>
@@ -3182,7 +3247,7 @@
<DIAGRAMID>1</DIAGRAMID>
<W>226</W>
<H>48</H>
-<L>746</L>
+<L>778</L>
<T>1</T>
<BRUSH>0,16777215</BRUSH>
<PEN>0,1,4,0</PEN>
@@ -3320,7 +3385,7 @@
<FROMRELATIVEX>5000</FROMRELATIVEX>
<FROMRELATIVEY>5000</FROMRELATIVEY>
<TORELATIVEX>5000</TORELATIVEX>
-<TORELATIVEY>4194</TORELATIVEY>
+<TORELATIVEY>3611</TORELATIVEY>
<POINTS>
<POINT>
<X>454</X>
@@ -3346,25 +3411,25 @@
<FONT>Arial,8,,0,clWindowText,0</FONT>
<PEN>1,1,4,0</PEN>
<FROMRELATIVEX>2840</FROMRELATIVEX>
-<FROMRELATIVEY>4259</FROMRELATIVEY>
+<FROMRELATIVEY>5000</FROMRELATIVEY>
<TORELATIVEX>5000</TORELATIVEX>
-<TORELATIVEY>4946</TORELATIVEY>
+<TORELATIVEY>5000</TORELATIVEY>
<POINTS>
<POINT>
-<X>735</X>
-<Y>374</Y>
+<X>753</X>
+<Y>382</Y>
</POINT>
<POINT>
<X>722</X>
-<Y>374</Y>
+<Y>382</Y>
</POINT>
<POINT>
<X>722</X>
-<Y>374</Y>
+<Y>382</Y>
</POINT>
<POINT>
-<X>685</X>
-<Y>374</Y>
+<X>702</X>
+<Y>382</Y>
</POINT>
</POINTS>
</RELC>
@@ -3463,19 +3528,19 @@
<TORELATIVEY>1296</TORELATIVEY>
<POINTS>
<POINT>
-<X>861</X>
+<X>879</X>
<Y>154</Y>
</POINT>
<POINT>
-<X>861</X>
+<X>879</X>
<Y>235</Y>
</POINT>
<POINT>
-<X>861</X>
+<X>879</X>
<Y>235</Y>
</POINT>
<POINT>
-<X>861</X>
+<X>879</X>
<Y>327</Y>
</POINT>
</POINTS>
@@ -3491,19 +3556,19 @@
<TORELATIVEY>3611</TORELATIVEY>
<POINTS>
<POINT>
-<X>861</X>
+<X>879</X>
<Y>479</Y>
</POINT>
<POINT>
-<X>861</X>
+<X>879</X>
<Y>447</Y>
</POINT>
<POINT>
-<X>861</X>
+<X>879</X>
<Y>447</Y>
</POINT>
<POINT>
-<X>861</X>
+<X>879</X>
<Y>436</Y>
</POINT>
</POINTS>
@@ -3519,7 +3584,7 @@
<TORELATIVEY>9167</TORELATIVEY>
<POINTS>
<POINT>
-<X>733</X>
+<X>751</X>
<Y>100</Y>
</POINT>
<POINT>
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploaderTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploaderTest.java
index 8a06e1477c25d1201f3a1c9e40e195b9e774d10d..71165afb4fc4d69657a9b0341b2ac3e633b03f11 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploaderTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploaderTest.java
@@ -211,9 +211,9 @@ public class ResultDataSetUploaderTest extends AssertJUnit
double probability = 1.0;
prepareForCreatingProtein(probability);
ProteinAnnotation a1 = createAnnotation(UNIPROT_ID1, PROTEIN_NAME1, SEQUENCE1);
- prepareForCreatingIdentifiedProtein(a1, false);
+ prepareForCreatingIdentifiedProtein(a1, false, true);
ProteinAnnotation a2 = createAnnotation(UNIPROT_ID2, PROTEIN_NAME2, SEQUENCE2);
- prepareForCreatingIdentifiedProtein(a2, true);
+ prepareForCreatingIdentifiedProtein(a2, true, false);
ProteinSummary summary = createProteinSummary();
Protein p1 = createProtein(probability, a1, a2);
@@ -232,7 +232,7 @@ public class ResultDataSetUploaderTest extends AssertJUnit
ProteinSummary summary = createProteinSummary();
prepareForCreatingProtein(probability);
ProteinAnnotation a1 = createAnnotation(UNIPROT_ID1, PROTEIN_NAME1, SEQUENCE1);
- prepareForCreatingIdentifiedProtein(a1, false);
+ prepareForCreatingIdentifiedProtein(a1, false, true);
Protein p1 = createProtein(probability, a1);
p1.setName(PROTEIN_NAME1);
p1.getParameters().add(createAbundance(CELL_LYSATE1, 2.5));
@@ -263,7 +263,7 @@ public class ResultDataSetUploaderTest extends AssertJUnit
prepareForCreatingProtein(probability);
summary.getProteinGroups().add(createProteinGroup(p1));
ProteinAnnotation a2 = createAnnotation(UNIPROT_ID2, PROTEIN_NAME2, SEQUENCE2);
- prepareForCreatingIdentifiedProtein(a2, false);
+ prepareForCreatingIdentifiedProtein(a2, false, true);
Protein p2 = createProtein(probability, a2);
p2.setName(PROTEIN_NAME1);
p2.getParameters().add(createAbundance(CELL_LYSATE1, 42.5));
@@ -345,7 +345,7 @@ public class ResultDataSetUploaderTest extends AssertJUnit
double probability = 1.0;
prepareForCreatingProtein(probability);
ProteinAnnotation a1 = createAnnotation(UNIPROT_ID1, PROTEIN_NAME1, SEQUENCE1);
- prepareForCreatingIdentifiedProtein(a1, false);
+ prepareForCreatingIdentifiedProtein(a1, false, true);
ProteinSummary summary = createProteinSummary();
Protein p1 = createProtein(probability, a1);
@@ -374,7 +374,7 @@ public class ResultDataSetUploaderTest extends AssertJUnit
double probability = 1.0;
prepareForCreatingProtein(probability);
ProteinAnnotation a1 = createAnnotation(UNIPROT_ID1, PROTEIN_NAME1, SEQUENCE1);
- prepareForCreatingIdentifiedProtein(a1, false);
+ prepareForCreatingIdentifiedProtein(a1, false, true);
ProteinSummary summary = createProteinSummary();
Protein p1 = createProtein(probability, a1);
@@ -468,7 +468,7 @@ public class ResultDataSetUploaderTest extends AssertJUnit
}
private void prepareForCreatingIdentifiedProtein(ProteinAnnotation annotation,
- final boolean referenceExist)
+ final boolean referenceExist, final boolean primary)
{
ProteinDescription proteinDescription = new ProteinDescription(annotation.getDescription());
final String uniprotID = proteinDescription.getAccessionNumber();
@@ -511,7 +511,7 @@ public class ResultDataSetUploaderTest extends AssertJUnit
will(returnValue(Arrays.asList(seq)));
}
- one(dao).createIdentifiedProtein(PROTEIN1_ID, SEQUENCE_ID, 0);
+ one(dao).createIdentifiedProtein(PROTEIN1_ID, SEQUENCE_ID, 0, primary);
}
});
}