From da6ff0235c03e10912cc8a7576a8e4c0499661f1 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Tue, 2 Jun 2009 09:10:59 +0000
Subject: [PATCH] SE-114 project created

SVN: 11213
---
 rtd_phosphonetx/.classpath                    |  16 ++
 rtd_phosphonetx/.project                      |  17 ++
 rtd_phosphonetx/build/build.xml               |  19 ++
 .../resource/dependency-structure.ddf         |   8 +
 .../ch/systemsx/cisd/phosphonetx/Main.java    |  36 +++
 .../cisd/phosphonetx/db/DBFactory.java        |  67 +++++
 .../source/sql/postgresql/001/model.txp       |  48 ++++
 .../source/sql/postgresql/001/schema-001.sql  | 269 ++++++++++++++++++
 .../ch/systemsx/cisd/phosphonetx}/.gitignore  |   0
 rtd_phosphonetx/sourceTest/java/tests.xml     |  12 +
 10 files changed, 492 insertions(+)
 create mode 100644 rtd_phosphonetx/.classpath
 create mode 100644 rtd_phosphonetx/.project
 create mode 100644 rtd_phosphonetx/build/build.xml
 create mode 100644 rtd_phosphonetx/resource/dependency-structure.ddf
 create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/phosphonetx/Main.java
 create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/phosphonetx/db/DBFactory.java
 create mode 100644 rtd_phosphonetx/source/sql/postgresql/001/model.txp
 create mode 100644 rtd_phosphonetx/source/sql/postgresql/001/schema-001.sql
 rename rtd_phosphonetx/{ => sourceTest/java/ch/systemsx/cisd/phosphonetx}/.gitignore (100%)
 create mode 100644 rtd_phosphonetx/sourceTest/java/tests.xml

diff --git a/rtd_phosphonetx/.classpath b/rtd_phosphonetx/.classpath
new file mode 100644
index 00000000000..5d08ad33f23
--- /dev/null
+++ b/rtd_phosphonetx/.classpath
@@ -0,0 +1,16 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" path="source/java"/>
+	<classpathentry kind="src" path="sourceTest/java"/>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/>
+	<classpathentry combineaccessrules="false" kind="src" path="/common"/>
+	<classpathentry combineaccessrules="false" kind="src" path="/dbmigration"/>
+	<classpathentry kind="lib" path="/libraries/cisd-base/cisd-base.jar" sourcepath="/libraries/cisd-base/cisd-base-src.zip"/>
+	<classpathentry kind="lib" path="/libraries/cisd-base/cisd-base-test.jar" sourcepath="/libraries/cisd-base/cisd-base-src.zip"/>
+	<classpathentry kind="lib" path="/libraries/testng/testng-jdk15.jar" sourcepath="/libraries/testng/src.zip"/>
+	<classpathentry kind="lib" path="/libraries/commons-lang/commons-lang.jar" sourcepath="/libraries/commons-lang/src.zip"/>
+	<classpathentry kind="lib" path="/libraries/log4j/log4j.jar" sourcepath="/libraries/log4j/src.zip"/>
+	<classpathentry kind="lib" path="/libraries/postgresql/postgresql.jar" sourcepath="/libraries/postgresql/postgresql-src.zip"/>
+	<classpathentry kind="lib" path="/libraries/eodsql/eodsql.jar" sourcepath="/libraries/eodsql/eodsql_src.zip"/>
+	<classpathentry kind="output" path="targets/classes"/>
+</classpath>
diff --git a/rtd_phosphonetx/.project b/rtd_phosphonetx/.project
new file mode 100644
index 00000000000..d1c9cd5f912
--- /dev/null
+++ b/rtd_phosphonetx/.project
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>rtd_phosphonetx</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+	</natures>
+</projectDescription>
diff --git a/rtd_phosphonetx/build/build.xml b/rtd_phosphonetx/build/build.xml
new file mode 100644
index 00000000000..3b2411005b7
--- /dev/null
+++ b/rtd_phosphonetx/build/build.xml
@@ -0,0 +1,19 @@
+<project name="phosphonetx" default="ci" basedir="..">
+	<import file="../../build_resources/ant/build-common.xml" />
+	<project-classpath name="ecp" classes="${classes}" />
+
+	<property name="original.dist" value="dist" />
+	<property name="mainfolder" value="rtd_phosphonetx" />
+
+	<target name="clean">
+		<delete dir="${dist}" />
+	</target>
+
+	<target name="compile" depends="build-common.compile, clean" />
+
+	<target name="run-tests">
+		<antcall target="build-common.run-tests">
+			<param name="test.suite" value="tests.xml" />
+		</antcall>
+	</target>
+</project>
\ No newline at end of file
diff --git a/rtd_phosphonetx/resource/dependency-structure.ddf b/rtd_phosphonetx/resource/dependency-structure.ddf
new file mode 100644
index 00000000000..5990357405e
--- /dev/null
+++ b/rtd_phosphonetx/resource/dependency-structure.ddf
@@ -0,0 +1,8 @@
+#
+#
+#
+#show allResults
+
+{root} = ch.systemsx.cisd
+{phosphonetx} = ${root}.phosphonetx
+
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/phosphonetx/Main.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/phosphonetx/Main.java
new file mode 100644
index 00000000000..024291312f4
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/phosphonetx/Main.java
@@ -0,0 +1,36 @@
+/*
+ * Copyright 2009 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.phosphonetx;
+
+import java.sql.Connection;
+import java.sql.SQLException;
+
+import ch.systemsx.cisd.phosphonetx.db.DBFactory;
+
+/**
+ * 
+ *
+ * @author Franz-Josef Elmer
+ */
+public class Main
+{
+    public static void main(String[] args) throws SQLException
+    {
+        DBFactory factory = new DBFactory();
+        Connection connection = factory.getConnection();
+    }
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/phosphonetx/db/DBFactory.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/phosphonetx/db/DBFactory.java
new file mode 100644
index 00000000000..3c595275129
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/phosphonetx/db/DBFactory.java
@@ -0,0 +1,67 @@
+/*
+ * Copyright 2009 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.phosphonetx.db;
+
+import java.sql.Connection;
+import java.sql.SQLException;
+
+import ch.systemsx.cisd.dbmigration.DBMigrationEngine;
+import ch.systemsx.cisd.dbmigration.DatabaseConfigurationContext;
+
+/**
+ * Factory for database connections.
+ *
+ * @author Bernd Rinn
+ */
+public class DBFactory
+{
+    /** Current version of the database. */
+    public static final String DATABASE_VERSION = "001";
+    
+    private final DatabaseConfigurationContext context;
+    
+    public DBFactory()
+    {
+        this(createDefaultDBContext());
+    }
+
+    DBFactory(DatabaseConfigurationContext context)
+    {
+        this.context = context;
+        DBMigrationEngine.createOrMigrateDatabaseAndGetScriptProvider(context, DATABASE_VERSION);
+    }
+    
+    static DatabaseConfigurationContext createDefaultDBContext()
+    {
+        final DatabaseConfigurationContext context = new DatabaseConfigurationContext();
+        context.setDatabaseEngineCode("postgresql");
+        context.setBasicDatabaseName("phosphonetx");
+        context.setDatabaseKind("dev");
+        context.setScriptFolder("source/sql");
+        context.setCreateFromScratch(true);
+        return context;
+    }
+    
+    public Connection getConnection() throws SQLException
+    {
+        final Connection conn = context.getDataSource().getConnection();
+        conn.setAutoCommit(false);
+        return conn;
+    }
+
+
+}
diff --git a/rtd_phosphonetx/source/sql/postgresql/001/model.txp b/rtd_phosphonetx/source/sql/postgresql/001/model.txp
new file mode 100644
index 00000000000..ead5815ba64
--- /dev/null
+++ b/rtd_phosphonetx/source/sql/postgresql/001/model.txp
@@ -0,0 +1,48 @@
+<?xml version="1.0" encoding="UTF-8"?>
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CSAOName="PERForeignKeyPG82"><Id>{911E8154-6F3F-420E-AF22-EA7217A185CD}</Id><Name>FK ID - SPEC_ID</Name><Ordinal>0</Ordinal><HistoryID>{BA26089D-3BEF-44C5-8BFF-9856AE426400}</HistoryID><GlobalOrder>0</GlobalOrder><GenerateCode>1</GenerateCode><BeforeScript></BeforeScript><AfterScript></AfterScript><Notes></Notes><Comments></Comments><AttrParent><Id>{85BCE757-9B63-4336-BD77-BB3A8EB9664D}</Id></AttrParent><AttrChild><Id>{EFBD75F7-5ADE-4C05-8A17-749F312AB35E}</Id></AttrChild><KeyConstraintItem><Id>{94492022-19BB-45A8-9F8F-28CC08E6CE09}</Id></KeyConstraintItem></PERForeignKeyPG82></ForeignKeys><ToDoItems/><Deferred>0</Deferred><Deferrable>0</Deferrable><MatchType>SIMPLE</MatchType><CreateIndexToFK>1</CreateIndexToFK></PERRelationPG82></Relations><Defaults/><Rules/><UserGroups/><Users/><InstanceUserGroupRelations/><Procedures/><Views/><Schemas/><Functions/><Synonyms/><MaterializedViews/><Sequences/><Tablespaces/><Aggregates/></PERModelPG82>
diff --git a/rtd_phosphonetx/source/sql/postgresql/001/schema-001.sql b/rtd_phosphonetx/source/sql/postgresql/001/schema-001.sql
new file mode 100644
index 00000000000..1286d7c610c
--- /dev/null
+++ b/rtd_phosphonetx/source/sql/postgresql/001/schema-001.sql
@@ -0,0 +1,269 @@
+/*
+Created: 06/05/2009
+Modified: 20/05/2009
+Model: Proteomics
+Database: PostgreSQL 8.2
+*/
+
+-- Create domain types section -------------------------------------------------
+
+CREATE DOMAIN BINARY_DATA AS Bytea
+;
+
+CREATE DOMAIN CHECKSUM AS Character varying(8)
+;
+
+CREATE DOMAIN CODE AS Character varying(40)
+;
+
+CREATE DOMAIN INTEGER_NUMBER AS Integer
+;
+
+CREATE DOMAIN REAL_NUMBER AS Double precision
+;
+
+CREATE DOMAIN SEQUENCE AS Text
+;
+
+CREATE DOMAIN SHORT_DESCRIPTION AS Character varying(200)
+;
+
+CREATE DOMAIN TECH_ID AS Bigint
+;
+
+-- Create tables section -------------------------------------------------
+
+-- Table ABUNDANCES
+
+CREATE TABLE ABUNDANCES(
+ ID TECH_ID NOT NULL,
+ ABTY_ID TECH_ID NOT NULL,
+ AMOUNT REAL_NUMBER NOT NULL
+)
+WITH (OIDS=FALSE)
+;
+
+-- Add keys for table ABUNDANCES
+
+ALTER TABLE ABUNDANCES ADD CONSTRAINT ABUN_PK PRIMARY KEY (ID)
+;
+
+-- Table ABUNDANCES_TYPES
+
+CREATE TABLE ABUNDANCES_TYPES(
+ ID TECH_ID NOT NULL,
+ CODE CODE NOT NULL,
+ DESCRIPTION SHORT_DESCRIPTION
+)
+WITH (OIDS=FALSE)
+;
+
+-- Add keys for table ABUNDANCES_TYPES
+
+ALTER TABLE ABUNDANCES_TYPES ADD CONSTRAINT ABTY_PK PRIMARY KEY (ID)
+;
+
+ALTER TABLE ABUNDANCES_TYPES ADD CONSTRAINT ABTY_CODE_BK UNIQUE (CODE)
+;
+
+-- Table IDENTIFICATION_DATA
+
+CREATE TABLE IDENTIFICATION_DATA(
+ ID TECH_ID NOT NULL,
+ SPEC_ID TECH_ID,
+ SPECTRA_COUNT INTEGER_NUMBER
+)
+WITH (OIDS=FALSE)
+;
+
+-- Table MODIFICATIONS
+
+CREATE TABLE MODIFICATIONS(
+ ID TECH_ID NOT NULL,
+ MOPE_ID TECH_ID NOT NULL,
+ MOTY_ID TECH_ID NOT NULL,
+ POSITION INTEGER_NUMBER NOT NULL,
+ MASS REAL_NUMBER NOT NULL
+)
+WITH (OIDS=FALSE)
+;
+
+-- Add keys for table MODIFICATIONS
+
+ALTER TABLE MODIFICATIONS ADD CONSTRAINT MODI_PK PRIMARY KEY (ID)
+;
+
+-- Table MODIFICATION_TYPES
+
+CREATE TABLE MODIFICATION_TYPES(
+ ID TECH_ID NOT NULL,
+ CODE CODE NOT NULL,
+ DESCRIPTION SHORT_DESCRIPTION,
+ MASS REAL_NUMBER,
+ DELTA_MASS REAL_NUMBER
+)
+WITH (OIDS=FALSE)
+;
+
+-- Add keys for table MODIFICATION_TYPES
+
+ALTER TABLE MODIFICATION_TYPES ADD CONSTRAINT MOTY_PK PRIMARY KEY (ID)
+;
+
+ALTER TABLE MODIFICATION_TYPES ADD CONSTRAINT MOTY_CODE_BK UNIQUE (CODE)
+;
+
+-- Table MODIFIED_PEPTIDES
+
+CREATE TABLE MODIFIED_PEPTIDES(
+ ID TECH_ID NOT NULL,
+ PEPT_ID TECH_ID NOT NULL,
+ ABUN_ID TECH_ID,
+ IDDA_ID TECH_ID,
+ CHARGE INTEGER_NUMBER NOT NULL
+)
+WITH (OIDS=FALSE)
+;
+
+-- Add keys for table MODIFIED_PEPTIDES
+
+ALTER TABLE MODIFIED_PEPTIDES ADD CONSTRAINT MOPE_PK PRIMARY KEY (ID)
+;
+
+-- Table PEPTIDES
+
+CREATE TABLE PEPTIDES(
+ ID TECH_ID NOT NULL,
+ PROT_ID TECH_ID NOT NULL,
+ SEQU_ID TECH_ID NOT NULL
+)
+WITH (OIDS=FALSE)
+;
+
+-- Add keys for table PEPTIDES
+
+ALTER TABLE PEPTIDES ADD CONSTRAINT PEPT_PK PRIMARY KEY (ID)
+;
+
+-- Table PROTEIN_STATISTICS
+
+CREATE TABLE PROTEIN_STATISTICS(
+ ID TECH_ID NOT NULL
+)
+WITH (OIDS=FALSE)
+;
+
+-- Add keys for table PROTEIN_STATISTICS
+
+ALTER TABLE PROTEIN_STATISTICS ADD CONSTRAINT PRST_PK PRIMARY KEY (ID)
+;
+
+-- Table PROTEINS
+
+CREATE TABLE PROTEINS(
+ ID TECH_ID NOT NULL,
+ SEQU_ID TECH_ID NOT NULL,
+ ABUN_ID TECH_ID,
+ PRST_ID TECH_ID
+)
+WITH (OIDS=FALSE)
+;
+
+-- Add keys for table PROTEINS
+
+ALTER TABLE PROTEINS ADD CONSTRAINT PROT_PK PRIMARY KEY (ID)
+;
+
+-- Table SEQUENCES
+
+CREATE TABLE SEQUENCES(
+ ID TECH_ID NOT NULL,
+ AMINO_ACID_SEQUENCE SEQUENCE NOT NULL,
+ CHECKSUM CHECKSUM NOT NULL
+)
+WITH (OIDS=FALSE)
+;
+
+-- Add keys for table SEQUENCES
+
+ALTER TABLE SEQUENCES ADD CONSTRAINT SEQU_PK PRIMARY KEY (ID)
+;
+
+-- Table SPECTRA
+
+CREATE TABLE SPECTRA(
+ ID TECH_ID NOT NULL,
+ DATA BINARY_DATA NOT NULL
+)
+WITH (OIDS=FALSE)
+;
+
+-- Add keys for table SPECTRA
+
+ALTER TABLE SPECTRA ADD CONSTRAINT SPEC_PK PRIMARY KEY (ID)
+;
+
+-- Create relationships section ------------------------------------------------- 
+
+CREATE INDEX IX_PE_PR_FK_PEPTIDES ON PEPTIDES (PROT_ID)
+;
+ALTER TABLE PEPTIDES ADD CONSTRAINT PE_PR_FK FOREIGN KEY (PROT_ID) REFERENCES PROTEINS (ID) ON DELETE NO ACTION ON UPDATE NO ACTION
+;
+
+CREATE INDEX IX_PE_SE_FK_PEPTIDES ON PEPTIDES (SEQU_ID)
+;
+ALTER TABLE PEPTIDES ADD CONSTRAINT PE_SE_FK FOREIGN KEY (SEQU_ID) REFERENCES SEQUENCES (ID) ON DELETE NO ACTION ON UPDATE NO ACTION
+;
+
+CREATE INDEX IX_PR_SE_FK_PROTEINS ON PROTEINS (SEQU_ID)
+;
+ALTER TABLE PROTEINS ADD CONSTRAINT PR_SE_FK FOREIGN KEY (SEQU_ID) REFERENCES SEQUENCES (ID) ON DELETE NO ACTION ON UPDATE NO ACTION
+;
+
+CREATE INDEX IX_MO_PE_FK_MODIFIED_PEPTIDES ON MODIFIED_PEPTIDES (PEPT_ID)
+;
+ALTER TABLE MODIFIED_PEPTIDES ADD CONSTRAINT MO_PE_FK FOREIGN KEY (PEPT_ID) REFERENCES PEPTIDES (ID) ON DELETE NO ACTION ON UPDATE NO ACTION
+;
+
+CREATE INDEX IX_MO_MP_FK_MODIFICATIONS ON MODIFICATIONS (MOPE_ID)
+;
+ALTER TABLE MODIFICATIONS ADD CONSTRAINT MO_MP_FK FOREIGN KEY (MOPE_ID) REFERENCES MODIFIED_PEPTIDES (ID) ON DELETE NO ACTION ON UPDATE NO ACTION
+;
+
+CREATE INDEX IX_MO_MT_FK_MODIFICATIONS ON MODIFICATIONS (MOTY_ID)
+;
+ALTER TABLE MODIFICATIONS ADD CONSTRAINT MO_MT_FK FOREIGN KEY (MOTY_ID) REFERENCES MODIFICATION_TYPES (ID) ON DELETE NO ACTION ON UPDATE NO ACTION
+;
+
+CREATE INDEX IX_AB_AT_FK_ABUNDANCES ON ABUNDANCES (ABTY_ID)
+;
+ALTER TABLE ABUNDANCES ADD CONSTRAINT AB_AT_FK FOREIGN KEY (ABTY_ID) REFERENCES ABUNDANCES_TYPES (ID) ON DELETE NO ACTION ON UPDATE NO ACTION
+;
+
+CREATE INDEX IX_PR_AB_FK_PROTEINS ON PROTEINS (ABUN_ID)
+;
+ALTER TABLE PROTEINS ADD CONSTRAINT PR_AB_FK FOREIGN KEY (ABUN_ID) REFERENCES ABUNDANCES (ID) ON DELETE NO ACTION ON UPDATE NO ACTION
+;
+
+CREATE INDEX IX_MP_AB_FK_MODIFIED_PEPTIDES ON MODIFIED_PEPTIDES (ABUN_ID)
+;
+ALTER TABLE MODIFIED_PEPTIDES ADD CONSTRAINT MP_AB_FK FOREIGN KEY (ABUN_ID) REFERENCES ABUNDANCES (ID) ON DELETE NO ACTION ON UPDATE NO ACTION
+;
+
+CREATE INDEX IX_PR_PS_FK_PROTEINS ON PROTEINS (PRST_ID)
+;
+ALTER TABLE PROTEINS ADD CONSTRAINT PR_PS_FK FOREIGN KEY (PRST_ID) REFERENCES PROTEIN_STATISTICS (ID) ON DELETE NO ACTION ON UPDATE NO ACTION
+;
+
+CREATE INDEX IX_MO_ID_FK_MODIFIED_PEPTIDES ON MODIFIED_PEPTIDES (IDDA_ID)
+;
+ALTER TABLE MODIFIED_PEPTIDES ADD CONSTRAINT MO_ID_FK FOREIGN KEY (IDDA_ID) REFERENCES IDENTIFICATION_DATA (ID) ON DELETE NO ACTION ON UPDATE NO ACTION
+;
+
+CREATE INDEX IX_ID_SP_FK_IDENTIFICATION_DATA ON IDENTIFICATION_DATA (SPEC_ID)
+;
+ALTER TABLE IDENTIFICATION_DATA ADD CONSTRAINT ID_SP_FK FOREIGN KEY (SPEC_ID) REFERENCES SPECTRA (ID) ON DELETE NO ACTION ON UPDATE NO ACTION
+;
+
+
+
diff --git a/rtd_phosphonetx/.gitignore b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/phosphonetx/.gitignore
similarity index 100%
rename from rtd_phosphonetx/.gitignore
rename to rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/phosphonetx/.gitignore
diff --git a/rtd_phosphonetx/sourceTest/java/tests.xml b/rtd_phosphonetx/sourceTest/java/tests.xml
new file mode 100644
index 00000000000..565cc7dc0c2
--- /dev/null
+++ b/rtd_phosphonetx/sourceTest/java/tests.xml
@@ -0,0 +1,12 @@
+<suite name="All" verbose="2" >
+  <test name="All" annotations="JDK">
+    <groups>
+      <run>
+        <exclude name="broken" />
+      </run>
+    </groups>
+    <packages>
+      <package name="ch.systemsx.cisd.phosphonetx.*" />
+   </packages>
+ </test>
+</suite>
-- 
GitLab