From af4c2c93a775a6a8a03fc06bc7c97c5ebc397009 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Tue, 8 Jun 2010 07:05:10 +0000
Subject: [PATCH] SE-256 MZ peaks now stored as text in metabol database
SVN: 16313
---
.../db/MetabolDatabaseVersionHolder.java | 2 +-
.../systemsx/cisd/yeastx/mzxml/IMzXmlDAO.java | 15 +-
.../cisd/yeastx/mzxml/MzXml2Database.java | 44 +--
.../cisd/yeastx/mzxml/dto/MzScanDTO.java | 47 ++-
.../source/sql/postgresql/005/schema-005.sql | 340 ++++++++++++++++++
.../migration/migration-004-005.sql | 3 +
.../cisd/yeastx/mzxml/MzXMLParserTest.java | 18 +-
.../cisd/yeastx/mzxml/MzXml2DatabaseTest.java | 34 --
8 files changed, 405 insertions(+), 98 deletions(-)
create mode 100644 rtd_yeastx/source/sql/postgresql/005/schema-005.sql
create mode 100644 rtd_yeastx/source/sql/postgresql/migration/migration-004-005.sql
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/MetabolDatabaseVersionHolder.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/MetabolDatabaseVersionHolder.java
index 6e4c4fb953e..d24e4ce2c28 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/MetabolDatabaseVersionHolder.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/MetabolDatabaseVersionHolder.java
@@ -26,7 +26,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.IDatabaseVersionHolder;
public class MetabolDatabaseVersionHolder implements IDatabaseVersionHolder
{
/** Current version of the database. */
- static final String DATABASE_VERSION = "004";
+ static final String DATABASE_VERSION = "005";
public String getDatabaseVersion()
{
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/mzxml/IMzXmlDAO.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/mzxml/IMzXmlDAO.java
index ab62445fa22..0916c920ffc 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/mzxml/IMzXmlDAO.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/mzxml/IMzXmlDAO.java
@@ -40,23 +40,18 @@ public interface IMzXmlDAO extends IDMGenericDAO
+ " returning ID")
public long addRun(DMDataSetDTO dataSet, MzInstrumentDTO instrument);
- @Select(sql = "insert into MZ_SCANS "
+ @Update(sql = "insert into MZ_SCANS "
+ " ( MZ_MS_RUN_ID, NUMBER, LEVEL, PEAKS_COUNT, POLARITY, "
+ " SCAN_TYPE, COLLISION_ENERGY, LOW_MZ, HIGH_MZ, "
- + " RETENTION_TIME, "
+ + " MZ_PEAK_POSITIONS, MZ_PEAK_INTENSITIES, RETENTION_TIME, "
+ " PRECURSOR1_MZ, PRECURSOR1_INTENSITY, PRECURSOR1_CHARGE, "
+ " PRECURSOR2_MZ, PRECURSOR2_INTENSITY, PRECURSOR2_CHARGE ) "
+ " values ( ?{1}, ?{2.number}, ?{2.level}, ?{2.peaksCount}, ?{2.polarity}, "
+ " ?{2.scanType}, ?{2.collisionEnergy}, ?{2.lowMz}, ?{2.highMz}, "
- + " ?{2.retentionTimeInSeconds}, "
+ + " ?{2.peakPositions}, ?{2.peakIntensities}, ?{2.retentionTimeInSeconds}, "
+ " ?{3.mz}, ?{3.intensity}, ?{3.charge}, "
- + " ?{4.mz}, ?{4.intensity}, ?{4.charge} ) "
- + " returning ID")
- public long addScan(long runId, MzScanDTO scan, MzPrecursorDTO precursor1,
+ + " ?{4.mz}, ?{4.intensity}, ?{4.charge} ) ")
+ public void addScan(long runId, MzScanDTO scan, MzPrecursorDTO precursor1,
MzPrecursorDTO precursor2);
- @Update(sql = "insert into MZ_PEAKS (MZ_SCAN_ID, MZ, INTENSITY) "
- + " values (?{1}, ?{2}, ?{3})", batchUpdate = true)
- public void addPeaks(long scanId, Iterable<Float> mzArray, Iterable<Float> intensityArray);
-
}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/mzxml/MzXml2Database.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/mzxml/MzXml2Database.java
index 9af38d4413e..85ad6cb7558 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/mzxml/MzXml2Database.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/mzxml/MzXml2Database.java
@@ -18,13 +18,11 @@ package ch.systemsx.cisd.yeastx.mzxml;
import java.io.File;
import java.sql.SQLException;
-import java.util.Iterator;
import java.util.List;
import javax.sql.DataSource;
import ch.rinn.restrictions.Private;
-import ch.systemsx.cisd.common.exceptions.NotImplementedException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.yeastx.db.AbstractDatasetLoader;
import ch.systemsx.cisd.yeastx.db.generic.DMDataSetDTO;
@@ -108,47 +106,7 @@ public class MzXml2Database extends AbstractDatasetLoader<IMzXmlDAO>
scan.getNumber(), precursors.size());
}
}
- long scanId = getDao().addScan(runId, scan, precursor1, precursor2);
- uploadPeaks(scanId, scan.getPeaks());
+ getDao().addScan(runId, scan, precursor1, precursor2);
}
- private void uploadPeaks(long scanId, float[] peaks)
- {
- Iterable<Float> mzArray = createEverySecondIterator(peaks, 0);
- Iterable<Float> intensityArray = createEverySecondIterator(peaks, 1);
- getDao().addPeaks(scanId, mzArray, intensityArray);
- }
-
- // iterates on every second element of an array starting from the specified initial index
- private static Iterable<Float> createEverySecondIterator(final float[] bytes,
- final int initialIndex)
- {
- return new Iterable<Float>()
- {
- public Iterator<Float> iterator()
- {
- return new Iterator<Float>()
- {
- private int nextIx = initialIndex;
-
- public boolean hasNext()
- {
- return nextIx < bytes.length;
- }
-
- public Float next()
- {
- int ix = nextIx;
- nextIx += 2;
- return bytes[ix];
- }
-
- public void remove()
- {
- throw new NotImplementedException();
- }
- };
- }
- };
- }
}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/mzxml/dto/MzScanDTO.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/mzxml/dto/MzScanDTO.java
index 10102f8399f..e3e61535491 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/mzxml/dto/MzScanDTO.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/mzxml/dto/MzScanDTO.java
@@ -33,6 +33,10 @@ public class MzScanDTO
private int level;
private int peaksCount;
+
+ private String peakPositions;
+
+ private String peakIntensities;
private String polarity;
@@ -178,9 +182,46 @@ public class MzScanDTO
return XmlUtils.tryAsSeconds(retentionTime);
}
- /** the array has mz on even positions and intensities on odd positions */
- public float[] getPeaks()
+ public final String getPeakPositions()
{
- return XmlUtils.asFloats(peaks.getPeaks());
+ initPeaks();
+ return peakPositions;
+ }
+
+ public final String getPeakIntensities()
+ {
+ initPeaks();
+ return peakIntensities;
+ }
+
+ private void initPeaks()
+ {
+ if (peakPositions == null)
+ {
+ float[] floats = XmlUtils.asFloats(peaks.getPeaks());
+ StringBuilder positions = new StringBuilder();
+ StringBuilder intensities = new StringBuilder();
+ for (int i = 0; i < floats.length; i++)
+ {
+ if (i % 2 == 0)
+ {
+ addTo(positions, floats[i]);
+ } else
+ {
+ addTo(intensities, floats[i]);
+ }
+ }
+ peakPositions = positions.toString();
+ peakIntensities = intensities.toString();
+ }
+ }
+
+ private void addTo(StringBuilder builder, float value)
+ {
+ if (builder.length() > 0)
+ {
+ builder.append(", ");
+ }
+ builder.append(value);
}
}
diff --git a/rtd_yeastx/source/sql/postgresql/005/schema-005.sql b/rtd_yeastx/source/sql/postgresql/005/schema-005.sql
new file mode 100644
index 00000000000..c4cc7a4293f
--- /dev/null
+++ b/rtd_yeastx/source/sql/postgresql/005/schema-005.sql
@@ -0,0 +1,340 @@
+-----------------------------------
+-- Version 004
+-----------------------------------
+
+-- Create domain types section -------------------------------------------------
+
+CREATE DOMAIN TECH_ID AS BIGINT;
+
+CREATE DOMAIN CODE AS VARCHAR(40);
+
+CREATE DOMAIN FILE_NAME as VARCHAR(255);
+
+CREATE DOMAIN FILE_PATH as VARCHAR(1000);
+
+CREATE DOMAIN SHORT_LABEL as VARCHAR(20);
+
+CREATE DOMAIN LONG_LABEL as VARCHAR(100);
+
+CREATE DOMAIN CHAR as VARCHAR(1);
+
+CREATE DOMAIN ms_quantification_software_kind AS character varying(40)
+ CONSTRAINT ms_quantification_software_kind_check CHECK (((VALUE)::text =
+ ANY ((ARRAY['msSoft'::character varying, 'Xcalibur'::character varying,
+ 'Analyst'::character varying, 'MassHunter'::character varying])::text[])));
+
+
+-- Create tables section -------------------------------------------------
+
+-- Table EXPERIMENTS
+
+CREATE TABLE EXPERIMENTS (
+ ID BIGSERIAL NOT NULL,
+ PERM_ID CODE NOT NULL,
+ NAME LONG_LABEL NOT NULL,
+ PRIMARY KEY (ID),
+ UNIQUE (PERM_ID)
+);
+
+-- Table SAMPLES
+
+CREATE TABLE SAMPLES (
+ ID BIGSERIAL NOT NULL,
+ PERM_ID CODE NOT NULL,
+ NAME LONG_LABEL NOT NULL,
+ EXPE_ID TECH_ID NOT NULL,
+ PRIMARY KEY (ID),
+ UNIQUE (PERM_ID),
+ CONSTRAINT FK_SAMPLE_1 FOREIGN KEY (EXPE_ID) REFERENCES EXPERIMENTS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+-- Table DATA_SETS
+
+CREATE TABLE DATA_SETS (
+ ID BIGSERIAL NOT NULL,
+ PERM_ID CODE NOT NULL,
+ EXPE_ID TECH_ID NOT NULL,
+ SAMP_ID TECH_ID,
+ PRIMARY KEY (ID),
+ UNIQUE (PERM_ID),
+ CONSTRAINT FK_DATA_SET_1 FOREIGN KEY (EXPE_ID) REFERENCES EXPERIMENTS (ID) ON DELETE CASCADE ON UPDATE CASCADE,
+ CONSTRAINT FK_DATA_SET_2 FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+-- Table EIC_MS_RUNS
+
+CREATE TABLE EIC_MS_RUNS (
+ ID BIGSERIAL NOT NULL,
+ EXPE_ID TECH_ID NOT NULL,
+ SAMP_ID TECH_ID,
+ DS_ID TECH_ID NOT NULL,
+ RAW_DATA_FILE_NAME FILE_NAME NOT NULL,
+ RAW_DATA_FILE_PATH FILE_PATH DEFAULT NULL,
+ ACQUISITION_DATE TIMESTAMP DEFAULT NULL,
+ INSTRUMENT_TYPE SHORT_LABEL DEFAULT NULL,
+ INSTRUMENT_MANUFACTURER LONG_LABEL DEFAULT NULL,
+ INSTRUMENT_MODEL LONG_LABEL DEFAULT NULL,
+ METHOD_IONISATION SHORT_LABEL DEFAULT NULL,
+ METHOD_SEPARATION LONG_LABEL DEFAULT NULL,
+ OPERATOR SHORT_LABEL DEFAULT NULL,
+ MS_RUN_ID BIGINT DEFAULT NULL,
+ SET_ID TECH_ID DEFAULT NULL,
+ START_TIME REAL NOT NULL,
+ END_TIME REAL NOT NULL,
+ PRIMARY KEY (ID),
+ CONSTRAINT FK_EIC_MS_RUN_1 FOREIGN KEY (EXPE_ID) REFERENCES EXPERIMENTS (ID) ON DELETE CASCADE ON UPDATE CASCADE,
+ CONSTRAINT FK_EIC_MS_RUN_2 FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID) ON DELETE CASCADE ON UPDATE CASCADE,
+ CONSTRAINT FK_EIC_MS_RUN_3 FOREIGN KEY (DS_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+CREATE INDEX EIC_MS_RUNS_FK_DS_ID_IDX ON EIC_MS_RUNS(DS_ID);
+CREATE INDEX EIC_MS_RUNS_FK_SAMP_ID_IDX ON EIC_MS_RUNS(SAMP_ID);
+CREATE INDEX EIC_MS_RUNS_FK_EXPE_ID_IDX ON EIC_MS_RUNS(EXPE_ID);
+
+-- Table EIC_CHROMATOGRAMS
+
+CREATE TABLE EIC_CHROMATOGRAMS (
+ ID BIGSERIAL NOT NULL,
+ EIC_MS_RUN_ID TECH_ID NOT NULL,
+ Q1_MZ REAL NOT NULL,
+ Q3_LOW_MZ REAL NOT NULL,
+ Q3_HIGH_MZ REAL NOT NULL,
+ LABEL LONG_LABEL DEFAULT NULL,
+ POLARITY CHAR DEFAULT NULL,
+ RUN_TIMES TEXT NOT NULL,
+ INTENSITIES TEXT NOT NULL,
+ PRIMARY KEY (ID),
+ CONSTRAINT FK_EIC_CHROMATOGRAM_1 FOREIGN KEY (EIC_MS_RUN_ID) REFERENCES EIC_MS_RUNS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+CREATE INDEX EIC_CHROMATOGRAM_FK_IDX ON EIC_CHROMATOGRAMS(EIC_MS_RUN_ID);
+
+-- Table FIA_MS_RUNS
+
+CREATE TABLE FIA_MS_RUNS (
+ ID BIGSERIAL NOT NULL,
+ EXPE_ID TECH_ID NOT NULL,
+ SAMP_ID TECH_ID,
+ DS_ID TECH_ID NOT NULL,
+ RAW_DATA_FILE_NAME FILE_NAME NOT NULL,
+ RAW_DATA_FILE_PATH FILE_PATH DEFAULT NULL,
+ ACQUISITION_DATE TIMESTAMP DEFAULT NULL,
+ INSTRUMENT_TYPE SHORT_LABEL DEFAULT NULL,
+ INSTRUMENT_MANUFACTURER LONG_LABEL DEFAULT NULL,
+ INSTRUMENT_MODEL LONG_LABEL DEFAULT NULL,
+ METHOD_IONISATION SHORT_LABEL DEFAULT NULL,
+ METHOD_SEPARATION LONG_LABEL DEFAULT NULL,
+ POLARITY VARCHAR(1) DEFAULT NULL,
+ LOW_MZ REAL NOT NULL,
+ HIGH_MZ REAL NOT NULL,
+ INTERNAL_STANDARD REAL NOT NULL,
+ -- Is this a good name?
+ OD REAL NOT NULL,
+ OPERATOR SHORT_LABEL DEFAULT NULL,
+ PRIMARY KEY (ID),
+ CONSTRAINT FK_FIA_MS_RUN_1 FOREIGN KEY (EXPE_ID) REFERENCES EXPERIMENTS (ID) ON DELETE CASCADE ON UPDATE CASCADE,
+ CONSTRAINT FK_EIA_MS_RUN_2 FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID) ON DELETE CASCADE ON UPDATE CASCADE,
+ CONSTRAINT FK_EIA_MS_RUN_3 FOREIGN KEY (DS_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+CREATE INDEX FIA_MS_RUNS_FK_DS_ID_IDX ON FIA_MS_RUNS(DS_ID);
+CREATE INDEX FIA_MS_RUNS_FK_SAMP_ID_IDX ON FIA_MS_RUNS(SAMP_ID);
+CREATE INDEX FIA_MS_RUNS_FK_EXPE_ID_IDX ON FIA_MS_RUNS(EXPE_ID);
+
+-- Table FIA_PROFILES
+
+CREATE TABLE FIA_PROFILES (
+ ID BIGSERIAL NOT NULL,
+ FIA_MS_RUN_ID TECH_ID NOT NULL,
+ LOW_MZ REAL NOT NULL,
+ HIGH_MZ REAL NOT NULL,
+ MZ TEXT NOT NULL,
+ INTENSITIES TEXT NOT NULL,
+ PRIMARY KEY (ID),
+ CONSTRAINT FK_FIA_PROFILE_1 FOREIGN KEY (FIA_MS_RUN_ID) REFERENCES FIA_MS_RUNS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+CREATE INDEX FIA_PROFILE_I_ID on FIA_PROFILES(FIA_MS_RUN_ID);
+CREATE INDEX FIA_PROFILE_I_ID_MZ on FIA_PROFILES(FIA_MS_RUN_ID, LOW_MZ, HIGH_MZ);
+
+-- Table FIA_CENTROIDS
+
+CREATE TABLE FIA_CENTROIDS (
+ ID BIGSERIAL NOT NULL,
+ FIA_MS_RUN_ID TECH_ID NOT NULL,
+ MZ REAL NOT NULL,
+ INTENSITY REAL NOT NULL,
+ CORRELATION REAL NOT NULL,
+ PRIMARY KEY (ID),
+ CONSTRAINT FK_FIA_CENTROID_1 FOREIGN KEY (FIA_MS_RUN_ID) REFERENCES FIA_MS_RUNS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+CREATE INDEX FIA_CENTROID_I_ID ON FIA_CENTROIDS(FIA_MS_RUN_ID);
+CREATE INDEX FIA_CENTROID_I_ID_MZ ON FIA_CENTROIDS(FIA_MS_RUN_ID, MZ);
+
+-- Table MS_QUANTIFICATIONS
+
+CREATE TABLE MS_QUANTIFICATIONS (
+ ID BIGSERIAL NOT NULL,
+ DS_ID TECH_ID NOT NULL,
+ EXPE_ID TECH_ID NOT NULL,
+ SOURCE MS_QUANTIFICATION_SOFTWARE_KIND NOT NULL,
+ VALID BOOLEAN NOT NULL,
+ COMMENT TEXT,
+ REGISTRATOR SHORT_LABEL DEFAULT NULL,
+ REGISTRATION_DATE TIMESTAMP DEFAULT NULL,
+ PRIMARY KEY (ID),
+ CONSTRAINT MS_QUANTIFICATION_1 FOREIGN KEY (EXPE_ID) REFERENCES EXPERIMENTS (ID) ON DELETE CASCADE ON UPDATE CASCADE,
+ CONSTRAINT MS_QUANTIFICATION_3 FOREIGN KEY (DS_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+CREATE INDEX MS_QUANTIFICATION_FK_DS_ID_IDX ON MS_QUANTIFICATIONS(DS_ID);
+CREATE INDEX MS_QUANTIFICATION_FK_EXPE_ID_IDX ON MS_QUANTIFICATIONS(EXPE_ID);
+
+-- Table MS_QUANT_CONCENTRATIONS
+
+CREATE TABLE MS_QUANT_CONCENTRATIONS (
+ ID BIGSERIAL NOT NULL,
+ MS_QUANTIFICATION_ID TECH_ID NOT NULL,
+ PARENT_DS_PERM_ID CODE NOT NULL,
+ AMOUNT REAL NOT NULL,
+ UNIT SHORT_LABEL NOT NULL,
+ VALID BOOLEAN NOT NULL,
+ COMMENT TEXT,
+ RETENTION_TIME REAL NOT NULL,
+ Q1 REAL NOT NULL,
+ Q3 REAL NOT NULL,
+ INTERNAL_STANDARD VARCHAR(30) NOT NULL,
+ PRIMARY KEY (ID),
+ CONSTRAINT FK_QUANT_CONCENTRATIONS_1 FOREIGN KEY (MS_QUANTIFICATION_ID) REFERENCES MS_QUANTIFICATIONS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+-- Table MS_QUANT_COMPOUND
+
+CREATE TABLE MS_QUANT_COMPOUNDS (
+ ID BIGSERIAL NOT NULL,
+ MS_QUANT_CONCENTRATION_ID TECH_ID NOT NULL,
+ COMPOUND_ID TECH_ID NOT NULL,
+ CONSTRAINT FK_QUANT_COMPOUND_1 FOREIGN KEY (MS_QUANT_CONCENTRATION_ID) REFERENCES MS_QUANT_CONCENTRATIONS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+--------------- mzXML file content
+CREATE TABLE MZ_MS_RUNS (
+ ID BIGSERIAL NOT NULL,
+ EXPE_ID TECH_ID NOT NULL,
+ SAMP_ID TECH_ID,
+ DS_ID TECH_ID NOT NULL,
+
+ INSTRUMENT_TYPE SHORT_LABEL DEFAULT NULL,
+ INSTRUMENT_MANUFACTURER LONG_LABEL DEFAULT NULL,
+ INSTRUMENT_MODEL LONG_LABEL DEFAULT NULL,
+ METHOD_IONISATION SHORT_LABEL DEFAULT NULL,
+
+ PRIMARY KEY (ID),
+ CONSTRAINT FK_MZ_MS_RUN_1 FOREIGN KEY (EXPE_ID) REFERENCES EXPERIMENTS (ID) ON DELETE CASCADE ON UPDATE CASCADE,
+ CONSTRAINT FK_MZ_MS_RUN_2 FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID) ON DELETE CASCADE ON UPDATE CASCADE,
+ CONSTRAINT FK_MZ_MS_RUN_3 FOREIGN KEY (DS_ID) REFERENCES DATA_SETS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+CREATE INDEX MZ_MS_RUNS_FK_DS_ID_IDX ON MZ_MS_RUNS(DS_ID);
+CREATE INDEX MZ_MS_RUNS_FK_SAMP_ID_IDX ON MZ_MS_RUNS(SAMP_ID);
+CREATE INDEX MZ_MS_RUNS_FK_EXPE_ID_IDX ON MZ_MS_RUNS(EXPE_ID);
+
+
+CREATE TABLE MZ_SCANS (
+ ID BIGSERIAL NOT NULL,
+ MZ_MS_RUN_ID TECH_ID NOT NULL,
+
+ NUMBER INTEGER NOT NULL CHECK (NUMBER > 0),
+ LEVEL INTEGER NOT NULL CHECK (LEVEL > 0),
+ PEAKS_COUNT INTEGER NOT NULL CHECK (PEAKS_COUNT >= 0),
+ MZ_PEAK_POSITIONS TEXT,
+ MZ_PEAK_INTENSITIES TEXT,
+ POLARITY CHAR (1) CHECK (POLARITY = '+' OR POLARITY = '-'),
+ SCAN_TYPE VARCHAR(10),
+ COLLISION_ENERGY REAL,
+ LOW_MZ REAL,
+ HIGH_MZ REAL,
+ RETENTION_TIME REAL,
+
+ PRECURSOR1_MZ REAL,
+ PRECURSOR1_INTENSITY REAL,
+ PRECURSOR1_CHARGE INTEGER CHECK (PRECURSOR1_CHARGE > 0),
+
+ PRECURSOR2_MZ REAL,
+ PRECURSOR2_INTENSITY REAL,
+ PRECURSOR2_CHARGE INTEGER CHECK (PRECURSOR2_CHARGE > 0),
+
+ CHECK (
+ (PRECURSOR1_MZ IS NULL AND PRECURSOR1_INTENSITY IS NULL AND PRECURSOR1_CHARGE IS NULL) OR
+ (PRECURSOR1_MZ IS NOT NULL AND PRECURSOR1_INTENSITY IS NOT NULL)
+ ),
+ CHECK (
+ (PRECURSOR2_MZ IS NULL AND PRECURSOR2_INTENSITY IS NULL AND PRECURSOR2_CHARGE IS NULL) OR
+ (PRECURSOR2_MZ IS NOT NULL AND PRECURSOR2_INTENSITY IS NOT NULL)
+ ),
+ PRIMARY KEY (ID),
+ CONSTRAINT FK_MZ_MS_RUN FOREIGN KEY (MZ_MS_RUN_ID) REFERENCES MZ_MS_RUNS (ID) ON DELETE CASCADE ON UPDATE CASCADE
+);
+
+--------------- END mzXML
+
+-- Table EVENTS
+
+CREATE TABLE EVENTS (
+ LAST_SEEN_DELETION_EVENT_ID TECH_ID NOT NULL
+);
+
+GRANT SELECT ON TABLE EXPERIMENTS TO GROUP metabol_readonly;
+GRANT SELECT ON TABLE SAMPLES TO GROUP metabol_readonly;
+GRANT SELECT ON TABLE DATA_SETS TO GROUP metabol_readonly;
+GRANT SELECT ON TABLE EIC_MS_RUNS TO GROUP metabol_readonly;
+GRANT SELECT ON TABLE EIC_CHROMATOGRAMS TO GROUP metabol_readonly;
+GRANT SELECT ON TABLE FIA_MS_RUNS TO GROUP metabol_readonly;
+GRANT SELECT ON TABLE FIA_PROFILES TO GROUP metabol_readonly;
+GRANT SELECT ON TABLE FIA_CENTROIDS TO GROUP metabol_readonly;
+GRANT SELECT ON TABLE MS_QUANTIFICATIONS TO GROUP metabol_readonly;
+GRANT SELECT ON TABLE MS_QUANT_CONCENTRATIONS TO GROUP metabol_readonly;
+GRANT SELECT ON TABLE MS_QUANT_COMPOUNDS TO GROUP metabol_readonly;
+GRANT SELECT ON TABLE EVENTS TO GROUP metabol_readonly;
+GRANT SELECT ON SEQUENCE EXPERIMENTS_ID_SEQ TO GROUP metabol_readonly;
+GRANT SELECT ON SEQUENCE SAMPLES_ID_SEQ TO GROUP metabol_readonly;
+GRANT SELECT ON SEQUENCE DATA_SETS_ID_SEQ TO GROUP metabol_readonly;
+GRANT SELECT ON SEQUENCE EIC_MS_RUNS_ID_SEQ TO GROUP metabol_readonly;
+GRANT SELECT ON SEQUENCE EIC_CHROMATOGRAMS_ID_SEQ TO GROUP metabol_readonly;
+GRANT SELECT ON SEQUENCE FIA_MS_RUNS_ID_SEQ TO GROUP metabol_readonly;
+GRANT SELECT ON SEQUENCE FIA_PROFILES_ID_SEQ TO GROUP metabol_readonly;
+GRANT SELECT ON SEQUENCE FIA_CENTROIDS_ID_SEQ TO GROUP metabol_readonly;
+GRANT SELECT ON SEQUENCE MS_QUANTIFICATIONS_ID_SEQ TO GROUP metabol_readonly;
+GRANT SELECT ON SEQUENCE MS_QUANT_CONCENTRATIONS_ID_SEQ TO GROUP metabol_readonly;
+GRANT SELECT ON TABLE MZ_MS_RUNS TO GROUP metabol_readonly;
+GRANT SELECT ON TABLE MZ_SCANS TO GROUP metabol_readonly;
+GRANT SELECT ON SEQUENCE MZ_MS_RUNS_ID_SEQ TO GROUP metabol_readonly;
+GRANT SELECT ON SEQUENCE MZ_SCANS_ID_SEQ TO GROUP metabol_readonly;
+
+GRANT ALL PRIVILEGES ON TABLE EXPERIMENTS TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON TABLE SAMPLES TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON TABLE DATA_SETS TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON TABLE EIC_MS_RUNS TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON TABLE EIC_CHROMATOGRAMS TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON TABLE FIA_MS_RUNS TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON TABLE FIA_PROFILES TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON TABLE FIA_CENTROIDS TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON TABLE MS_QUANTIFICATIONS TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON TABLE MS_QUANT_CONCENTRATIONS TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON TABLE MS_QUANT_COMPOUNDS TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON TABLE EVENTS TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON SEQUENCE EXPERIMENTS_ID_SEQ TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON SEQUENCE SAMPLES_ID_SEQ TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON SEQUENCE DATA_SETS_ID_SEQ TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON SEQUENCE EIC_MS_RUNS_ID_SEQ TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON SEQUENCE EIC_CHROMATOGRAMS_ID_SEQ TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON SEQUENCE FIA_MS_RUNS_ID_SEQ TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON SEQUENCE FIA_PROFILES_ID_SEQ TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON SEQUENCE FIA_CENTROIDS_ID_SEQ TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON SEQUENCE MS_QUANTIFICATIONS_ID_SEQ TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON SEQUENCE MS_QUANT_CONCENTRATIONS_ID_SEQ TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON TABLE MZ_MS_RUNS TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON TABLE MZ_SCANS TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON SEQUENCE MZ_MS_RUNS_ID_SEQ TO GROUP metabol_readwrite;
+GRANT ALL PRIVILEGES ON SEQUENCE MZ_SCANS_ID_SEQ TO GROUP metabol_readwrite;
diff --git a/rtd_yeastx/source/sql/postgresql/migration/migration-004-005.sql b/rtd_yeastx/source/sql/postgresql/migration/migration-004-005.sql
new file mode 100644
index 00000000000..f4fc3090b64
--- /dev/null
+++ b/rtd_yeastx/source/sql/postgresql/migration/migration-004-005.sql
@@ -0,0 +1,3 @@
+DROP TABLE MZ_PEAKS;
+ALTER TABLE MZ_SCANS ADD COLUMN MZ_PEAK_POSITIONS TEXT;
+ALTER TABLE MZ_SCANS ADD COLUMN MZ_PEAK_INTENSITIES TEXT;
\ No newline at end of file
diff --git a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/mzxml/MzXMLParserTest.java b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/mzxml/MzXMLParserTest.java
index 711d37d9d3a..acef5b8e7a5 100644
--- a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/mzxml/MzXMLParserTest.java
+++ b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/mzxml/MzXMLParserTest.java
@@ -74,12 +74,16 @@ public class MzXMLParserTest extends AssertJUnit
assertEquals(32333300.0, precursor.getIntensity());
assertNull(precursor.getCharge());
- float[] peakFloats = scan.getPeaks();
- assertEquals(scan.getPeaksCount() * 2, peakFloats.length);
-
- assertEquals(174.6F, peakFloats[0]);
- assertEquals(16666.666F, peakFloats[1]);
- assertEquals(695.88F, peakFloats[peakFloats.length - 2]);
- assertEquals(16666.666F, peakFloats[peakFloats.length - 1]);
+ assertNumbers("174.6", "695.88", scan.getPeaksCount(), scan.getPeakPositions());
+ assertNumbers("16666.666", "16666.666", scan.getPeaksCount(), scan.getPeakIntensities());
+ }
+
+ private void assertNumbers(String firstNumber, String lastNumber, int count, String numbers)
+ {
+ String[] numberArray = numbers.split(",");
+ assertEquals(firstNumber, numberArray[0].trim());
+ assertEquals(lastNumber, numberArray[numberArray.length - 1].trim());
+ assertEquals(count, numberArray.length);
}
+
}
diff --git a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/mzxml/MzXml2DatabaseTest.java b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/mzxml/MzXml2DatabaseTest.java
index 6b6f24028c9..99aed660af8 100644
--- a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/mzxml/MzXml2DatabaseTest.java
+++ b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/mzxml/MzXml2DatabaseTest.java
@@ -17,12 +17,8 @@
package ch.systemsx.cisd.yeastx.mzxml;
import java.util.Arrays;
-import java.util.Iterator;
import java.util.List;
-import org.hamcrest.BaseMatcher;
-import org.hamcrest.Description;
-import org.hamcrest.Matcher;
import org.jmock.Expectations;
import org.jmock.Mockery;
import org.testng.annotations.Test;
@@ -77,36 +73,6 @@ public class MzXml2DatabaseTest
will(returnValue(runId));
exactly(2).of(dao).addScan(runId, scan, precursor, precursor);
- long scanId = 333;
- will(returnValue(scanId));
-
- exactly(2).of(dao).addPeaks(with(scanId), with(createFloatIteratorMatcher(mz)),
- with(createFloatIteratorMatcher(intensity)));
- }
-
- // checks that iterator has exactly one value
- private Matcher<Iterable<Float>> createFloatIteratorMatcher(final float value)
- {
- return new BaseMatcher<Iterable<Float>>()
- {
- public boolean matches(Object item)
- {
- Iterator<Float> iterator = asIterator(item);
- Float number = iterator.next();
- return number.equals(value) && iterator.hasNext() == false;
- }
-
- @SuppressWarnings("unchecked")
- private Iterator<Float> asIterator(Object item)
- {
- return ((Iterable<Float>) item).iterator();
- }
-
- public void describeTo(Description description)
- {
- description.appendValue("iterator with one value '" + value + "'");
- }
- };
}
});
--
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