From c7cf1459a2a73db505c3f15bd88f56d5af5227e4 Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Tue, 29 Sep 2009 19:14:39 +0000
Subject: [PATCH] LMS-1180 YeastX: support metabolomics quantification datasets
SVN: 12773
---
rtd_yeastx/.classpath | 1 +
.../TEST&TEST_PROJECT&TEST_EXP.quantML | 735 ++++++++++++++++++
.../resource/examples/allFields.quantML | 25 +
.../ch/systemsx/cisd/yeastx/db/DBUtils.java | 2 +-
.../yeastx/eicml/EICMLFilenameFilter.java | 6 +-
.../cisd/yeastx/etl/ConstantsYeastX.java | 2 +
.../cisd/yeastx/etl/ML2DatabaseUploader.java | 14 +
.../yeastx/fiaml/FIAMLFilenameFilter.java | 6 +-
.../cisd/yeastx/quant/IQuantMSDAO.java | 50 ++
.../cisd/yeastx/quant/QuantML2Database.java | 135 ++++
.../quant/QuantMLDataSetInfoExtractor.java | 74 ++
.../cisd/yeastx/quant/QuantMLParser.java | 100 +++
.../cisd/yeastx/quant/XmlDateAdapter.java | 43 +
.../quant/dto/ConcentrationCompounds.java | 42 +
.../yeastx/quant/dto/MSConcentrationDTO.java | 157 ++++
.../yeastx/quant/dto/MSQuantificationDTO.java | 112 +++
.../quant/dto/MSQuantificationsDTO.java | 47 ++
.../source/sql/postgresql/003/schema-003.sql | 3 +-
.../migration/migration-002-003.sql | 3 +-
.../cisd/yeastx/quant/QuantMLParserTest.java | 94 +++
.../cisd/yeastx/quant/QuantMSDAOTest.java | 63 ++
21 files changed, 1707 insertions(+), 7 deletions(-)
create mode 100644 rtd_yeastx/resource/examples/TEST&TEST_PROJECT&TEST_EXP.quantML
create mode 100644 rtd_yeastx/resource/examples/allFields.quantML
create mode 100644 rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/IQuantMSDAO.java
create mode 100644 rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/QuantML2Database.java
create mode 100644 rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/QuantMLDataSetInfoExtractor.java
create mode 100644 rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/QuantMLParser.java
create mode 100644 rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/XmlDateAdapter.java
create mode 100644 rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/dto/ConcentrationCompounds.java
create mode 100644 rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/dto/MSConcentrationDTO.java
create mode 100644 rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/dto/MSQuantificationDTO.java
create mode 100644 rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/dto/MSQuantificationsDTO.java
create mode 100644 rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/quant/QuantMLParserTest.java
create mode 100644 rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/quant/QuantMSDAOTest.java
diff --git a/rtd_yeastx/.classpath b/rtd_yeastx/.classpath
index fcb08714a47..ea7f89f9fff 100644
--- a/rtd_yeastx/.classpath
+++ b/rtd_yeastx/.classpath
@@ -21,5 +21,6 @@
<classpathentry kind="lib" path="/libraries/spring/spring.jar" sourcepath="/libraries/spring/src.jar"/>
<classpathentry kind="lib" path="/libraries/eodsql/eodsql.jar" sourcepath="/libraries/eodsql/eodsql_src.zip"/>
<classpathentry kind="lib" path="/libraries/gwt1.5/gwt-isserializable.jar"/>
+ <classpathentry kind="lib" path="/libraries/jaxb/jaxb-api.jar" sourcepath="/libraries/jaxb/jaxb-api-src.zip"/>
<classpathentry kind="output" path="targets/classes"/>
</classpath>
diff --git a/rtd_yeastx/resource/examples/TEST&TEST_PROJECT&TEST_EXP.quantML b/rtd_yeastx/resource/examples/TEST&TEST_PROJECT&TEST_EXP.quantML
new file mode 100644
index 00000000000..145bf0afe5a
--- /dev/null
+++ b/rtd_yeastx/resource/examples/TEST&TEST_PROJECT&TEST_EXP.quantML
@@ -0,0 +1,735 @@
+<?xml version="1.0" encoding="utf-8"?>
+<quantML>
+ <msQuantification>
+ <source>msSoft</source>
+ <valid>true</valid>
+ <concentration>
+ <datasetParent>20090822211007858-23605</datasetParent>
+ <amount>0.689155</amount>
+ <unit/>
+ <comment/>
+ <valid>true</valid>
+ <retentionTime>939.5</retentionTime>
+ <Q1>664.1</Q1>
+ <Q3>408</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23806</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211016773-23606</datasetParent>
+ <amount>3.775339</amount>
+ <unit/>
+ <comment/>
+ <valid>true</valid>
+ <retentionTime>922.2</retentionTime>
+ <Q1>664.1</Q1>
+ <Q3>408</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23806</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211024338-23607</datasetParent>
+ <amount>3.909032</amount>
+ <unit/>
+ <comment/>
+ <valid>true</valid>
+ <retentionTime>922.6</retentionTime>
+ <Q1>664.1</Q1>
+ <Q3>408</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23806</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211027473-23608</datasetParent>
+ <amount>4.181345</amount>
+ <unit/>
+ <comment/>
+ <valid>true</valid>
+ <retentionTime>921.6</retentionTime>
+ <Q1>664.1</Q1>
+ <Q3>408</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23806</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211029837-23609</datasetParent>
+ <amount>4.210279</amount>
+ <unit/>
+ <comment/>
+ <valid>true</valid>
+ <retentionTime>922.8</retentionTime>
+ <Q1>664.1</Q1>
+ <Q3>408</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23806</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211032103-23610</datasetParent>
+ <amount>4.209338</amount>
+ <unit/>
+ <comment/>
+ <valid>true</valid>
+ <retentionTime>923.5</retentionTime>
+ <Q1>664.1</Q1>
+ <Q3>408</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23806</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211040739-23611</datasetParent>
+ <amount>3.303593</amount>
+ <unit/>
+ <comment/>
+ <valid>true</valid>
+ <retentionTime>922.2</retentionTime>
+ <Q1>664.1</Q1>
+ <Q3>408</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23806</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211044547-23612</datasetParent>
+ <amount>-4.328958</amount>
+ <unit/>
+ <comment>signal high</comment>
+ <valid>false</valid>
+ <retentionTime>920.9</retentionTime>
+ <Q1>664.1</Q1>
+ <Q3>408</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23806</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211049391-23613</datasetParent>
+ <amount>-16.153122</amount>
+ <unit/>
+ <comment>signal high</comment>
+ <valid>false</valid>
+ <retentionTime>919.7</retentionTime>
+ <Q1>664.1</Q1>
+ <Q3>408</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23806</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211052411-23614</datasetParent>
+ <amount>0.361582</amount>
+ <unit/>
+ <comment>signal high</comment>
+ <valid>false</valid>
+ <retentionTime>922.2</retentionTime>
+ <Q1>664.1</Q1>
+ <Q3>408</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23806</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211056619-23615</datasetParent>
+ <amount>2.614341</amount>
+ <unit/>
+ <comment/>
+ <valid>true</valid>
+ <retentionTime>922.2</retentionTime>
+ <Q1>664.1</Q1>
+ <Q3>408</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23806</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211100743-23616</datasetParent>
+ <amount>3.298259</amount>
+ <unit/>
+ <comment/>
+ <valid>true</valid>
+ <retentionTime>924.1</retentionTime>
+ <Q1>664.1</Q1>
+ <Q3>408</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23806</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211104731-23617</datasetParent>
+ <amount>3.899307</amount>
+ <unit/>
+ <comment/>
+ <valid>true</valid>
+ <retentionTime>922.8</retentionTime>
+ <Q1>664.1</Q1>
+ <Q3>408</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23806</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211111839-23618</datasetParent>
+ <amount>3.724714</amount>
+ <unit/>
+ <comment/>
+ <valid>true</valid>
+ <retentionTime>922.2</retentionTime>
+ <Q1>664.1</Q1>
+ <Q3>408</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23806</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211119852-23619</datasetParent>
+ <amount>2.494577</amount>
+ <unit/>
+ <comment/>
+ <valid>true</valid>
+ <retentionTime>922.2</retentionTime>
+ <Q1>664.1</Q1>
+ <Q3>408</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23806</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211122021-23620</datasetParent>
+ <amount>3.652310</amount>
+ <unit/>
+ <comment/>
+ <valid>true</valid>
+ <retentionTime>922.2</retentionTime>
+ <Q1>664.1</Q1>
+ <Q3>408</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23806</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211124186-23621</datasetParent>
+ <amount>4.230794</amount>
+ <unit/>
+ <comment>signal low</comment>
+ <valid>false</valid>
+ <retentionTime>951.6</retentionTime>
+ <Q1>664.1</Q1>
+ <Q3>408</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23806</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211127046-23622</datasetParent>
+ <amount>4.230957</amount>
+ <unit/>
+ <comment>signal low</comment>
+ <valid>false</valid>
+ <retentionTime>941.4</retentionTime>
+ <Q1>664.1</Q1>
+ <Q3>408</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23806</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211131542-23623</datasetParent>
+ <amount>4.230698</amount>
+ <unit/>
+ <comment>signal low</comment>
+ <valid>false</valid>
+ <retentionTime>933.0</retentionTime>
+ <Q1>664.1</Q1>
+ <Q3>408</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23806</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211135837-23624</datasetParent>
+ <amount>4.230236</amount>
+ <unit/>
+ <comment>signal low</comment>
+ <valid>false</valid>
+ <retentionTime>940.1</retentionTime>
+ <Q1>664.1</Q1>
+ <Q3>408</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23806</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211139038-23625</datasetParent>
+ <amount>4.230934</amount>
+ <unit/>
+ <comment>signal low</comment>
+ <valid>false</valid>
+ <retentionTime>940.1</retentionTime>
+ <Q1>664.1</Q1>
+ <Q3>408</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23806</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211142289-23626</datasetParent>
+ <amount>4.230776</amount>
+ <unit/>
+ <comment>signal low</comment>
+ <valid>false</valid>
+ <retentionTime>942.7</retentionTime>
+ <Q1>664.1</Q1>
+ <Q3>408</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23806</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211144528-23627</datasetParent>
+ <amount>4.231008</amount>
+ <unit/>
+ <comment>signal low</comment>
+ <valid>false</valid>
+ <retentionTime>932.4</retentionTime>
+ <Q1>664.1</Q1>
+ <Q3>408</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23806</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211146631-23628</datasetParent>
+ <amount>3.942793</amount>
+ <unit/>
+ <comment/>
+ <valid>true</valid>
+ <retentionTime>922.2</retentionTime>
+ <Q1>664.1</Q1>
+ <Q3>408</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23806</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211148831-23629</datasetParent>
+ <amount>4.230723</amount>
+ <unit/>
+ <comment>signal low</comment>
+ <valid>false</valid>
+ <retentionTime>943.3</retentionTime>
+ <Q1>664.1</Q1>
+ <Q3>408</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23806</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211151102-23630</datasetParent>
+ <amount>4.118647</amount>
+ <unit/>
+ <comment/>
+ <valid>true</valid>
+ <retentionTime>923.5</retentionTime>
+ <Q1>664.1</Q1>
+ <Q3>408</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23806</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211007858-23605</datasetParent>
+ <amount>0.726202</amount>
+ <unit/>
+ <comment/>
+ <valid>true</valid>
+ <retentionTime>941.5</retentionTime>
+ <Q1>742.1</Q1>
+ <Q3>620</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23808</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211016773-23606</datasetParent>
+ <amount>3.697735</amount>
+ <unit/>
+ <comment/>
+ <valid>true</valid>
+ <retentionTime>927.3</retentionTime>
+ <Q1>742.1</Q1>
+ <Q3>620</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23808</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211024338-23607</datasetParent>
+ <amount>3.981213</amount>
+ <unit/>
+ <comment/>
+ <valid>true</valid>
+ <retentionTime>928.7</retentionTime>
+ <Q1>742.1</Q1>
+ <Q3>620</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23808</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211027473-23608</datasetParent>
+ <amount>4.213055</amount>
+ <unit/>
+ <comment/>
+ <valid>true</valid>
+ <retentionTime>938.3</retentionTime>
+ <Q1>742.1</Q1>
+ <Q3>620</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23808</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211029837-23609</datasetParent>
+ <amount>4.226762</amount>
+ <unit/>
+ <comment/>
+ <valid>true</valid>
+ <retentionTime>949.3</retentionTime>
+ <Q1>742.1</Q1>
+ <Q3>620</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23808</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211032103-23610</datasetParent>
+ <amount>4.118463</amount>
+ <unit/>
+ <comment/>
+ <valid>true</valid>
+ <retentionTime>929.3</retentionTime>
+ <Q1>742.1</Q1>
+ <Q3>620</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23808</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211040739-23611</datasetParent>
+ <amount>3.243816</amount>
+ <unit/>
+ <comment/>
+ <valid>true</valid>
+ <retentionTime>927.4</retentionTime>
+ <Q1>742.1</Q1>
+ <Q3>620</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23808</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211044547-23612</datasetParent>
+ <amount>-5.900209</amount>
+ <unit/>
+ <comment>signal high</comment>
+ <valid>false</valid>
+ <retentionTime>926.7</retentionTime>
+ <Q1>742.1</Q1>
+ <Q3>620</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23808</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211049391-23613</datasetParent>
+ <amount>-4.422907</amount>
+ <unit/>
+ <comment>signal high</comment>
+ <valid>false</valid>
+ <retentionTime>925.4</retentionTime>
+ <Q1>742.1</Q1>
+ <Q3>620</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23808</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211052411-23614</datasetParent>
+ <amount>-0.271409</amount>
+ <unit/>
+ <comment>signal high</comment>
+ <valid>false</valid>
+ <retentionTime>926.7</retentionTime>
+ <Q1>742.1</Q1>
+ <Q3>620</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23808</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211056619-23615</datasetParent>
+ <amount>-0.057087</amount>
+ <unit/>
+ <comment>signal high</comment>
+ <valid>false</valid>
+ <retentionTime>927.4</retentionTime>
+ <Q1>742.1</Q1>
+ <Q3>620</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23808</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211100743-23616</datasetParent>
+ <amount>3.122158</amount>
+ <unit/>
+ <comment/>
+ <valid>true</valid>
+ <retentionTime>929.3</retentionTime>
+ <Q1>742.1</Q1>
+ <Q3>620</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23808</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211104731-23617</datasetParent>
+ <amount>3.421073</amount>
+ <unit/>
+ <comment/>
+ <valid>true</valid>
+ <retentionTime>928.0</retentionTime>
+ <Q1>742.1</Q1>
+ <Q3>620</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23808</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211111839-23618</datasetParent>
+ <amount>3.109696</amount>
+ <unit/>
+ <comment/>
+ <valid>true</valid>
+ <retentionTime>928.0</retentionTime>
+ <Q1>742.1</Q1>
+ <Q3>620</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23808</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211119852-23619</datasetParent>
+ <amount>1.051402</amount>
+ <unit/>
+ <comment/>
+ <valid>true</valid>
+ <retentionTime>927.3</retentionTime>
+ <Q1>742.1</Q1>
+ <Q3>620</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23808</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211122021-23620</datasetParent>
+ <amount>3.594872</amount>
+ <unit/>
+ <comment/>
+ <valid>true</valid>
+ <retentionTime>927.4</retentionTime>
+ <Q1>742.1</Q1>
+ <Q3>620</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23808</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211124186-23621</datasetParent>
+ <amount>4.251867</amount>
+ <unit/>
+ <comment>signal low</comment>
+ <valid>false</valid>
+ <retentionTime>944.7</retentionTime>
+ <Q1>742.1</Q1>
+ <Q3>620</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23808</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211127046-23622</datasetParent>
+ <amount>4.255881</amount>
+ <unit/>
+ <comment>signal low</comment>
+ <valid>false</valid>
+ <retentionTime>941.5</retentionTime>
+ <Q1>742.1</Q1>
+ <Q3>620</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23808</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211131542-23623</datasetParent>
+ <amount>4.252812</amount>
+ <unit/>
+ <comment>signal low</comment>
+ <valid>false</valid>
+ <retentionTime>925.4</retentionTime>
+ <Q1>742.1</Q1>
+ <Q3>620</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23808</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211135837-23624</datasetParent>
+ <amount>4.255647</amount>
+ <unit/>
+ <comment>signal low</comment>
+ <valid>false</valid>
+ <retentionTime>934.4</retentionTime>
+ <Q1>742.1</Q1>
+ <Q3>620</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23808</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211139038-23625</datasetParent>
+ <amount>4.255907</amount>
+ <unit/>
+ <comment>signal low</comment>
+ <valid>false</valid>
+ <retentionTime>947.3</retentionTime>
+ <Q1>742.1</Q1>
+ <Q3>620</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23808</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211142289-23626</datasetParent>
+ <amount>4.255880</amount>
+ <unit/>
+ <comment>signal low</comment>
+ <valid>false</valid>
+ <retentionTime>929.3</retentionTime>
+ <Q1>742.1</Q1>
+ <Q3>620</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23808</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211144528-23627</datasetParent>
+ <amount>4.255628</amount>
+ <unit/>
+ <comment>signal low</comment>
+ <valid>false</valid>
+ <retentionTime>948.6</retentionTime>
+ <Q1>742.1</Q1>
+ <Q3>620</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23808</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211146631-23628</datasetParent>
+ <amount>3.911377</amount>
+ <unit/>
+ <comment/>
+ <valid>true</valid>
+ <retentionTime>927.6</retentionTime>
+ <Q1>742.1</Q1>
+ <Q3>620</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23808</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211148831-23629</datasetParent>
+ <amount>4.248650</amount>
+ <unit/>
+ <comment>signal low</comment>
+ <valid>false</valid>
+ <retentionTime>939.6</retentionTime>
+ <Q1>742.1</Q1>
+ <Q3>620</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23808</cmpdId>
+ </identity>
+ </concentration>
+ <concentration>
+ <datasetParent>20090822211151102-23630</datasetParent>
+ <amount>4.102364</amount>
+ <unit/>
+ <comment/>
+ <valid>true</valid>
+ <retentionTime>929.3</retentionTime>
+ <Q1>742.1</Q1>
+ <Q3>620</Q3>
+ <internalStandard/>
+ <identity number="1">
+ <cmpdId>23808</cmpdId>
+ </identity>
+ </concentration>
+ </msQuantification>
+</quantML>
\ No newline at end of file
diff --git a/rtd_yeastx/resource/examples/allFields.quantML b/rtd_yeastx/resource/examples/allFields.quantML
new file mode 100644
index 00000000000..f66be98c85e
--- /dev/null
+++ b/rtd_yeastx/resource/examples/allFields.quantML
@@ -0,0 +1,25 @@
+<?xml version="1.0" encoding="utf-8"?>
+<quantML>
+ <msQuantification>
+ <source>msSoft</source>
+ <valid>true</valid>
+ <comment>no comment</comment>
+ <registrationDate>2009-04-07 12:00:21</registrationDate>
+ <registrator>John Doe</registrator>
+ <concentration>
+ <datasetParent>20090822211007858-23605</datasetParent>
+ <amount>0.689155</amount>
+ <unit>kg</unit>
+ <comment>concentration comment</comment>
+ <valid>true</valid>
+ <retentionTime>939.5</retentionTime>
+ <Q1>664.1</Q1>
+ <Q3>408</Q3>
+ <internalStandard>value1</internalStandard>
+ <identity number="1">
+ <cmpdId>1</cmpdId>
+ <cmpdId>2</cmpdId>
+ </identity>
+ </concentration>
+ </msQuantification>
+</quantML>
\ No newline at end of file
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DBUtils.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DBUtils.java
index 86f09faf0ae..b69f0441fec 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DBUtils.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/db/DBUtils.java
@@ -31,7 +31,7 @@ import ch.systemsx.cisd.dbmigration.DatabaseConfigurationContext;
public class DBUtils
{
/** Current version of the database. */
- public static final String DATABASE_VERSION = "002";
+ public static final String DATABASE_VERSION = "003";
static
{
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLFilenameFilter.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLFilenameFilter.java
index 44940b080f6..3957d1133d4 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLFilenameFilter.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLFilenameFilter.java
@@ -19,15 +19,17 @@ package ch.systemsx.cisd.yeastx.eicml;
import java.io.File;
import java.io.FilenameFilter;
+import ch.systemsx.cisd.yeastx.etl.ConstantsYeastX;
+
/**
* A {@link FilenameFilter} for <code>eicML</code> files.
- *
+ *
* @author Bernd Rinn
*/
final class EICMLFilenameFilter implements FilenameFilter
{
public boolean accept(File myDir, String name)
{
- return name.endsWith(".eicML");
+ return name.endsWith("." + ConstantsYeastX.EICML_EXT);
}
}
\ No newline at end of file
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/ConstantsYeastX.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/ConstantsYeastX.java
index 81d62cf0744..ceea820ce92 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/ConstantsYeastX.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/ConstantsYeastX.java
@@ -29,5 +29,7 @@ public class ConstantsYeastX
public static final String EICML_EXT = "eicML";
+ public static final String QUANTML_EXT = "quantML";
+
public static final String MZXML_EXT = "mzXML";
}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/ML2DatabaseUploader.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/ML2DatabaseUploader.java
index 9ae705e61b0..701b810fc2f 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/ML2DatabaseUploader.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/ML2DatabaseUploader.java
@@ -36,6 +36,7 @@ import ch.systemsx.cisd.yeastx.db.DBUtils;
import ch.systemsx.cisd.yeastx.db.DMDataSetDTO;
import ch.systemsx.cisd.yeastx.eicml.EICML2Database;
import ch.systemsx.cisd.yeastx.fiaml.FIAML2Database;
+import ch.systemsx.cisd.yeastx.quant.QuantML2Database;
/**
* Extracts and uploads information from dataset files (like <code>eicML</code> or
@@ -53,6 +54,8 @@ public class ML2DatabaseUploader implements IDataSetUploader
private final FIAML2Database fiaML2Database;
+ private final QuantML2Database quantML2Database;
+
private final String uniqueSampleNamePropertyCode;
private final String uniqueExperimentNamePropertyCode;
@@ -67,6 +70,7 @@ public class ML2DatabaseUploader implements IDataSetUploader
DBUtils.init(dbContext);
this.eicML2Database = new EICML2Database(dbContext.getDataSource());
this.fiaML2Database = new FIAML2Database(dbContext.getDataSource());
+ this.quantML2Database = new QuantML2Database(dbContext.getDataSource());
this.uniqueExperimentNamePropertyCode =
DatasetMappingResolver.getUniqueExperimentNamePropertyCode(properties);
this.uniqueSampleNamePropertyCode =
@@ -86,6 +90,9 @@ public class ML2DatabaseUploader implements IDataSetUploader
} else if (extension.equalsIgnoreCase(ConstantsYeastX.EICML_EXT))
{
translateEIC(dataSet, dataSetInformation);
+ } else if (extension.equalsIgnoreCase(ConstantsYeastX.QUANTML_EXT))
+ {
+ translateQuant(dataSet, dataSetInformation);
} else
{
// do nothing
@@ -100,6 +107,13 @@ public class ML2DatabaseUploader implements IDataSetUploader
}
}
+ private void translateQuant(File dataSet, DataSetInformation dataSetInformation)
+ throws SQLException
+ {
+ DMDataSetDTO openbisBacklink = createBacklink(dataSetInformation);
+ quantML2Database.uploadQuantMLFile(dataSet, openbisBacklink);
+ }
+
private void translateEIC(File dataSet, DataSetInformation dataSetInformation)
throws SQLException
{
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/FIAMLFilenameFilter.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/FIAMLFilenameFilter.java
index c861b8ca58b..06e498c8cac 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/FIAMLFilenameFilter.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/fiaml/FIAMLFilenameFilter.java
@@ -19,15 +19,17 @@ package ch.systemsx.cisd.yeastx.fiaml;
import java.io.File;
import java.io.FilenameFilter;
+import ch.systemsx.cisd.yeastx.etl.ConstantsYeastX;
+
/**
* A {@link FilenameFilter} for <code>fiaML</code> files.
- *
+ *
* @author Bernd Rinn
*/
final class FIAMLFilenameFilter implements FilenameFilter
{
public boolean accept(File myDir, String name)
{
- return name.endsWith(".fiaML");
+ return name.endsWith("." + ConstantsYeastX.FIAML_EXT);
}
}
\ No newline at end of file
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/IQuantMSDAO.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/IQuantMSDAO.java
new file mode 100644
index 00000000000..511baa92640
--- /dev/null
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/IQuantMSDAO.java
@@ -0,0 +1,50 @@
+/*
+ * 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.yeastx.quant;
+
+import net.lemnik.eodsql.Select;
+import net.lemnik.eodsql.Update;
+
+import ch.systemsx.cisd.yeastx.db.IGenericDAO;
+import ch.systemsx.cisd.yeastx.quant.dto.MSConcentrationDTO;
+import ch.systemsx.cisd.yeastx.quant.dto.MSQuantificationDTO;
+
+/**
+ * Creates MS Quantifications records.
+ *
+ * @author Tomasz Pylak
+ */
+public interface IQuantMSDAO extends IGenericDAO
+{
+ @Select(sql = "insert into MS_QUANTIFICATIONS "
+ + "( DS_ID, EXPE_ID, SOURCE, VALID, COMMENT, REGISTRATOR, REGISTRATION_DATE ) "
+ + "values (?{1}, ?{2}, ?{3.source}, ?{3.valid}, ?{3.comment}, "
+ + " ?{3.registrator}, ?{3.registrationDate} ) returning ID")
+ public long addQuantification(long datasetId, long experimentId,
+ MSQuantificationDTO quantification);
+
+ @Select(sql = "insert into MS_QUANT_CONCENTRATIONS "
+ + "( MS_QUANTIFICATION_ID, PARENT_DS_PERM_ID, AMOUNT, UNIT, VALID, COMMENT, "
+ + " RETENTION_TIME, Q1, Q3, INTERNAL_STANDARD ) "
+ + "values (?{1}, ?{2.parentDatasetCode}, ?{2.amount}, ?{2.unit}, ?{2.valid}, ?{2.comment}, "
+ + " ?{2.retentionTime}, ?{2.q1}, ?{2.q3}, ?{2.internalStandard} ) returning ID")
+ public long addConcentration(long quantMSId, MSConcentrationDTO concentration);
+
+ @Update(sql = "insert into MS_QUANT_COMPOUNDS (MS_QUANT_CONCENTRATION_ID, COMPOUND_ID) "
+ + "values (?{1}, ?{2})", batchUpdate = true)
+ public void addCompoundIds(long concentrationId, Iterable<Long> compoundIds);
+}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/QuantML2Database.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/QuantML2Database.java
new file mode 100644
index 00000000000..ac3fc367b1e
--- /dev/null
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/QuantML2Database.java
@@ -0,0 +1,135 @@
+/*
+ * 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.yeastx.quant;
+
+import java.io.File;
+import java.io.FilenameFilter;
+import java.sql.SQLException;
+import java.util.List;
+
+import javax.sql.DataSource;
+
+import net.lemnik.eodsql.QueryTool;
+import net.lemnik.eodsql.TransactionQuery;
+
+import org.springframework.dao.DataAccessException;
+
+import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
+import ch.systemsx.cisd.yeastx.db.DBUtils;
+import ch.systemsx.cisd.yeastx.db.DMDataSetDTO;
+import ch.systemsx.cisd.yeastx.etl.ConstantsYeastX;
+import ch.systemsx.cisd.yeastx.quant.dto.ConcentrationCompounds;
+import ch.systemsx.cisd.yeastx.quant.dto.MSConcentrationDTO;
+import ch.systemsx.cisd.yeastx.quant.dto.MSQuantificationDTO;
+import ch.systemsx.cisd.yeastx.quant.dto.MSQuantificationsDTO;
+
+/**
+ * Tool for uploading <code>quantML</code> files to the database.
+ *
+ * @author Tomasz Pylak
+ */
+public class QuantML2Database
+{
+
+ private final IQuantMSDAO dao;
+
+ public QuantML2Database(DataSource datasource)
+ {
+ this.dao = QueryTool.getQuery(datasource, IQuantMSDAO.class);
+ }
+
+ /**
+ * Method for uploading an <var>fiaMLFile</var> to the database.
+ */
+ public void uploadQuantMLFile(final File file, final DMDataSetDTO dataSet) throws SQLException
+ {
+ TransactionQuery transaction = null;
+ try
+ {
+ transaction = dao;
+ DBUtils.createDataSet(dao, dataSet);
+ MSQuantificationsDTO quantifications = QuantMLParser.parseQuantifications(file);
+ uploadQuantifications(quantifications, dataSet);
+ transaction.close(true);
+ } catch (Throwable th)
+ {
+ try
+ {
+ DBUtils.rollbackAndClose(transaction);
+ } catch (DataAccessException ex)
+ {
+ // Avoid this exception shadowing the original exception.
+ }
+ throw CheckedExceptionTunnel.wrapIfNecessary(th);
+ }
+ }
+
+ private void uploadQuantifications(MSQuantificationsDTO quantifications, DMDataSetDTO dataSet)
+ {
+ for (MSQuantificationDTO quantification : quantifications.getQuantifications())
+ {
+ long quantificationId =
+ dao.addQuantification(dataSet.getId(), dataSet.getExperimentId(),
+ quantification);
+ uploadConcentrations(quantificationId, quantification.getConcentrations());
+ }
+ }
+
+ private void uploadConcentrations(long quantificationId,
+ List<MSConcentrationDTO> concentrations)
+ {
+ for (MSConcentrationDTO concentration : concentrations)
+ {
+ long concentrationId = dao.addConcentration(quantificationId, concentration);
+ uploadCompoundIds(concentrationId, concentration.getCompounds());
+ }
+ }
+
+ private void uploadCompoundIds(long concentrationId, ConcentrationCompounds compounds)
+ {
+ dao.addCompoundIds(concentrationId, compounds.getCompoundIds());
+ }
+
+ public static void main(String[] args) throws SQLException
+ {
+ final long start = System.currentTimeMillis();
+ final QuantML2Database quantML2Database =
+ new QuantML2Database(DBUtils.createDefaultDBContext().getDataSource());
+ final String dir = args[0];
+ int permId = 0;
+ for (String f : new File(dir).list(createQuantFilter()))
+ {
+ System.out.println(f);
+ quantML2Database.uploadQuantMLFile(new File(dir, f), new DMDataSetDTO(Integer
+ .toString(++permId), "sample perm id", "sample name", "experiment perm id",
+ "experiment name"));
+ }
+ System.out.println((System.currentTimeMillis() - start) / 1000.0);
+ }
+
+ private static FilenameFilter createQuantFilter()
+ {
+ return new FilenameFilter()
+ {
+ public boolean accept(File dir, String name)
+ {
+ return name.endsWith("." + ConstantsYeastX.QUANTML_EXT);
+ }
+ };
+ }
+
+}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/QuantMLDataSetInfoExtractor.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/QuantMLDataSetInfoExtractor.java
new file mode 100644
index 00000000000..260157e6752
--- /dev/null
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/QuantMLDataSetInfoExtractor.java
@@ -0,0 +1,74 @@
+/*
+ * 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.yeastx.quant;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Properties;
+
+import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor;
+import ch.systemsx.cisd.etlserver.IDataSetInfoExtractor;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+import ch.systemsx.cisd.yeastx.quant.dto.MSConcentrationDTO;
+import ch.systemsx.cisd.yeastx.quant.dto.MSQuantificationDTO;
+import ch.systemsx.cisd.yeastx.quant.dto.MSQuantificationsDTO;
+
+/**
+ * A default data set info extractor enriched with parent dataset codes.
+ *
+ * @author Tomasz Pylak
+ */
+public class QuantMLDataSetInfoExtractor implements IDataSetInfoExtractor
+{
+ private final IDataSetInfoExtractor defaultExtractor;
+
+ public QuantMLDataSetInfoExtractor(final Properties globalProperties)
+ {
+ this.defaultExtractor = new DefaultDataSetInfoExtractor(globalProperties);
+ }
+
+ public DataSetInformation getDataSetInformation(File incomingDataSetPath,
+ IEncapsulatedOpenBISService openbisService) throws UserFailureException,
+ EnvironmentFailureException
+ {
+ DataSetInformation dataSetInformation =
+ defaultExtractor.getDataSetInformation(incomingDataSetPath, openbisService);
+ List<String> parentDatasetCodes = extractParentDatasetCodes(incomingDataSetPath);
+ dataSetInformation.setParentDataSetCodes(parentDatasetCodes);
+ return dataSetInformation;
+ }
+
+ private static List<String> extractParentDatasetCodes(File incomingDataSetPath)
+ {
+ MSQuantificationsDTO quantifications =
+ QuantMLParser.parseQuantifications(incomingDataSetPath);
+ List<String> parentDatasets = new ArrayList<String>();
+ for (MSQuantificationDTO q : quantifications.getQuantifications())
+ {
+ for (MSConcentrationDTO c : q.getConcentrations())
+ {
+ parentDatasets.add(c.getParentDatasetCode());
+ }
+ }
+ return parentDatasets;
+ }
+
+}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/QuantMLParser.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/QuantMLParser.java
new file mode 100644
index 00000000000..d91ed30160d
--- /dev/null
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/QuantMLParser.java
@@ -0,0 +1,100 @@
+/*
+ * 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.yeastx.quant;
+
+import java.io.File;
+import java.io.IOException;
+
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBException;
+import javax.xml.bind.SchemaOutputResolver;
+import javax.xml.bind.Unmarshaller;
+import javax.xml.transform.Result;
+import javax.xml.transform.stream.StreamResult;
+
+import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
+import ch.systemsx.cisd.yeastx.quant.dto.MSQuantificationsDTO;
+
+/**
+ * Loader of MS Quantifications (*.quantML) XML file.
+ *
+ * @author Tomasz Pylak
+ */
+class QuantMLParser
+{
+ public static MSQuantificationsDTO parseQuantifications(File dataSet)
+ {
+ return new QuantMLParser().doParseMSQuantifications(dataSet);
+ }
+
+ private final Unmarshaller unmarshaller;
+
+ private QuantMLParser()
+ {
+ this.unmarshaller = createUnmarshaller();
+ }
+
+ private static Unmarshaller createUnmarshaller()
+ {
+ try
+ {
+ JAXBContext context = JAXBContext.newInstance(MSQuantificationsDTO.class);
+
+ return context.createUnmarshaller();
+ } catch (JAXBException ex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ }
+ }
+
+ public static void debugGenerateXmlSchema(JAXBContext context)
+ {
+ try
+ {
+ context.generateSchema(new SchemaOutputResolver()
+ {
+ @Override
+ public Result createOutput(String namespaceUri, String schemaName)
+ throws IOException
+ {
+ return new StreamResult(new File(".", schemaName));
+ }
+ });
+ } catch (IOException ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ private MSQuantificationsDTO doParseMSQuantifications(File dataSet)
+ {
+
+ try
+ {
+ Object object = unmarshaller.unmarshal(dataSet);
+ if (object instanceof MSQuantificationsDTO == false)
+ {
+ throw new IllegalArgumentException("Wrong type: " + object);
+ }
+ return (MSQuantificationsDTO) object;
+ } catch (JAXBException ex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ }
+ }
+
+}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/XmlDateAdapter.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/XmlDateAdapter.java
new file mode 100644
index 00000000000..0a8efd546c2
--- /dev/null
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/XmlDateAdapter.java
@@ -0,0 +1,43 @@
+/*
+ * 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.yeastx.quant;
+
+import java.text.SimpleDateFormat;
+import java.util.Date;
+
+import javax.xml.bind.annotation.adapters.XmlAdapter;
+
+/**
+ * @author Tomasz Pylak
+ */
+public class XmlDateAdapter extends XmlAdapter<String, Date>
+{
+ static String PATTERN = "yyyy-MM-dd HH:mm:ss";
+
+ @Override
+ public String marshal(Date date) throws Exception
+ {
+ return new SimpleDateFormat(PATTERN).format(date);
+ }
+
+ @Override
+ public Date unmarshal(String dateString) throws Exception
+ {
+ return new SimpleDateFormat(PATTERN).parse(dateString);
+ }
+
+}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/dto/ConcentrationCompounds.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/dto/ConcentrationCompounds.java
new file mode 100644
index 00000000000..dc07a43885c
--- /dev/null
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/dto/ConcentrationCompounds.java
@@ -0,0 +1,42 @@
+/*
+ * 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.yeastx.quant.dto;
+
+import java.util.List;
+
+import javax.xml.bind.annotation.XmlElement;
+
+/**
+ * Stores all the compound ids of one concentration.
+ *
+ * @author Tomasz Pylak
+ */
+public class ConcentrationCompounds
+{
+ private List<Long> compoundIds;
+
+ @XmlElement(name = "cmpdId", required = true)
+ public List<Long> getCompoundIds()
+ {
+ return compoundIds;
+ }
+
+ public void setCompoundIds(List<Long> compoundIds)
+ {
+ this.compoundIds = compoundIds;
+ }
+}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/dto/MSConcentrationDTO.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/dto/MSConcentrationDTO.java
new file mode 100644
index 00000000000..7f7f921ed27
--- /dev/null
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/dto/MSConcentrationDTO.java
@@ -0,0 +1,157 @@
+/*
+ * 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.yeastx.quant.dto;
+
+import javax.xml.bind.annotation.XmlElement;
+
+/**
+ * Stores the content of one concentration.
+ *
+ * @author Tomasz Pylak
+ */
+public class MSConcentrationDTO
+{
+ private String parentDatasetCode; // not null
+
+ private double amount; // not null
+
+ private String unit;// not null, can be empty
+
+ private boolean valid;// not null
+
+ private String comment; // can be null
+
+ private double retentionTime;// not null
+
+ private double q1; // not null
+
+ private double q3;// not null
+
+ private String internalStandard;// not null, can be empty
+
+ private ConcentrationCompounds compounds;
+
+ @XmlElement(required = true, name = "datasetParent")
+ public String getParentDatasetCode()
+ {
+ return parentDatasetCode;
+ }
+
+ public void setParentDatasetCode(String parentDatasetCode)
+ {
+ this.parentDatasetCode = parentDatasetCode;
+ }
+
+ @XmlElement(required = true, name = "amount")
+ public double getAmount()
+ {
+ return amount;
+ }
+
+ public void setAmount(double amount)
+ {
+ this.amount = amount;
+ }
+
+ @XmlElement(required = true, name = "unit")
+ public String getUnit()
+ {
+ return unit;
+ }
+
+ public void setUnit(String unit)
+ {
+ this.unit = unit;
+ }
+
+ @XmlElement(required = true, name = "valid")
+ public boolean isValid()
+ {
+ return valid;
+ }
+
+ public void setValid(boolean valid)
+ {
+ this.valid = valid;
+ }
+
+ @XmlElement(name = "comment")
+ public String getComment()
+ {
+ return comment;
+ }
+
+ public void setComment(String comment)
+ {
+ this.comment = comment;
+ }
+
+ @XmlElement(required = true, name = "retentionTime")
+ public double getRetentionTime()
+ {
+ return retentionTime;
+ }
+
+ public void setRetentionTime(double retentionTime)
+ {
+ this.retentionTime = retentionTime;
+ }
+
+ @XmlElement(required = true, name = "Q1")
+ public double getQ1()
+ {
+ return q1;
+ }
+
+ public void setQ1(double q1)
+ {
+ this.q1 = q1;
+ }
+
+ @XmlElement(required = true, name = "Q3")
+ public double getQ3()
+ {
+ return q3;
+ }
+
+ public void setQ3(double q3)
+ {
+ this.q3 = q3;
+ }
+
+ @XmlElement(required = true, name = "internalStandard")
+ public String getInternalStandard()
+ {
+ return internalStandard;
+ }
+
+ public void setInternalStandard(String internalStandard)
+ {
+ this.internalStandard = internalStandard;
+ }
+
+ @XmlElement(required = true, name = "identity")
+ public ConcentrationCompounds getCompounds()
+ {
+ return compounds;
+ }
+
+ public void setCompounds(ConcentrationCompounds compounds)
+ {
+ this.compounds = compounds;
+ }
+}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/dto/MSQuantificationDTO.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/dto/MSQuantificationDTO.java
new file mode 100644
index 00000000000..bb54fe84da8
--- /dev/null
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/dto/MSQuantificationDTO.java
@@ -0,0 +1,112 @@
+/*
+ * 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.yeastx.quant.dto;
+
+import java.util.Date;
+import java.util.List;
+
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
+
+import ch.systemsx.cisd.yeastx.quant.XmlDateAdapter;
+
+/**
+ * Stores the content of one quantification.
+ *
+ * @author Tomasz Pylak
+ */
+public class MSQuantificationDTO
+{
+ private String source;
+
+ private boolean valid;
+
+ private String comment;
+
+ private String registrator;
+
+ private Date registrationDate;
+
+ private List<MSConcentrationDTO> concentrations;
+
+ @XmlElement(required = true, name = "source")
+ public String getSource()
+ {
+ return source;
+ }
+
+ public void setSource(String source)
+ {
+ this.source = source;
+ }
+
+ @XmlElement(required = true, name = "valid")
+ public boolean isValid()
+ {
+ return valid;
+ }
+
+ public void setValid(boolean valid)
+ {
+ this.valid = valid;
+ }
+
+ @XmlElement(name = "comment")
+ public String getComment()
+ {
+ return comment;
+ }
+
+ public void setComment(String comment)
+ {
+ this.comment = comment;
+ }
+
+ @XmlElement(name = "registrator")
+ public String getRegistrator()
+ {
+ return registrator;
+ }
+
+ public void setRegistrator(String registrator)
+ {
+ this.registrator = registrator;
+ }
+
+ @XmlElement(name = "registrationDate")
+ @XmlJavaTypeAdapter(value = XmlDateAdapter.class, type = Date.class)
+ public Date getRegistrationDate()
+ {
+ return registrationDate;
+ }
+
+ public void setRegistrationDate(Date registrationDate)
+ {
+ this.registrationDate = registrationDate;
+ }
+
+ @XmlElement(required = true, name = "concentration")
+ public List<MSConcentrationDTO> getConcentrations()
+ {
+ return concentrations;
+ }
+
+ public void setConcentrations(List<MSConcentrationDTO> concetrations)
+ {
+ this.concentrations = concetrations;
+ }
+}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/dto/MSQuantificationsDTO.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/dto/MSQuantificationsDTO.java
new file mode 100644
index 00000000000..56365034192
--- /dev/null
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/quant/dto/MSQuantificationsDTO.java
@@ -0,0 +1,47 @@
+/*
+ * 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.yeastx.quant.dto;
+
+import java.util.List;
+
+import javax.xml.bind.annotation.XmlElement;
+import javax.xml.bind.annotation.XmlRootElement;
+import javax.xml.bind.annotation.XmlType;
+
+/**
+ * Stores the content of the whole *.quantML file (all quantifications).
+ *
+ * @author Tomasz Pylak
+ */
+@XmlRootElement(name = "quantML")
+@XmlType
+public class MSQuantificationsDTO
+{
+ private List<MSQuantificationDTO> quantifications;
+
+ @XmlElement(name = "msQuantification")
+ public List<MSQuantificationDTO> getQuantifications()
+ {
+ return quantifications;
+ }
+
+ public void setQuantifications(List<MSQuantificationDTO> quantifications)
+ {
+ this.quantifications = quantifications;
+ }
+
+}
diff --git a/rtd_yeastx/source/sql/postgresql/003/schema-003.sql b/rtd_yeastx/source/sql/postgresql/003/schema-003.sql
index df0fd975512..65aff18ca8b 100644
--- a/rtd_yeastx/source/sql/postgresql/003/schema-003.sql
+++ b/rtd_yeastx/source/sql/postgresql/003/schema-003.sql
@@ -196,7 +196,7 @@ CREATE INDEX MS_QUANTIFICATION_FK_EXPE_ID_IDX ON MS_QUANTIFICATIONS(EXPE_ID);
CREATE TABLE MS_QUANT_CONCENTRATIONS (
ID BIGSERIAL NOT NULL,
MS_QUANTIFICATION_ID TECH_ID NOT NULL,
- PARENT_DS_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,
@@ -212,6 +212,7 @@ CREATE TABLE MS_QUANT_CONCENTRATIONS (
-- 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
diff --git a/rtd_yeastx/source/sql/postgresql/migration/migration-002-003.sql b/rtd_yeastx/source/sql/postgresql/migration/migration-002-003.sql
index bbaece7368c..fd4fa370bee 100644
--- a/rtd_yeastx/source/sql/postgresql/migration/migration-002-003.sql
+++ b/rtd_yeastx/source/sql/postgresql/migration/migration-002-003.sql
@@ -31,7 +31,7 @@ CREATE INDEX MS_QUANTIFICATION_FK_EXPE_ID_IDX ON MS_QUANTIFICATIONS(EXPE_ID);
CREATE TABLE MS_QUANT_CONCENTRATIONS (
ID BIGSERIAL NOT NULL,
MS_QUANTIFICATION_ID TECH_ID NOT NULL,
- PARENT_DS_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,
@@ -47,6 +47,7 @@ CREATE TABLE MS_QUANT_CONCENTRATIONS (
-- 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
diff --git a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/quant/QuantMLParserTest.java b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/quant/QuantMLParserTest.java
new file mode 100644
index 00000000000..45ef8ad8ba3
--- /dev/null
+++ b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/quant/QuantMLParserTest.java
@@ -0,0 +1,94 @@
+/*
+ * 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.yeastx.quant;
+
+import java.io.File;
+import java.util.Date;
+import java.util.List;
+
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.yeastx.quant.dto.MSConcentrationDTO;
+import ch.systemsx.cisd.yeastx.quant.dto.MSQuantificationDTO;
+import ch.systemsx.cisd.yeastx.quant.dto.MSQuantificationsDTO;
+
+/**
+ * @author Tomasz Pylak
+ */
+public class QuantMLParserTest extends AssertJUnit
+{
+ @Test
+ public void testParseQuantFileRealContent()
+ {
+ File file = new File("resource/examples/TEST&TEST_PROJECT&TEST_EXP.quantML");
+ MSQuantificationsDTO quantifications = QuantMLParser.parseQuantifications(file);
+ assertEquals(1, quantifications.getQuantifications().size());
+ MSQuantificationDTO quantification = quantifications.getQuantifications().get(0);
+ assertEquals("msSoft", quantification.getSource());
+ assertTrue(quantification.isValid());
+ assertNull(quantification.getComment());
+ assertNull(quantification.getRegistrator());
+ assertNull(quantification.getRegistrationDate());
+
+ assertEquals(52, quantification.getConcentrations().size());
+ MSConcentrationDTO concentration = quantification.getConcentrations().get(0);
+ assertEquals(0.689155, concentration.getAmount());
+ assertEquals("", concentration.getComment());
+ assertTrue(concentration.isValid());
+ assertEquals("20090822211007858-23605", concentration.getParentDatasetCode());
+ assertEquals("", concentration.getInternalStandard());
+ assertEquals("", concentration.getUnit());
+ assertEquals(664.1, concentration.getQ1());
+ assertEquals(408.0, concentration.getQ3());
+ assertEquals(939.5, concentration.getRetentionTime());
+ List<Long> compoundIds = concentration.getCompounds().getCompoundIds();
+ assertEquals(1, compoundIds.size());
+ assertEquals(23806, compoundIds.get(0).longValue());
+ }
+
+ @Test
+ public void testParseQuantFileFullContent() throws Exception
+ {
+ File file = new File("resource/examples/allFields.quantML");
+ MSQuantificationsDTO quantifications = QuantMLParser.parseQuantifications(file);
+ assertEquals(1, quantifications.getQuantifications().size());
+ MSQuantificationDTO quantification = quantifications.getQuantifications().get(0);
+ assertEquals("msSoft", quantification.getSource());
+ assertTrue(quantification.isValid());
+ assertEquals("no comment", quantification.getComment());
+ assertEquals("John Doe", quantification.getRegistrator());
+ Date expectedDate = new XmlDateAdapter().unmarshal("2009-04-07 12:00:21");
+ assertEquals(expectedDate, quantification.getRegistrationDate());
+
+ assertEquals(1, quantification.getConcentrations().size());
+ MSConcentrationDTO concentration = quantification.getConcentrations().get(0);
+ assertEquals(0.689155, concentration.getAmount());
+ assertEquals("concentration comment", concentration.getComment());
+ assertTrue(concentration.isValid());
+ assertEquals("20090822211007858-23605", concentration.getParentDatasetCode());
+ assertEquals("value1", concentration.getInternalStandard());
+ assertEquals("kg", concentration.getUnit());
+ assertEquals(664.1, concentration.getQ1());
+ assertEquals(408.0, concentration.getQ3());
+ assertEquals(939.5, concentration.getRetentionTime());
+ List<Long> compundIds = concentration.getCompounds().getCompoundIds();
+ assertEquals(2, compundIds.size());
+ assertEquals(1, compundIds.get(0).longValue());
+ assertEquals(2, compundIds.get(1).longValue());
+ }
+}
diff --git a/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/quant/QuantMSDAOTest.java b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/quant/QuantMSDAOTest.java
new file mode 100644
index 00000000000..2885f5fde54
--- /dev/null
+++ b/rtd_yeastx/sourceTest/java/ch/systemsx/cisd/yeastx/quant/QuantMSDAOTest.java
@@ -0,0 +1,63 @@
+/*
+ * 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.yeastx.quant;
+
+import java.io.File;
+import java.sql.SQLException;
+
+import net.lemnik.eodsql.QueryTool;
+
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.yeastx.db.AbstractDBTest;
+import ch.systemsx.cisd.yeastx.db.DMDataSetDTO;
+
+/**
+ * @author Tomasz Pylak
+ */
+public class QuantMSDAOTest extends AbstractDBTest
+{
+ private IQuantMSDAO quantmsDAO;
+
+ @BeforeMethod(alwaysRun = true)
+ public void setDAO() throws SQLException
+ {
+ quantmsDAO = QueryTool.getQuery(datasource, IQuantMSDAO.class);
+ }
+
+ @AfterMethod(alwaysRun = true)
+ public void close()
+ {
+ if (quantmsDAO != null)
+ {
+ quantmsDAO.close();
+ }
+ }
+
+ @Test
+ public void testUploadFiaML() throws SQLException
+ {
+ QuantML2Database uploader = new QuantML2Database(datasource);
+ DMDataSetDTO dataSetDTO =
+ new DMDataSetDTO("data set perm id", "sample perm id", "sample name",
+ "experiment perm id", "experiment name");
+ uploader.uploadQuantMLFile(new File("resource/examples/allFields.quantML"), dataSetDTO);
+ }
+
+}
--
GitLab