diff --git a/rtd_phosphonetx/etc/service.properties b/rtd_phosphonetx/etc/service.properties
index 329e6d66589a39ed408bfaa942c2c34f8682887d..9e1e0b93990cbe36c81c2786d70a556fae6f10bc 100644
--- a/rtd_phosphonetx/etc/service.properties
+++ b/rtd_phosphonetx/etc/service.properties
@@ -1,4 +1,4 @@
-# Unique code of this Data Store Server. Not more than 40 characters.
+testtt# Unique code of this Data Store Server. Not more than 40 characters.
data-store-server-code = DSS1
# The root directory of the data store
@@ -111,6 +111,7 @@ main-thread.data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetI
main-thread.data-set-info-extractor.strip-file-extension = true
main-thread.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator}
main-thread.data-set-info-extractor.group-code = TEST
+main-thread.data-set-info-extractor.index-of-experiment-identifier = 0
# Location of file containing data set properties
#main-thread.data-set-info-extractor.data-set-properties-file-name = data-set.properties
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploader.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploader.java
index a4e8829e7f4470f89797b8022ac2699916f2cc7c..341800e89773540a5d639cbf3aa173741286ed4b 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploader.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploader.java
@@ -46,6 +46,7 @@ import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinSummaryDataFilt
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Sample;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Sequence;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Group;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
/**
@@ -82,16 +83,30 @@ class ResultDataSetUploader extends AbstractHandler
Experiment experiment = getOrCreateExperiment(dataSetInfo.tryToGetExperiment().getPermId());
ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample dataSetInfoSample =
dataSetInfo.tryToGetSample();
- if (dataSetInfoSample == null)
+ Sample sample = null;
+ GroupIdentifier groupIdentifier = null;
+ if (dataSetInfoSample != null)
{
- throw new UserFailureException("Missing sample in " + dataSetInfo);
+ sample = getOrCreateSample(experiment, dataSetInfoSample.getPermId());
+ Group group = dataSetInfoSample.getGroup();
+ groupIdentifier = new GroupIdentifier(group.getInstance().getCode(), group.getCode());
+ } else
+ {
+ ExperimentIdentifier experimentIdentifier = dataSetInfo.getExperimentIdentifier();
+ if (experimentIdentifier == null)
+ {
+ throw new UserFailureException(
+ "Neither sample nor experiment identifier specified: " + dataSetInfo);
+ }
+ groupIdentifier =
+ new GroupIdentifier(experimentIdentifier.getDatabaseInstanceCode(),
+ experimentIdentifier.getGroupCode());
}
- Sample sample = getOrCreateSample(experiment, dataSetInfoSample.getPermId());
String referenceDatabase = summary.getSummaryHeader().getReferenceDatabase();
Database database = getOrGreateDatabase(referenceDatabase);
DataSet ds =
getOrCreateDataSet(experiment, sample, database, dataSetInfo.getDataSetCode());
- addToDatabase(ds, experiment, dataSetInfoSample.getGroup(), summary);
+ addToDatabase(ds, experiment, groupIdentifier, summary);
if (errorMessages.length() == 0)
{
connection.commit();
@@ -136,7 +151,7 @@ class ResultDataSetUploader extends AbstractHandler
return database;
}
- private DataSet getOrCreateDataSet(Experiment experiment, Sample sample, Database database,
+ private DataSet getOrCreateDataSet(Experiment experiment, Sample sampleOrNull, Database database,
String dataSetPermID)
{
DataSet dataSet = dao.tryToGetDataSetByPermID(dataSetPermID);
@@ -146,8 +161,12 @@ class ResultDataSetUploader extends AbstractHandler
dataSet.setPermID(dataSetPermID);
long experimentID = experiment.getId();
dataSet.setExperimentID(experimentID);
- long sampleID = sample.getId();
- dataSet.setSampleID(sampleID);
+ Long sampleID = null;
+ if (sampleOrNull != null)
+ {
+ sampleID = sampleOrNull.getId();
+ dataSet.setSampleID(sampleID);
+ }
long databaseID = database.getId();
dataSet.setDatabaseID(databaseID);
dataSet.setId(dao.createDataSet(experimentID, sampleID, dataSetPermID, databaseID));
@@ -167,13 +186,11 @@ class ResultDataSetUploader extends AbstractHandler
return experiment;
}
- private void addToDatabase(DataSet dataSet, Experiment experiment, Group group,
+ private void addToDatabase(DataSet dataSet, Experiment experiment, GroupIdentifier groupIdentifier,
ProteinSummary summary)
{
long dataSetID = dataSet.getId();
Long databaseID = dataSet.getDatabaseID();
- GroupIdentifier groupIdentifier =
- new GroupIdentifier(group.getInstance().getCode(), group.getCode());
AbundanceHandler abundanceHandler =
new AbundanceHandler(openbisService, dao, groupIdentifier, experiment);
createProbabilityToFDRMapping(dataSetID, summary);
@@ -339,5 +356,5 @@ class ResultDataSetUploader extends AbstractHandler
}
throw new UserFailureException("Missing Protein Prophet details.");
}
-
}
+
diff --git a/rtd_phosphonetx/source/sql/postgresql/001/schema-001.dez b/rtd_phosphonetx/source/sql/postgresql/001/schema-001.dez
index 80c885dcde0f9c875086b09a7ed026e47b4ae028..8fb86063bc3c09ea2b676e3bd6a8348b31683cd4 100644
--- a/rtd_phosphonetx/source/sql/postgresql/001/schema-001.dez
+++ b/rtd_phosphonetx/source/sql/postgresql/001/schema-001.dez
@@ -4,14 +4,14 @@
<VERSION>
<PROJECTSETTINGS>
<PROJECTFILENAME>D:\User\felmer\dev-workspace\rtd_phosphonetx\source\sql\postgresql\phosphonetx.dez</PROJECTFILENAME>
-<MODIFIED>2009-08-27</MODIFIED>
+<MODIFIED>2009-09-28</MODIFIED>
<CREATED>2009-06-29</CREATED>
<CREATED2></CREATED2>
<PROJECTNAME></PROJECTNAME>
<DESCRIPTION></DESCRIPTION>
<AUTHOR></AUTHOR>
<COPYRIGHT></COPYRIGHT>
-<LASTGENERATEDFILES>N:\user\cisd\felmer\phosphonetx\schema-001.sql;N:\user\cisd\felmer\phosphonetx\drop.sql;C:\Users\felmer\Documents\CreateDBLog_200908271.txt</LASTGENERATEDFILES>
+<LASTGENERATEDFILES>N:\user\cisd\felmer\phosphonetx\schema-001.sql;N:\user\cisd\felmer\phosphonetx\drop.sql;C:\Users\felmer\Documents\CreateDBLog_200909281.txt</LASTGENERATEDFILES>
</PROJECTSETTINGS>
<CONNECTIONSETTINGS>
<SQLFILE>D:\User\felmer\dev-workspace\rtd_phosphonetx\source\sql\postgresql\001\schema-001.sql</SQLFILE>
@@ -20,7 +20,7 @@
</CONNECTIONSETTINGS>
<DATADICT>
<DBID>postgresql8</DBID>
-<LASTID>159</LASTID>
+<LASTID>175</LASTID>
<DDSETTINGS>
<PKCONNAMETEMPLATE>PK_%table%</PKCONNAMETEMPLATE>
<FKCONNAMETEMPLATE>%relname%</FKCONNAMETEMPLATE>
@@ -187,6 +187,19 @@
<INC>1</INC>
</DT>
</DOMAIN>
+<DOMAIN>
+<NAME>SPECTRUM_REFERENCE</NAME>
+<ID>171</ID>
+<POSNR>0</POSNR>
+<SCHEMA></SCHEMA>
+<DESC></DESC>
+<DT>
+<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
+<LE>100</LE>
+<SD>0</SD>
+<INC>1</INC>
+</DT>
+</DOMAIN>
</DOMAINS>
<ENTITIES>
<ENT>
@@ -373,19 +386,6 @@
<SD>0</SD>
<INC>1</INC>
</DT>
-<NNCON>
-<NAME></NAME>
-<ID>1</ID>
-<POSNR>0</POSNR>
-<SCHEMA></SCHEMA>
-<DESC></DESC>
-<VALUE>1</VALUE>
-<CONLEVEL>1</CONLEVEL>
-<CONTYPE>5</CONTYPE>
-<ATTRIBUTEIDS>
-<ATTRIBUTEID>5</ATTRIBUTEID>
-</ATTRIBUTEIDS>
-</NNCON>
</ATTR>
<ATTR>
<NAME>DB_ID</NAME>
@@ -1962,6 +1962,231 @@
</ATTR>
</ATTRIBUTES>
</ENT>
+<ENT>
+<NAME>SPECTRUM_REFERENCES</NAME>
+<ID>160</ID>
+<POSNR>0</POSNR>
+<SCHEMA></SCHEMA>
+<DESC></DESC>
+<ATTRLASTID>4</ATTRLASTID>
+<IDXLASTID>1</IDXLASTID>
+<TRGLASTID>1</TRGLASTID>
+<CONLASTID>1</CONLASTID>
+<PKCON>
+<NAME>PK_SPECTRUM_REFERENCES</NAME>
+<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
+<ID>1</ID>
+<POSNR>0</POSNR>
+<SCHEMA></SCHEMA>
+<DESC></DESC>
+<CONLEVEL>2</CONLEVEL>
+<CONTYPE>3</CONTYPE>
+<ATTRIBUTEIDS>
+<ATTRIBUTEID>4</ATTRIBUTEID>
+</ATTRIBUTEIDS>
+</PKCON>
+<ATTRIBUTES>
+<ATTR>
+<NAME>ID</NAME>
+<ID>4</ID>
+<POSNR>0</POSNR>
+<SCHEMA></SCHEMA>
+<DESC></DESC>
+<DOMAINID>-1</DOMAINID>
+<DT>
+<DTLISTNAME>BIGSERIAL</DTLISTNAME>
+<SD>0</SD>
+<INC>1</INC>
+</DT>
+<NNCON>
+<NAME></NAME>
+<ID>1</ID>
+<POSNR>0</POSNR>
+<SCHEMA></SCHEMA>
+<DESC></DESC>
+<VALUE>1</VALUE>
+<CONLEVEL>1</CONLEVEL>
+<CONTYPE>5</CONTYPE>
+<ATTRIBUTEIDS>
+<ATTRIBUTEID>4</ATTRIBUTEID>
+</ATTRIBUTEIDS>
+</NNCON>
+</ATTR>
+<ATTR>
+<NAME>PEPT_ID</NAME>
+<ID>2</ID>
+<POSNR>0</POSNR>
+<SCHEMA></SCHEMA>
+<DESC></DESC>
+<DOMAINID>12</DOMAINID>
+<DT>
+<DTLISTNAME>BIGINT</DTLISTNAME>
+<SD>0</SD>
+<INC>1</INC>
+</DT>
+<NNCON>
+<NAME></NAME>
+<ID>1</ID>
+<POSNR>0</POSNR>
+<SCHEMA></SCHEMA>
+<DESC></DESC>
+<VALUE>1</VALUE>
+<CONLEVEL>1</CONLEVEL>
+<CONTYPE>5</CONTYPE>
+<ATTRIBUTEIDS>
+<ATTRIBUTEID>2</ATTRIBUTEID>
+</ATTRIBUTEIDS>
+</NNCON>
+</ATTR>
+<ATTR>
+<NAME>REFERENCE</NAME>
+<ID>3</ID>
+<POSNR>0</POSNR>
+<SCHEMA></SCHEMA>
+<DESC></DESC>
+<DOMAINID>171</DOMAINID>
+<DT>
+<DTLISTNAME>CHARACTER VARYING</DTLISTNAME>
+<LE>100</LE>
+<SD>0</SD>
+<INC>1</INC>
+</DT>
+<NNCON>
+<NAME></NAME>
+<ID>1</ID>
+<POSNR>0</POSNR>
+<SCHEMA></SCHEMA>
+<DESC></DESC>
+<VALUE>1</VALUE>
+<CONLEVEL>1</CONLEVEL>
+<CONTYPE>5</CONTYPE>
+<ATTRIBUTEIDS>
+<ATTRIBUTEID>3</ATTRIBUTEID>
+</ATTRIBUTEIDS>
+</NNCON>
+</ATTR>
+</ATTRIBUTES>
+</ENT>
+<ENT>
+<NAME>MODIFICATION_FRACTIONS</NAME>
+<ID>173</ID>
+<POSNR>0</POSNR>
+<SCHEMA></SCHEMA>
+<DESC></DESC>
+<ATTRLASTID>5</ATTRLASTID>
+<IDXLASTID>1</IDXLASTID>
+<TRGLASTID>1</TRGLASTID>
+<CONLASTID>1</CONLASTID>
+<PKCON>
+<NAME>PK_MODIFICATION_FRACTIONS</NAME>
+<NAMETEMPLATE>PK_%table%</NAMETEMPLATE>
+<ID>1</ID>
+<POSNR>0</POSNR>
+<SCHEMA></SCHEMA>
+<DESC></DESC>
+<CONLEVEL>2</CONLEVEL>
+<CONTYPE>3</CONTYPE>
+<ATTRIBUTEIDS>
+<ATTRIBUTEID>2</ATTRIBUTEID>
+</ATTRIBUTEIDS>
+</PKCON>
+<ATTRIBUTES>
+<ATTR>
+<NAME>ID</NAME>
+<ID>2</ID>
+<POSNR>0</POSNR>
+<SCHEMA></SCHEMA>
+<DESC></DESC>
+<DOMAINID>-1</DOMAINID>
+<DT>
+<DTLISTNAME>BIGSERIAL</DTLISTNAME>
+<SD>0</SD>
+<INC>1</INC>
+</DT>
+<NNCON>
+<NAME></NAME>
+<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
+<ID>1</ID>
+<POSNR>0</POSNR>
+<SCHEMA></SCHEMA>
+<DESC></DESC>
+<VALUE>1</VALUE>
+<CONLEVEL>1</CONLEVEL>
+<CONTYPE>5</CONTYPE>
+<ATTRIBUTEIDS>
+<ATTRIBUTEID>2</ATTRIBUTEID>
+</ATTRIBUTEIDS>
+</NNCON>
+</ATTR>
+<ATTR>
+<NAME>MODI_ID</NAME>
+<ID>3</ID>
+<POSNR>0</POSNR>
+<SCHEMA></SCHEMA>
+<DESC></DESC>
+<DOMAINID>12</DOMAINID>
+<DT>
+<DTLISTNAME>BIGINT</DTLISTNAME>
+<SD>0</SD>
+<INC>1</INC>
+</DT>
+<NNCON>
+<NAME></NAME>
+<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
+<ID>1</ID>
+<POSNR>0</POSNR>
+<SCHEMA></SCHEMA>
+<DESC></DESC>
+<VALUE>1</VALUE>
+<CONLEVEL>1</CONLEVEL>
+<CONTYPE>5</CONTYPE>
+<ATTRIBUTEIDS>
+<ATTRIBUTEID>3</ATTRIBUTEID>
+</ATTRIBUTEIDS>
+</NNCON>
+</ATTR>
+<ATTR>
+<NAME>SAMP_ID</NAME>
+<ID>4</ID>
+<POSNR>0</POSNR>
+<SCHEMA></SCHEMA>
+<DESC></DESC>
+<DOMAINID>12</DOMAINID>
+<DT>
+<DTLISTNAME>BIGINT</DTLISTNAME>
+<SD>0</SD>
+<INC>1</INC>
+</DT>
+</ATTR>
+<ATTR>
+<NAME>FRACTION</NAME>
+<ID>5</ID>
+<POSNR>0</POSNR>
+<SCHEMA></SCHEMA>
+<DESC></DESC>
+<DOMAINID>8</DOMAINID>
+<DT>
+<DTLISTNAME>DOUBLE PRECISION</DTLISTNAME>
+<SD>0</SD>
+<INC>1</INC>
+</DT>
+<NNCON>
+<NAME></NAME>
+<NAMETEMPLATE>NN_%column%</NAMETEMPLATE>
+<ID>1</ID>
+<POSNR>0</POSNR>
+<SCHEMA></SCHEMA>
+<DESC></DESC>
+<VALUE>1</VALUE>
+<CONLEVEL>1</CONLEVEL>
+<CONTYPE>5</CONTYPE>
+<ATTRIBUTEIDS>
+<ATTRIBUTEID>5</ATTRIBUTEID>
+</ATTRIBUTEIDS>
+</NNCON>
+</ATTR>
+</ATTRIBUTES>
+</ENT>
</ENTITIES>
<SUBCATEGORIES>
</SUBCATEGORIES>
@@ -2028,7 +2253,7 @@
<CHILDOBJECTID>17</CHILDOBJECTID>
<CARDINALITY>0</CARDINALITY>
<RELTYPE>1</RELTYPE>
-<MANDATORYPARENT>1</MANDATORYPARENT>
+<MANDATORYPARENT>0</MANDATORYPARENT>
<UPDATERULE>0</UPDATERULE>
<DELETERULE>0</DELETERULE>
<CONSTRAINT>
@@ -2524,6 +2749,123 @@
</PAIR>
</PAIRS>
</REL>
+<REL>
+<NAME>PEPTIDES_SPECTRUM_REFERENCES</NAME>
+<NAMETEMPLATE>%parent%_%child%</NAMETEMPLATE>
+<ID>172</ID>
+<POSNR>0</POSNR>
+<SCHEMA></SCHEMA>
+<DESC></DESC>
+<PARENTOBJECTID>21</PARENTOBJECTID>
+<CHILDOBJECTID>160</CHILDOBJECTID>
+<CARDINALITY>0</CARDINALITY>
+<RELTYPE>1</RELTYPE>
+<MANDATORYPARENT>1</MANDATORYPARENT>
+<UPDATERULE>0</UPDATERULE>
+<DELETERULE>0</DELETERULE>
+<CONSTRAINT>
+<NAME>PEPTIDES_SPECTRUM_REFERENCES</NAME>
+<NAMETEMPLATE>%relname%</NAMETEMPLATE>
+<ID>1</ID>
+<POSNR>0</POSNR>
+<SCHEMA></SCHEMA>
+<DESC></DESC>
+<CONLEVEL>2</CONLEVEL>
+<CONTYPE>4</CONTYPE>
+<ATTRIBUTEIDS>
+<ATTRIBUTEID>2</ATTRIBUTEID>
+</ATTRIBUTEIDS>
+</CONSTRAINT>
+<PAIRS>
+<PAIR>
+<NAME></NAME>
+<ID>0</ID>
+<POSNR>0</POSNR>
+<SCHEMA></SCHEMA>
+<DESC></DESC>
+<KEYID>2</KEYID>
+<FOREIGNKEYID>2</FOREIGNKEYID>
+</PAIR>
+</PAIRS>
+</REL>
+<REL>
+<NAME>MODIFICATIONS_MODIFICATION_FRACTIONS</NAME>
+<NAMETEMPLATE>%parent%_%child%</NAMETEMPLATE>
+<ID>174</ID>
+<POSNR>0</POSNR>
+<SCHEMA></SCHEMA>
+<DESC></DESC>
+<PARENTOBJECTID>19</PARENTOBJECTID>
+<CHILDOBJECTID>173</CHILDOBJECTID>
+<CARDINALITY>0</CARDINALITY>
+<RELTYPE>1</RELTYPE>
+<MANDATORYPARENT>1</MANDATORYPARENT>
+<UPDATERULE>0</UPDATERULE>
+<DELETERULE>0</DELETERULE>
+<CONSTRAINT>
+<NAME>MODIFICATIONS_MODIFICATION_FRACTIONS</NAME>
+<NAMETEMPLATE>%relname%</NAMETEMPLATE>
+<ID>1</ID>
+<POSNR>0</POSNR>
+<SCHEMA></SCHEMA>
+<DESC></DESC>
+<CONLEVEL>2</CONLEVEL>
+<CONTYPE>4</CONTYPE>
+<ATTRIBUTEIDS>
+<ATTRIBUTEID>3</ATTRIBUTEID>
+</ATTRIBUTEIDS>
+</CONSTRAINT>
+<PAIRS>
+<PAIR>
+<NAME></NAME>
+<ID>0</ID>
+<POSNR>0</POSNR>
+<SCHEMA></SCHEMA>
+<DESC></DESC>
+<KEYID>2</KEYID>
+<FOREIGNKEYID>3</FOREIGNKEYID>
+</PAIR>
+</PAIRS>
+</REL>
+<REL>
+<NAME>SAMPLES_MODIFICATION_FRACTIONS</NAME>
+<NAMETEMPLATE>%parent%_%child%</NAMETEMPLATE>
+<ID>175</ID>
+<POSNR>0</POSNR>
+<SCHEMA></SCHEMA>
+<DESC></DESC>
+<PARENTOBJECTID>24</PARENTOBJECTID>
+<CHILDOBJECTID>173</CHILDOBJECTID>
+<CARDINALITY>0</CARDINALITY>
+<RELTYPE>1</RELTYPE>
+<MANDATORYPARENT>0</MANDATORYPARENT>
+<UPDATERULE>0</UPDATERULE>
+<DELETERULE>0</DELETERULE>
+<CONSTRAINT>
+<NAME>SAMPLES_MODIFICATION_FRACTIONS</NAME>
+<NAMETEMPLATE>%relname%</NAMETEMPLATE>
+<ID>1</ID>
+<POSNR>0</POSNR>
+<SCHEMA></SCHEMA>
+<DESC></DESC>
+<CONLEVEL>2</CONLEVEL>
+<CONTYPE>4</CONTYPE>
+<ATTRIBUTEIDS>
+<ATTRIBUTEID>4</ATTRIBUTEID>
+</ATTRIBUTEIDS>
+</CONSTRAINT>
+<PAIRS>
+<PAIR>
+<NAME></NAME>
+<ID>0</ID>
+<POSNR>0</POSNR>
+<SCHEMA></SCHEMA>
+<DESC></DESC>
+<KEYID>2</KEYID>
+<FOREIGNKEYID>4</FOREIGNKEYID>
+</PAIR>
+</PAIRS>
+</REL>
</RELATIONSHIPS>
<SUBCATEGORYCONNECTIONS>
</SUBCATEGORYCONNECTIONS>
@@ -2585,8 +2927,8 @@
<DIAGRAMID>1</DIAGRAMID>
<W>136</W>
<H>63</H>
-<L>647</L>
-<T>24</T>
+<L>544</L>
+<T>11</T>
<BRUSH>0,16777215</BRUSH>
<PEN>0,1,4,0</PEN>
<FONT>Arial,8,,0,clWindowText,0</FONT>
@@ -2596,10 +2938,10 @@
<ENTC>
<ID>17</ID>
<DIAGRAMID>1</DIAGRAMID>
-<W>141</W>
+<W>139</W>
<H>108</H>
-<L>297</L>
-<T>24</T>
+<L>295</L>
+<T>11</T>
<BRUSH>0,16777215</BRUSH>
<PEN>0,1,4,0</PEN>
<FONT>Arial,8,,0,clWindowText,0</FONT>
@@ -2611,8 +2953,8 @@
<DIAGRAMID>1</DIAGRAMID>
<W>177</W>
<H>93</H>
-<L>526</L>
-<T>585</T>
+<L>12</L>
+<T>628</T>
<BRUSH>0,16777215</BRUSH>
<PEN>0,1,4,0</PEN>
<FONT>Arial,8,,0,clWindowText,0</FONT>
@@ -2624,8 +2966,8 @@
<DIAGRAMID>1</DIAGRAMID>
<W>187</W>
<H>93</H>
-<L>274</L>
-<T>442</T>
+<L>271</L>
+<T>480</T>
<BRUSH>0,16777215</BRUSH>
<PEN>0,1,4,0</PEN>
<FONT>Arial,8,,0,clWindowText,0</FONT>
@@ -2637,8 +2979,8 @@
<DIAGRAMID>1</DIAGRAMID>
<W>180</W>
<H>78</H>
-<L>277</L>
-<T>289</T>
+<L>274</L>
+<T>328</T>
<BRUSH>0,16777215</BRUSH>
<PEN>0,1,4,0</PEN>
<FONT>Arial,8,,0,clWindowText,0</FONT>
@@ -2650,8 +2992,8 @@
<DIAGRAMID>1</DIAGRAMID>
<W>136</W>
<H>78</H>
-<L>15</L>
-<T>24</T>
+<L>12</L>
+<T>11</T>
<BRUSH>0,16777215</BRUSH>
<PEN>0,1,4,0</PEN>
<FONT>Arial,8,,0,clWindowText,0</FONT>
@@ -2663,8 +3005,8 @@
<DIAGRAMID>1</DIAGRAMID>
<W>250</W>
<H>108</H>
-<L>731</L>
-<T>289</T>
+<L>736</L>
+<T>328</T>
<BRUSH>0,16777215</BRUSH>
<PEN>0,1,4,0</PEN>
<FONT>Arial,8,,0,clWindowText,0</FONT>
@@ -2676,8 +3018,8 @@
<DIAGRAMID>1</DIAGRAMID>
<W>142</W>
<H>78</H>
-<L>526</L>
-<T>289</T>
+<L>541</L>
+<T>328</T>
<BRUSH>0,16777215</BRUSH>
<PEN>0,1,4,0</PEN>
<FONT>Arial,8,,0,clWindowText,0</FONT>
@@ -2689,8 +3031,8 @@
<DIAGRAMID>1</DIAGRAMID>
<W>161</W>
<H>93</H>
-<L>15</L>
-<T>289</T>
+<L>114</L>
+<T>182</T>
<BRUSH>0,16777215</BRUSH>
<PEN>0,1,4,0</PEN>
<FONT>Arial,8,,0,clWindowText,0</FONT>
@@ -2702,8 +3044,8 @@
<DIAGRAMID>1</DIAGRAMID>
<W>245</W>
<H>93</H>
-<L>457</L>
-<T>176</T>
+<L>490</L>
+<T>182</T>
<BRUSH>0,16777215</BRUSH>
<PEN>0,1,4,0</PEN>
<FONT>Arial,8,,0,clWindowText,0</FONT>
@@ -2715,8 +3057,8 @@
<DIAGRAMID>1</DIAGRAMID>
<W>252</W>
<H>78</H>
-<L>730</L>
-<T>442</T>
+<L>734</L>
+<T>480</T>
<BRUSH>0,16777215</BRUSH>
<PEN>0,1,4,0</PEN>
<FONT>Arial,8,,0,clWindowText,0</FONT>
@@ -2728,7 +3070,7 @@
<DIAGRAMID>1</DIAGRAMID>
<W>252</W>
<H>63</H>
-<L>730</L>
+<L>734</L>
<T>107</T>
<BRUSH>0,16777215</BRUSH>
<PEN>0,1,4,0</PEN>
@@ -2741,8 +3083,34 @@
<DIAGRAMID>1</DIAGRAMID>
<W>183</W>
<H>93</H>
-<L>276</L>
-<T>585</T>
+<L>273</L>
+<T>628</T>
+<BRUSH>0,16777215</BRUSH>
+<PEN>0,1,4,0</PEN>
+<FONT>Arial,8,,0,clWindowText,0</FONT>
+<TR>0</TR>
+<AS>1</AS>
+</ENTC>
+<ENTC>
+<ID>160</ID>
+<DIAGRAMID>1</DIAGRAMID>
+<W>214</W>
+<H>78</H>
+<L>505</L>
+<T>480</T>
+<BRUSH>0,16777215</BRUSH>
+<PEN>0,1,4,0</PEN>
+<FONT>Arial,8,,0,clWindowText,0</FONT>
+<TR>0</TR>
+<AS>1</AS>
+</ENTC>
+<ENTC>
+<ID>173</ID>
+<DIAGRAMID>1</DIAGRAMID>
+<W>164</W>
+<H>93</H>
+<L>12</L>
+<T>480</T>
<BRUSH>0,16777215</BRUSH>
<PEN>0,1,4,0</PEN>
<FONT>Arial,8,,0,clWindowText,0</FONT>
@@ -2770,20 +3138,20 @@
<TORELATIVEY>2870</TORELATIVEY>
<POINTS>
<POINT>
-<X>646</X>
-<Y>55</Y>
+<X>543</X>
+<Y>42</Y>
</POINT>
<POINT>
-<X>493</X>
-<Y>55</Y>
+<X>480</X>
+<Y>42</Y>
</POINT>
<POINT>
-<X>493</X>
-<Y>55</Y>
+<X>480</X>
+<Y>42</Y>
</POINT>
<POINT>
-<X>438</X>
-<Y>55</Y>
+<X>434</X>
+<Y>42</Y>
</POINT>
</POINTS>
</RELC>
@@ -2798,20 +3166,20 @@
<TORELATIVEY>3611</TORELATIVEY>
<POINTS>
<POINT>
-<X>151</X>
-<Y>63</Y>
+<X>148</X>
+<Y>50</Y>
</POINT>
<POINT>
-<X>233</X>
-<Y>63</Y>
+<X>219</X>
+<Y>50</Y>
</POINT>
<POINT>
-<X>233</X>
-<Y>63</Y>
+<X>219</X>
+<Y>50</Y>
</POINT>
<POINT>
-<X>296</X>
-<Y>63</Y>
+<X>294</X>
+<Y>50</Y>
</POINT>
</POINTS>
</RELC>
@@ -2826,20 +3194,20 @@
<TORELATIVEY>5000</TORELATIVEY>
<POINTS>
<POINT>
-<X>367</X>
-<Y>367</Y>
+<X>364</X>
+<Y>406</Y>
</POINT>
<POINT>
-<X>367</X>
-<Y>403</Y>
+<X>364</X>
+<Y>428</Y>
</POINT>
<POINT>
-<X>367</X>
-<Y>403</Y>
+<X>364</X>
+<Y>428</Y>
</POINT>
<POINT>
-<X>367</X>
-<Y>441</Y>
+<X>364</X>
+<Y>479</Y>
</POINT>
</POINTS>
</RELC>
@@ -2848,26 +3216,26 @@
<DIAGRAMID>1</DIAGRAMID>
<FONT>Arial,8,,0,clWindowText,0</FONT>
<PEN>1,1,4,0</PEN>
-<FROMRELATIVEX>4965</FROMRELATIVEX>
+<FROMRELATIVEX>4964</FROMRELATIVEX>
<FROMRELATIVEY>5000</FROMRELATIVEY>
<TORELATIVEX>5000</TORELATIVEX>
<TORELATIVEY>5000</TORELATIVEY>
<POINTS>
<POINT>
-<X>367</X>
-<Y>132</Y>
+<X>364</X>
+<Y>119</Y>
</POINT>
<POINT>
-<X>367</X>
-<Y>210</Y>
+<X>364</X>
+<Y>183</Y>
</POINT>
<POINT>
-<X>367</X>
-<Y>210</Y>
+<X>364</X>
+<Y>183</Y>
</POINT>
<POINT>
-<X>367</X>
-<Y>288</Y>
+<X>364</X>
+<Y>327</Y>
</POINT>
</POINTS>
</RELC>
@@ -2882,20 +3250,20 @@
<TORELATIVEY>5000</TORELATIVEY>
<POINTS>
<POINT>
-<X>457</X>
-<Y>328</Y>
+<X>454</X>
+<Y>367</Y>
</POINT>
<POINT>
-<X>471</X>
-<Y>328</Y>
+<X>489</X>
+<Y>367</Y>
</POINT>
<POINT>
-<X>471</X>
-<Y>328</Y>
+<X>489</X>
+<Y>367</Y>
</POINT>
<POINT>
-<X>525</X>
-<Y>328</Y>
+<X>540</X>
+<Y>367</Y>
</POINT>
</POINTS>
</RELC>
@@ -2910,20 +3278,20 @@
<TORELATIVEY>5000</TORELATIVEY>
<POINTS>
<POINT>
-<X>730</X>
-<Y>328</Y>
+<X>735</X>
+<Y>367</Y>
</POINT>
<POINT>
-<X>690</X>
-<Y>328</Y>
+<X>705</X>
+<Y>367</Y>
</POINT>
<POINT>
-<X>690</X>
-<Y>328</Y>
+<X>705</X>
+<Y>367</Y>
</POINT>
<POINT>
-<X>668</X>
-<Y>328</Y>
+<X>683</X>
+<Y>367</Y>
</POINT>
</POINTS>
</RELC>
@@ -2932,26 +3300,26 @@
<DIAGRAMID>1</DIAGRAMID>
<FONT>Arial,8,,0,clWindowText,0</FONT>
<PEN>1,1,4,0</PEN>
-<FROMRELATIVEX>5000</FROMRELATIVEX>
+<FROMRELATIVEX>8750</FROMRELATIVEX>
<FROMRELATIVEY>5000</FROMRELATIVEY>
-<TORELATIVEX>4224</TORELATIVEX>
+<TORELATIVEX>1056</TORELATIVEX>
<TORELATIVEY>5000</TORELATIVEY>
<POINTS>
<POINT>
-<X>83</X>
-<Y>102</Y>
+<X>131</X>
+<Y>89</Y>
</POINT>
<POINT>
-<X>83</X>
+<X>131</X>
<Y>143</Y>
</POINT>
<POINT>
-<X>83</X>
+<X>131</X>
<Y>143</Y>
</POINT>
<POINT>
-<X>83</X>
-<Y>288</Y>
+<X>131</X>
+<Y>181</Y>
</POINT>
</POINTS>
</RELC>
@@ -2960,26 +3328,26 @@
<DIAGRAMID>1</DIAGRAMID>
<FONT>Arial,8,,0,clWindowText,0</FONT>
<PEN>1,1,4,0</PEN>
-<FROMRELATIVEX>7341</FROMRELATIVEX>
+<FROMRELATIVEX>0</FROMRELATIVEX>
<FROMRELATIVEY>5000</FROMRELATIVEY>
-<TORELATIVEX>5000</TORELATIVEX>
+<TORELATIVEX>9938</TORELATIVEX>
<TORELATIVEY>4194</TORELATIVEY>
<POINTS>
<POINT>
-<X>276</X>
-<Y>328</Y>
+<X>274</X>
+<Y>327</Y>
</POINT>
<POINT>
-<X>231</X>
-<Y>328</Y>
+<X>274</X>
+<Y>299</Y>
</POINT>
<POINT>
-<X>231</X>
-<Y>328</Y>
+<X>274</X>
+<Y>299</Y>
</POINT>
<POINT>
-<X>176</X>
-<Y>328</Y>
+<X>274</X>
+<Y>275</Y>
</POINT>
</POINTS>
</RELC>
@@ -2994,20 +3362,20 @@
<TORELATIVEY>5000</TORELATIVEY>
<POINTS>
<POINT>
-<X>415</X>
-<Y>132</Y>
+<X>411</X>
+<Y>119</Y>
</POINT>
<POINT>
-<X>415</X>
-<Y>149</Y>
+<X>411</X>
+<Y>161</Y>
</POINT>
<POINT>
-<X>579</X>
-<Y>149</Y>
+<X>612</X>
+<Y>161</Y>
</POINT>
<POINT>
-<X>579</X>
-<Y>175</Y>
+<X>612</X>
+<Y>181</Y>
</POINT>
</POINTS>
</RELC>
@@ -3016,26 +3384,26 @@
<DIAGRAMID>1</DIAGRAMID>
<FONT>Arial,8,,0,clWindowText,0</FONT>
<PEN>1,1,4,0</PEN>
-<FROMRELATIVEX>5000</FROMRELATIVEX>
+<FROMRELATIVEX>5040</FROMRELATIVEX>
<FROMRELATIVEY>7619</FROMRELATIVEY>
<TORELATIVEX>5000</TORELATIVEX>
<TORELATIVEY>1296</TORELATIVEY>
<POINTS>
<POINT>
-<X>856</X>
+<X>861</X>
<Y>170</Y>
</POINT>
<POINT>
-<X>856</X>
+<X>861</X>
<Y>235</Y>
</POINT>
<POINT>
-<X>856</X>
+<X>861</X>
<Y>235</Y>
</POINT>
<POINT>
-<X>856</X>
-<Y>288</Y>
+<X>861</X>
+<Y>327</Y>
</POINT>
</POINTS>
</RELC>
@@ -3044,26 +3412,26 @@
<DIAGRAMID>1</DIAGRAMID>
<FONT>Arial,8,,0,clWindowText,0</FONT>
<PEN>1,1,4,0</PEN>
-<FROMRELATIVEX>5000</FROMRELATIVEX>
+<FROMRELATIVEX>5040</FROMRELATIVEX>
<FROMRELATIVEY>5000</FROMRELATIVEY>
<TORELATIVEX>5000</TORELATIVEX>
<TORELATIVEY>3611</TORELATIVEY>
<POINTS>
<POINT>
-<X>856</X>
-<Y>441</Y>
+<X>861</X>
+<Y>479</Y>
</POINT>
<POINT>
-<X>856</X>
-<Y>421</Y>
+<X>861</X>
+<Y>447</Y>
</POINT>
<POINT>
-<X>856</X>
-<Y>421</Y>
+<X>861</X>
+<Y>447</Y>
</POINT>
<POINT>
-<X>856</X>
-<Y>397</Y>
+<X>861</X>
+<Y>436</Y>
</POINT>
</POINTS>
</RELC>
@@ -3073,25 +3441,25 @@
<FONT>Arial,8,,0,clWindowText,0</FONT>
<PEN>1,1,4,0</PEN>
<FROMRELATIVEX>5000</FROMRELATIVEX>
-<FROMRELATIVEY>1905</FROMRELATIVEY>
+<FROMRELATIVEY>952</FROMRELATIVEY>
<TORELATIVEX>5000</TORELATIVEX>
-<TORELATIVEY>8796</TORELATIVEY>
+<TORELATIVEY>9444</TORELATIVEY>
<POINTS>
<POINT>
-<X>729</X>
-<Y>119</Y>
+<X>733</X>
+<Y>113</Y>
</POINT>
<POINT>
-<X>644</X>
-<Y>119</Y>
+<X>578</X>
+<Y>113</Y>
</POINT>
<POINT>
-<X>644</X>
-<Y>119</Y>
+<X>578</X>
+<Y>113</Y>
</POINT>
<POINT>
-<X>438</X>
-<Y>119</Y>
+<X>434</X>
+<Y>113</Y>
</POINT>
</POINTS>
</RELC>
@@ -3106,20 +3474,20 @@
<TORELATIVEY>5000</TORELATIVEY>
<POINTS>
<POINT>
-<X>367</X>
-<Y>535</Y>
+<X>364</X>
+<Y>573</Y>
</POINT>
<POINT>
-<X>367</X>
-<Y>563</Y>
+<X>364</X>
+<Y>585</Y>
</POINT>
<POINT>
-<X>367</X>
-<Y>563</Y>
+<X>364</X>
+<Y>585</Y>
</POINT>
<POINT>
-<X>367</X>
-<Y>584</Y>
+<X>364</X>
+<Y>627</Y>
</POINT>
</POINTS>
</RELC>
@@ -3128,26 +3496,110 @@
<DIAGRAMID>1</DIAGRAMID>
<FONT>Arial,8,,0,clWindowText,0</FONT>
<PEN>1,1,4,0</PEN>
-<FROMRELATIVEX>5000</FROMRELATIVEX>
+<FROMRELATIVEX>929</FROMRELATIVEX>
<FROMRELATIVEY>4946</FROMRELATIVEY>
<TORELATIVEX>5000</TORELATIVEX>
<TORELATIVEY>4946</TORELATIVEY>
<POINTS>
<POINT>
-<X>459</X>
-<Y>631</Y>
+<X>272</X>
+<Y>674</Y>
+</POINT>
+<POINT>
+<X>237</X>
+<Y>674</Y>
+</POINT>
+<POINT>
+<X>237</X>
+<Y>674</Y>
+</POINT>
+<POINT>
+<X>189</X>
+<Y>674</Y>
+</POINT>
+</POINTS>
+</RELC>
+<RELC>
+<ID>172</ID>
+<DIAGRAMID>1</DIAGRAMID>
+<FONT>Arial,8,,0,clWindowText,0</FONT>
+<PEN>1,1,4,0</PEN>
+<FROMRELATIVEX>5000</FROMRELATIVEX>
+<FROMRELATIVEY>4194</FROMRELATIVEY>
+<TORELATIVEX>5000</TORELATIVEX>
+<TORELATIVEY>5000</TORELATIVEY>
+<POINTS>
+<POINT>
+<X>458</X>
+<Y>519</Y>
+</POINT>
+<POINT>
+<X>469</X>
+<Y>519</Y>
+</POINT>
+<POINT>
+<X>469</X>
+<Y>519</Y>
+</POINT>
+<POINT>
+<X>504</X>
+<Y>519</Y>
+</POINT>
+</POINTS>
+</RELC>
+<RELC>
+<ID>174</ID>
+<DIAGRAMID>1</DIAGRAMID>
+<FONT>Arial,8,,0,clWindowText,0</FONT>
+<PEN>1,1,4,0</PEN>
+<FROMRELATIVEX>4633</FROMRELATIVEX>
+<FROMRELATIVEY>5000</FROMRELATIVEY>
+<TORELATIVEX>5000</TORELATIVEX>
+<TORELATIVEY>5000</TORELATIVEY>
+<POINTS>
+<POINT>
+<X>94</X>
+<Y>627</Y>
+</POINT>
+<POINT>
+<X>94</X>
+<Y>585</Y>
+</POINT>
+<POINT>
+<X>94</X>
+<Y>585</Y>
+</POINT>
+<POINT>
+<X>94</X>
+<Y>573</Y>
+</POINT>
+</POINTS>
+</RELC>
+<RELC>
+<ID>175</ID>
+<DIAGRAMID>1</DIAGRAMID>
+<FONT>Arial,8,,0,clWindowText,0</FONT>
+<PEN>1,1,4,0</PEN>
+<FROMRELATIVEX>5000</FROMRELATIVEX>
+<FROMRELATIVEY>5000</FROMRELATIVEY>
+<TORELATIVEX>4146</TORELATIVEX>
+<TORELATIVEY>5000</TORELATIVEY>
+<POINTS>
+<POINT>
+<X>80</X>
+<Y>89</Y>
</POINT>
<POINT>
-<X>492</X>
-<Y>631</Y>
+<X>80</X>
+<Y>202</Y>
</POINT>
<POINT>
-<X>492</X>
-<Y>631</Y>
+<X>80</X>
+<Y>202</Y>
</POINT>
<POINT>
-<X>525</X>
-<Y>631</Y>
+<X>80</X>
+<Y>479</Y>
</POINT>
</POINTS>
</RELC>
diff --git a/rtd_phosphonetx/source/sql/postgresql/001/schema-001.png b/rtd_phosphonetx/source/sql/postgresql/001/schema-001.png
index 84c5a177c879021beacb52d4070ae887bcb89a7c..69f33d205fd55433318b8e294148b3eb20267d5d 100644
Binary files a/rtd_phosphonetx/source/sql/postgresql/001/schema-001.png and b/rtd_phosphonetx/source/sql/postgresql/001/schema-001.png differ
diff --git a/rtd_phosphonetx/source/sql/postgresql/001/schema-001.sql b/rtd_phosphonetx/source/sql/postgresql/001/schema-001.sql
index d32bd77ea7c5452063134fd2aa5d7d58006aadb7..5aaa048555bba96d45fcc2fa27e0976638a3de3c 100644
--- a/rtd_phosphonetx/source/sql/postgresql/001/schema-001.sql
+++ b/rtd_phosphonetx/source/sql/postgresql/001/schema-001.sql
@@ -5,8 +5,8 @@
/* Project name: */
/* Author: */
/* Script type: Database creation script */
-/* Created on: 2009-08-27 11:01 */
-/* Model version: Version 2009-08-27 */
+/* Created on: 2009-09-28 08:43 */
+/* Model version: Version 2009-09-28 */
/* ---------------------------------------------------------------------- */
@@ -34,6 +34,8 @@ CREATE DOMAIN SHORT_SEQUENCE AS CHARACTER VARYING(1000);
CREATE DOMAIN ACCESSION_NUMBER AS CHARACTER VARYING(256);
+CREATE DOMAIN SPECTRUM_REFERENCE AS CHARACTER VARYING(100);
+
/* ---------------------------------------------------------------------- */
/* Tables */
/* ---------------------------------------------------------------------- */
@@ -56,7 +58,7 @@ CREATE TABLE EXPERIMENTS (
CREATE TABLE DATA_SETS (
ID BIGSERIAL NOT NULL,
EXPE_ID TECH_ID NOT NULL,
- SAMP_ID TECH_ID NOT NULL,
+ SAMP_ID TECH_ID,
DB_ID TECH_ID NOT NULL,
PERM_ID CODE NOT NULL,
CONSTRAINT PK_DATA_SETS PRIMARY KEY (ID),
@@ -203,6 +205,29 @@ CREATE TABLE MODIFIED_PEPTIDES (
CONSTRAINT PK_MODIFIED_PEPTIDES PRIMARY KEY (ID)
);
+/* ---------------------------------------------------------------------- */
+/* Add table "SPECTRUM_REFERENCES" */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE SPECTRUM_REFERENCES (
+ ID BIGSERIAL NOT NULL,
+ PEPT_ID TECH_ID NOT NULL,
+ REFERENCE SPECTRUM_REFERENCE NOT NULL,
+ CONSTRAINT PK_SPECTRUM_REFERENCES PRIMARY KEY (ID)
+);
+
+/* ---------------------------------------------------------------------- */
+/* Add table "MODIFICATION_FRACTIONS" */
+/* ---------------------------------------------------------------------- */
+
+CREATE TABLE MODIFICATION_FRACTIONS (
+ ID BIGSERIAL NOT NULL,
+ MODI_ID TECH_ID NOT NULL,
+ SAMP_ID TECH_ID,
+ FRACTION REAL_NUMBER NOT NULL,
+ CONSTRAINT PK_MODIFICATION_FRACTIONS PRIMARY KEY (ID)
+);
+
/* ---------------------------------------------------------------------- */
/* Foreign key constraints */
/* ---------------------------------------------------------------------- */
@@ -248,3 +273,12 @@ ALTER TABLE PROBABILITY_FDR_MAPPINGS ADD CONSTRAINT DATA_SETS_PROBABILITY_FDR_MA
ALTER TABLE MODIFIED_PEPTIDES ADD CONSTRAINT PEPTIDES_MODIFIED_PEPTIDES
FOREIGN KEY (PEPT_ID) REFERENCES PEPTIDES (ID);
+
+ALTER TABLE SPECTRUM_REFERENCES ADD CONSTRAINT PEPTIDES_SPECTRUM_REFERENCES
+ FOREIGN KEY (PEPT_ID) REFERENCES PEPTIDES (ID);
+
+ALTER TABLE MODIFICATION_FRACTIONS ADD CONSTRAINT MODIFICATIONS_MODIFICATION_FRACTIONS
+ FOREIGN KEY (MODI_ID) REFERENCES MODIFICATIONS (ID);
+
+ALTER TABLE MODIFICATION_FRACTIONS ADD CONSTRAINT SAMPLES_MODIFICATION_FRACTIONS
+ FOREIGN KEY (SAMP_ID) REFERENCES SAMPLES (ID);