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arteymixarteymix
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Merge branch 'release-1.31.0'
2 parents c2d29b4 + 712827f commit 659cabe

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‎.editorconfig

+17-1
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@@ -1,11 +1,24 @@
11
root = true
22

3+
[Jenkinsfile]
4+
indent_style=space
5+
indent_size=4
6+
7+
[init-indices.sql]
8+
indent_size=2
9+
310
[/pom.xml]
411
indent_style=tab
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613
[/gemma-web/pom.xml]
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indent_style=tab
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16+
[BioMaterial.hbm.xml]
17+
indent_size=3
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19+
[BioAssay.hbm.xml]
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indent_size=3
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[Investigation.hbm.xml]
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indent_style=tab
1124

@@ -25,4 +38,7 @@ indent_size=3
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indent_style=tab
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[gemma-web/**/applicationContext-security.xml]
28-
indent_style=tab
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indent_style=tab
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[dwrServices.js]
44+
indent_size=4

‎.idea/codeStyles/Project.xml

+5
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‎.idea/runConfigurations/Gemma_CLI.xml

+1-1
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‎.jenkins/Jenkinsfile

+3-3
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@@ -165,8 +165,8 @@ pipeline {
165165
}
166166
steps {
167167
sh 'mvn -B site-deploy'
168-
sh "ln -sf ${siteDir}/gemma/gemma-${gemmaVersion} ${dataDir}/gemma-devsite"
169-
sh "ln -sf ${siteDir}/baseCode/baseCode-${baseCodeVersion} ${dataDir}/basecode-site"
168+
sh "ln -Tsf ${siteDir}/gemma/gemma-${gemmaVersion} ${dataDir}/gemma-devsite"
169+
sh "ln -Tsf ${siteDir}/baseCode/baseCode-${baseCodeVersion} ${dataDir}/baseCode-site"
170170
}
171171
}
172172
stage ('Deploy Gemma Web') {
@@ -192,7 +192,7 @@ pipeline {
192192
}
193193
}
194194
steps {
195-
sh "rsync -adv gemma-cli/target/appassembler ${cliDir}"
195+
sh "rsync -av --delete gemma-cli/target/appassembler/ ${cliDir}/"
196196
}
197197
}
198198
}

‎.jenkins/README.md

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@@ -0,0 +1,8 @@
1+
This folder contains a configuration for Jenkins and a script to validate the
2+
Jenkinsfile.
3+
4+
Run the following before pushing any changes to the CI configuration:
5+
6+
```bash
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.jenkins/validate-jenkinsfile
8+
```

‎.jenkins/validate-jenkinsfile

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@@ -0,0 +1,4 @@
1+
#!/bin/bash
2+
JENKINS_URL=https://jenkins.pavlab.msl.ubc.ca
3+
JENKINS_CRUMB=`curl "$JENKINS_URL/crumbIssuer/api/xml?xpath=concat(//crumbRequestField,\":\",//crumb)"`
4+
curl -X POST -H $JENKINS_CRUMB -F "jenkinsfile=<$(dirname "${BASH_SOURCE[0]}")/Jenkinsfile" $JENKINS_URL/pipeline-model-converter/validate

‎gemma-cli/pom.xml

+1-1
Original file line numberDiff line numberDiff line change
@@ -3,7 +3,7 @@
33
<parent>
44
<artifactId>gemma</artifactId>
55
<groupId>gemma</groupId>
6-
<version>1.30.6</version>
6+
<version>1.31.0</version>
77
</parent>
88
<modelVersion>4.0.0</modelVersion>
99
<artifactId>gemma-cli</artifactId>

‎gemma-cli/src/main/java/ubic/gemma/core/apps/AffyDataFromCelCli.java

+2-1
Original file line numberDiff line numberDiff line change
@@ -22,6 +22,7 @@
2222
import org.apache.commons.cli.CommandLine;
2323
import org.apache.commons.cli.Option;
2424
import org.apache.commons.cli.Options;
25+
import org.apache.commons.cli.ParseException;
2526
import org.apache.commons.lang3.StringUtils;
2627
import ubic.gemma.core.loader.expression.DataUpdater;
2728
import ubic.gemma.core.loader.expression.geo.model.GeoPlatform;
@@ -182,7 +183,7 @@ protected void doWork() throws Exception {
182183
}
183184

184185
@Override
185-
protected void processOptions( CommandLine commandLine ) {
186+
protected void processOptions( CommandLine commandLine ) throws ParseException {
186187
super.processOptions( commandLine );
187188
if ( commandLine.hasOption( AffyDataFromCelCli.APT_FILE_OPT ) ) {
188189
this.aptFile = commandLine.getOptionValue( AffyDataFromCelCli.APT_FILE_OPT );

‎gemma-cli/src/main/java/ubic/gemma/core/apps/AffyProbeCollapseCli.java

+2-1
Original file line numberDiff line numberDiff line change
@@ -22,6 +22,7 @@
2222
import org.apache.commons.cli.CommandLine;
2323
import org.apache.commons.cli.Option;
2424
import org.apache.commons.cli.Options;
25+
import org.apache.commons.cli.ParseException;
2526
import ubic.gemma.core.analysis.sequence.SequenceManipulation;
2627
import ubic.gemma.core.loader.expression.arrayDesign.AffyProbeReader;
2728
import ubic.gemma.model.expression.designElement.CompositeSequence;
@@ -69,7 +70,7 @@ protected void buildOptions( Options options ) {
6970
}
7071

7172
@Override
72-
protected void processOptions( CommandLine commandLine ) {
73+
protected void processOptions( CommandLine commandLine ) throws ParseException {
7374
super.processOptions( commandLine );
7475
affyProbeFileName = commandLine.getOptionValue( "affyProbeFile" );
7576
}

‎gemma-cli/src/main/java/ubic/gemma/core/apps/ArrayDesignAlternativePopulateCli.java

+3-3
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@@ -24,7 +24,7 @@
2424
import org.apache.commons.lang3.StringUtils;
2525
import org.springframework.core.io.ClassPathResource;
2626
import ubic.gemma.core.apps.GemmaCLI.CommandGroup;
27-
import ubic.gemma.core.util.AbstractCLIContextCLI;
27+
import ubic.gemma.core.util.AbstractAuthenticatedCLI;
2828
import ubic.gemma.model.expression.arrayDesign.ArrayDesign;
2929
import ubic.gemma.persistence.service.expression.arrayDesign.ArrayDesignService;
3030

@@ -38,7 +38,7 @@
3838
*
3939
* @author paul
4040
*/
41-
public class ArrayDesignAlternativePopulateCli extends AbstractCLIContextCLI {
41+
public class ArrayDesignAlternativePopulateCli extends AbstractAuthenticatedCLI {
4242

4343
@Override
4444
public CommandGroup getCommandGroup() {
@@ -61,7 +61,7 @@ protected boolean requireLogin() {
6161
}
6262

6363
@Override
64-
protected void processOptions( CommandLine commandLine ) throws Exception {
64+
protected void processOptions( CommandLine commandLine ) {
6565

6666
}
6767

‎gemma-cli/src/main/java/ubic/gemma/core/apps/ArrayDesignAnnotationFileCli.java

+9-14
Original file line numberDiff line numberDiff line change
@@ -18,21 +18,11 @@
1818
*/
1919
package ubic.gemma.core.apps;
2020

21-
import java.io.BufferedReader;
22-
import java.io.FileInputStream;
23-
import java.io.IOException;
24-
import java.io.InputStream;
25-
import java.io.InputStreamReader;
26-
import java.io.PrintWriter;
27-
import java.util.ArrayList;
28-
import java.util.Collection;
29-
import java.util.HashSet;
30-
3121
import org.apache.commons.cli.CommandLine;
3222
import org.apache.commons.cli.Option;
3323
import org.apache.commons.cli.Options;
24+
import org.apache.commons.cli.ParseException;
3425
import org.apache.commons.lang3.StringUtils;
35-
3626
import ubic.gemma.core.analysis.service.ArrayDesignAnnotationService;
3727
import ubic.gemma.core.apps.GemmaCLI.CommandGroup;
3828
import ubic.gemma.core.genome.gene.service.GeneService;
@@ -45,6 +35,11 @@
4535
import ubic.gemma.model.genome.Taxon;
4636
import ubic.gemma.persistence.service.genome.taxon.TaxonService;
4737

38+
import java.io.*;
39+
import java.util.ArrayList;
40+
import java.util.Collection;
41+
import java.util.HashSet;
42+
4843
/**
4944
* Given an array design creates a Gene Ontology Annotation file Given a batch file creates all the Annotation files for
5045
* the AD's specified in the batch file Given nothing creates annotation files for every AD that isn't subsumed or
@@ -107,9 +102,9 @@ protected void buildOptions( Options options ) {
107102
}
108103

109104
@Override
110-
protected void processOptions( CommandLine commandLine ) {
105+
protected void processOptions( CommandLine commandLine ) throws ParseException {
111106

112-
if ( autoSeek ) {
107+
if ( isAutoSeek() ) {
113108
throw new IllegalArgumentException( "This CLI doesn't support the auto option" );
114109
}
115110

@@ -333,7 +328,7 @@ private void processFromListInFile() throws IOException {
333328
continue;
334329
}
335330

336-
ArrayDesign arrayDesign = this.locateArrayDesign( accession, getArrayDesignService() );
331+
ArrayDesign arrayDesign = this.locateArrayDesign( accession );
337332

338333
try {
339334
this.processAD( arrayDesign );

‎gemma-cli/src/main/java/ubic/gemma/core/apps/ArrayDesignBioSequenceDetachCli.java

+2-2
Original file line numberDiff line numberDiff line change
@@ -21,8 +21,8 @@
2121
import org.apache.commons.cli.CommandLine;
2222
import org.apache.commons.cli.Option;
2323
import org.apache.commons.cli.Options;
24+
import org.apache.commons.cli.ParseException;
2425
import ubic.gemma.model.common.auditAndSecurity.eventType.ArrayDesignSequenceRemoveEvent;
25-
import ubic.gemma.model.common.auditAndSecurity.eventType.AuditEventType;
2626
import ubic.gemma.model.expression.arrayDesign.ArrayDesign;
2727
import ubic.gemma.model.expression.designElement.CompositeSequence;
2828
import ubic.gemma.model.genome.biosequence.BioSequence;
@@ -61,7 +61,7 @@ protected void buildOptions( Options options ) {
6161
}
6262

6363
@Override
64-
protected void processOptions( CommandLine commandLine ) {
64+
protected void processOptions( CommandLine commandLine ) throws ParseException {
6565
super.processOptions( commandLine );
6666
this.delete = commandLine.hasOption( "delete" );
6767
}

‎gemma-cli/src/main/java/ubic/gemma/core/apps/ArrayDesignBlatCli.java

+5-3
Original file line numberDiff line numberDiff line change
@@ -21,6 +21,7 @@
2121
import org.apache.commons.cli.CommandLine;
2222
import org.apache.commons.cli.Option;
2323
import org.apache.commons.cli.Options;
24+
import org.apache.commons.cli.ParseException;
2425
import ubic.gemma.core.apps.GemmaCLI.CommandGroup;
2526
import ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceAlignmentService;
2627
import ubic.gemma.core.loader.genome.BlatResultParser;
@@ -36,7 +37,7 @@
3637
import java.util.ArrayList;
3738
import java.util.Collection;
3839
import java.util.Date;
39-
import java.util.concurrent.*;
40+
import java.util.concurrent.Callable;
4041

4142
/**
4243
* Command line interface to run blat on the sequences for a microarray; the results are persisted in the DB. You must
@@ -72,6 +73,7 @@ protected void buildOptions( Options options ) {
7273
.desc(
7374
"Threshold (0-1.0) for acceptance of BLAT alignments [Default = " + this.blatScoreThreshold + "]" )
7475
.longOpt( "scoreThresh" )
76+
.type( Double.class )
7577
.build();
7678

7779
options.addOption( Option.builder( "sensitive" ).desc( "Run on more sensitive server, if available" ).build() );
@@ -89,7 +91,7 @@ protected void buildOptions( Options options ) {
8991
}
9092

9193
@Override
92-
protected void processOptions( CommandLine commandLine ) {
94+
protected void processOptions( CommandLine commandLine ) throws ParseException {
9395
super.processOptions( commandLine );
9496

9597
if ( commandLine.hasOption( "sensitive" ) ) {
@@ -105,7 +107,7 @@ protected void processOptions( CommandLine commandLine ) {
105107
// }
106108

107109
if ( commandLine.hasOption( 's' ) ) {
108-
this.blatScoreThreshold = this.getDoubleOptionValue( commandLine, 's' );
110+
this.blatScoreThreshold = ( Double ) commandLine.getParsedOptionValue( 's' );
109111
}
110112

111113
TaxonService taxonService = this.getBean( TaxonService.class );

‎gemma-cli/src/main/java/ubic/gemma/core/apps/ArrayDesignMergeCli.java

+3-2
Original file line numberDiff line numberDiff line change
@@ -21,6 +21,7 @@
2121
import org.apache.commons.cli.CommandLine;
2222
import org.apache.commons.cli.Option;
2323
import org.apache.commons.cli.Options;
24+
import org.apache.commons.cli.ParseException;
2425
import org.apache.commons.lang3.StringUtils;
2526
import ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignMergeService;
2627
import ubic.gemma.model.expression.arrayDesign.ArrayDesign;
@@ -95,14 +96,14 @@ protected void buildOptions( Options options ) {
9596
}
9697

9798
@Override
98-
protected void processOptions( CommandLine commandLine ) {
99+
protected void processOptions( CommandLine commandLine ) throws ParseException {
99100
super.processOptions( commandLine );
100101
if ( commandLine.hasOption( 'o' ) ) {// required
101102
String otherArrayDesignName = commandLine.getOptionValue( 'o' );
102103
String[] names = StringUtils.split( otherArrayDesignName, ',' );
103104
this.otherArrayDesigns = new HashSet<>();
104105
for ( String string : names ) {
105-
ArrayDesign o = this.locateArrayDesign( string, getArrayDesignService() );
106+
ArrayDesign o = this.locateArrayDesign( string );
106107
if ( o == null ) {
107108
throw new IllegalArgumentException( "Array design " + string + " not found" );
108109
}

‎gemma-cli/src/main/java/ubic/gemma/core/apps/ArrayDesignProbeCleanupCLI.java

+2-3
Original file line numberDiff line numberDiff line change
@@ -21,9 +21,9 @@
2121
import org.apache.commons.cli.CommandLine;
2222
import org.apache.commons.cli.Option;
2323
import org.apache.commons.cli.Options;
24+
import org.apache.commons.cli.ParseException;
2425
import org.apache.commons.lang3.StringUtils;
2526
import org.springframework.beans.factory.annotation.Autowired;
26-
import org.springframework.stereotype.Component;
2727
import ubic.gemma.core.util.AbstractCLI;
2828
import ubic.gemma.model.expression.arrayDesign.ArrayDesign;
2929
import ubic.gemma.model.expression.designElement.CompositeSequence;
@@ -38,7 +38,6 @@
3838
*
3939
* @author Paul
4040
*/
41-
@Component
4241
public class ArrayDesignProbeCleanupCLI extends ArrayDesignSequenceManipulatingCli {
4342

4443
@Autowired
@@ -59,7 +58,7 @@ protected void buildOptions( Options options ) {
5958
}
6059

6160
@Override
62-
protected void processOptions( CommandLine commandLine ) {
61+
protected void processOptions( CommandLine commandLine ) throws ParseException {
6362
super.processOptions( commandLine );
6463
if ( commandLine.hasOption( 'f' ) ) {
6564
file = commandLine.getOptionValue( 'f' );

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