Merge pull request #289 from ISA-tools/development

1.7.8 pre release with ENA submission tool.

isatab files/BII-I-1/i_Investigation.txt

@@ -9,9 +9,8 @@ Investigation Title	"Growth control of the eukaryote cell: a systems biology stu
 Investigation Description	"Background Cell growth underlies many key cellular and developmental processes, yet a limited number of studies have been carried out on cell-growth regulation. Comprehensive studies at the transcriptional, proteomic and metabolic levels under defined controlled conditions are currently lacking. Results Metabolic control analysis is being exploited in a systems biology study of the eukaryotic cell. Using chemostat culture, we have measured the impact of changes in flux (growth rate) on the transcriptome, proteome, endometabolome and exometabolome of the yeast Saccharomyces cerevisiae. Each functional genomic level shows clear growth-rate-associated trends and discriminates between carbon-sufficient and carbon-limited conditions. Genes consistently and significantly upregulated with increasing growth rate are frequently essential and encode evolutionarily conserved proteins of known function that participate in many protein-protein interactions. In contrast, more unknown, and fewer essential, genes are downregulated with increasing growth rate; their protein products rarely interact with one another. A large proportion of yeast genes under positive growth-rate control share orthologs with other eukaryotes, including humans. Significantly, transcription of genes encoding components of the TOR complex (a major controller of eukaryotic cell growth) is not subject to growth-rate regulation. Moreover, integrative studies reveal the extent and importance of post-transcriptional control, patterns of control of metabolic fluxes at the level of enzyme synthesis, and the relevance of specific enzymatic reactions in the control of metabolic fluxes during cell growth. Conclusion This work constitutes a first comprehensive systems biology study on growth-rate control in the eukaryotic cell. The results have direct implications for advanced studies on cell growth, in vivo regulation of metabolic fluxes for comprehensive metabolic engineering, and for the design of genome-scale systems biology models of the eukaryotic cell."
 Investigation Submission Date	"2007-04-30"
 Investigation Public Release Date	"2009-03-10"
-Comment[Created with configuration]	""
-Comment[Last Opened With Configuration]	""
 Comment[Created With Configuration]	""
+Comment[Last Opened With Configuration]	""
 Comment[Owning Organisation URI]	""
 Comment[Consortium URI]	""
 Comment[Principal Investigator URI]	""

package.sh

@@ -3,18 +3,19 @@
 # More details in the POM. 
 #
 
-# should be used by passing in either 'scidata' or 'all' as a parameter, e.g. ./package.sh scidata
+# should be used by passing in either 'scidata', 'mixs' or 'all' as a parameter, e.g. ./package.sh scidata
 # switching these will result in different actions being performed on packaging.
 
 PACKAGE_TYPE=$1
-echo $PACKAGE_TYPE
+echo "ISAcreator packaging for type " $PACKAGE_TYPE
+
+MIXS_DATASETS=mixs-datasets-v2.zip
 
 if [ "$PACKAGE_TYPE" = ""  ]
 then
     PACKAGE_TYPE="all"
 fi
 
-alias mvn='/Users/eamonnmaguire/dev/maven/bin/mvn'
 #MVNOPTS="--offline"
 get_tag_data () {
     local tag=$1
@@ -37,25 +38,39 @@ VERSION=${VERSIONSPLIT[0]}
 if [ "$VERSION" = "" ]
 then
   echo "Couldn't extract version from pom.xml. Exiting."
+  exit 1
 fi
 
-
 rm -rf src/main/resources/Configurations
 
 mkdir src/main/resources/Configurations
 
 if [ "$PACKAGE_TYPE" = "scidata"  ]
 then
     CONFIGURATION=isaconfig-Scientific-Data-v1.1.zip
+fi
+
+if [ "$PACKAGE_TYPE" = "mixs"  ]
+then
+    CONFIGURATION=isaconfig-mixs-v4.zip
 else
     CONFIGURATION=isaconfig-default_v2014-01-16.zip
 fi
 
-wget https://bitbucket.org/eamonnmag/isatools-downloads/downloads/"$CONFIGURATION" --no-check-certificate
+echo "Configuration file: " $CONFIGURATION
 
-cp $CONFIGURATION src/main/resources/Configurations/
+if hash curl 2>/dev/null; then
+   echo "curl is installed, will download configurations next"
+else
+   echo "curl is not installed, install it and then run package.sh again"
+   exit 1
+fi
+
+curl -L -O http://bitbucket.org/eamonnmag/isatools-downloads/downloads/"$CONFIGURATION"
 
 
+cp $CONFIGURATION src/main/resources/Configurations/
+
 WD=$(pwd)
 
 pwd
@@ -68,8 +83,14 @@ cd $WD
 echo "Changing back to target..."
 pwd
 
+##Building ISAcreator
 mvn $MVNOPTS -Dmaven.test.skip=true clean assembly:assembly -Pbuild
 
+if [ "$?" -ne 0 ]; then
+    echo "Maven Build Unsuccessful!"
+    exit 1
+fi
+
 
 mkdir target/Configurations
 cp $CONFIGURATION target/Configurations/
@@ -86,10 +107,18 @@ mkdir "isatab files"
 if [ "$PACKAGE_TYPE" = "scidata" ]
 then
     cd "isatab files"
-    wget https://bitbucket.org/eamonnmag/isatools-downloads/downloads/SciData-Datasets-1-and-2.zip --no-check-certificate
+    curl -L -O https://bitbucket.org/eamonnmag/isatools-downloads/downloads/SciData-Datasets-1-and-2.zip
     unzip SciData-Datasets-1-and-2.zip
     rm -f SciData-Datasets-1-and-2.zip
     cd ../
+fi
+if [ "$PACKAGE_TYPE" = "mixs" ]
+then
+    cd "isatab files"
+    curl -L -O https://bitbucket.org/eamonnmag/isatools-downloads/downloads/$MIXS_DATASETS
+    unzip $MIXS_DATASETS
+    rm -f $MIXS_DATASETS
+    cd ../
 else
     cp -r ../"isatab files"/* "isatab files"
 fi

pom.xml

@@ -4,7 +4,7 @@
     <groupId>org.isatools</groupId>
     <artifactId>ISAcreator</artifactId>
     <packaging>bundle</packaging>
-    <version>1.7.7</version>
+    <version>1.7.8</version>
     <name>ISAcreator</name>
     <url>http://www.isa-tools.org</url>
 
@@ -24,7 +24,6 @@
             <organization>ISA tools team</organization>
             <organizationUrl>http://isa-tools.org</organizationUrl>
         </developer>
-
     </developers>
 
     <licenses>
@@ -388,6 +387,11 @@
                     <artifactId>slf4j-api</artifactId>
                     <groupId>org.slf4j</groupId>
                 </exclusion>
+
+                <exclusion>
+                    <groupId>org.slf4j</groupId>
+                    <artifactId>slf4j-log4j12</artifactId>
+                </exclusion>
             </exclusions>
 
         </dependency>
@@ -402,7 +406,7 @@
         <dependency>
             <groupId>org.isatools</groupId>
             <artifactId>import_layer</artifactId>
-            <version>1.6.5</version>
+            <version>1.6.8</version>
             <exclusions>
                 <exclusion>
                     <groupId>uk.ac.ebi</groupId>
@@ -485,6 +489,18 @@
                     </artifactId>
                     <groupId>org.apache.commons</groupId>
                 </exclusion>
+
+
+                <exclusion>
+                    <groupId>org.slf4j</groupId>
+                    <artifactId>slf4j-api</artifactId>
+                </exclusion>
+
+                <exclusion>
+                    <groupId>org.slf4j</groupId>
+                    <artifactId>slf4j-log4j12</artifactId>
+                </exclusion>
+
             </exclusions>
             <!--<scope>runtime</scope>-->
         </dependency>
@@ -503,6 +519,12 @@
              <version>1.11</version>
         </dependency>
 
+        <dependency>
+            <groupId>com.sun.jersey.contribs</groupId>
+            <artifactId>jersey-multipart</artifactId>
+            <version>1.18</version>
+        </dependency>
+
         <dependency>
             <groupId>com.sun.jersey</groupId>
             <artifactId>jersey-json</artifactId>

src/main/java/org/isatools/isacreator/api/utils/SpreadsheetUtils.java

@@ -40,12 +40,18 @@ The ISA Team and the ISA software suite have been funded by the EU Carcinogenomi
 import org.apache.commons.collections15.map.ListOrderedMap;
 import org.apache.commons.collections15.set.ListOrderedSet;
 import org.isatools.isacreator.configuration.DataTypes;
+import org.isatools.isacreator.configuration.FieldObject;
+import org.isatools.isacreator.configuration.TableConfiguration;
+import org.isatools.isacreator.managers.ConfigurationManager;
 import org.isatools.isacreator.model.Assay;
+import org.isatools.isacreator.ontologymanager.OntologyManager;
 import org.isatools.isacreator.ontologymanager.common.OntologyTerm;
 import org.isatools.isacreator.ontologyselectiontool.OntologyCellEditor;
 import org.isatools.isacreator.sampleselection.SampleInformation;
+import org.isatools.isacreator.settings.ISAcreatorProperties;
 import org.isatools.isacreator.spreadsheet.Spreadsheet;
 import org.isatools.isacreator.spreadsheet.Utils;
+import org.isatools.isacreator.spreadsheet.model.TableReferenceObject;
 
 import javax.swing.*;
 import javax.swing.table.TableColumn;
@@ -399,13 +405,65 @@ public static Set<String> findValuesForColumnInSpreadsheet(Spreadsheet spreadshe
 
     public static StringBuilder outputAssayAsString(Assay assay) {
         StringBuilder output = new StringBuilder();
+        TableReferenceObject tableReferenceObject = assay.getTableReferenceObject();
         Object[][] content = assay.getTableReferenceObject().getDataAsArray();
 
+        String separator = "\t";
+        String newline = "\n";
+
+        int row_number = 0;
+
         for (Object[] row : content) {
             for (int columnIndex = 0; columnIndex < row.length; columnIndex++) {
-                output.append(row[columnIndex].toString());
-                output.append(columnIndex != row.length - 1 ? "\t" : "\n");
+
+                output.append("\""+row[columnIndex].toString()+"\"");
+                output.append(columnIndex != row.length - 1 ? separator : newline);
+
+                if (columnIndex < content[0].length) {
+                    FieldObject field = tableReferenceObject.getFieldByName(content[0][columnIndex].toString());
+
+                    if (field != null) {
+                        if (row_number == 0) {
+
+                            if (field.getDatatype().equals(DataTypes.ONTOLOGY_TERM)) {
+                                output.append("\"Term Source REF\"" + separator);
+                                output.append("\"Term Accession Number\"" + separator);
+                            }
+
+                        } else {
+                            //add the ontology values
+
+                            if (field.getDatatype().equals(DataTypes.ONTOLOGY_TERM)) {
+
+                                String val = (String) row[columnIndex];
+                                OntologyTerm oo = OntologyManager.getOntologyTerm(val);
+                                String source = "", termAccession = "";
+
+
+                                if (oo != null) {
+                                    if (ISAcreatorProperties.getProperty("ontologyTermURI").equals("true"))
+                                        termAccession = oo.getOntologyTermURI();
+                                    else
+                                        termAccession = oo.getOntologyTermAccession();
+                                }
+
+                                if (val.contains(":")) {
+                                    source = val.substring(0, val.indexOf(":"));
+                                    val = val.substring(val.indexOf(":") + 1);
+                                }
+
+                                if (oo!=null && source.equals(""))
+                                    source = oo.getOntologySource();
+
+                                output.append("\""+source + "\""+ separator);
+                                output.append("\""+ termAccession + "\"" + separator);
+
+                            }
+                        } //else
+                    } //field not null
+                }
             }
+            row_number++;
         }
 
         return output;

src/main/java/org/isatools/isacreator/api/utils/StudyUtils.java

@@ -144,6 +144,9 @@ private static String generateUniqueAssayReference(Study study, String assayRefe
 
         String candidateRef = cycleCount == 0 ? assayReference + ".txt" : assayReference + "-" + cycleCount + ".txt";
 
+        candidateRef = candidateRef.replaceAll("\\s+","_");
+
+
         if (study.getAssays().containsKey(candidateRef)) {
             // generate the id using a recursive method
             return generateUniqueAssayReference(study, assayReference, cycleCount + 1);

src/main/java/org/isatools/isacreator/common/UIHelper.java

@@ -97,7 +97,7 @@ public class UIHelper {
     public static final RoundedBorder GREY_ROUNDED_BORDER = new RoundedBorder(UIHelper.GREY_COLOR, 2);
     public static final RoundedBorder DARK_GREEN_ROUNDED_BORDER = new RoundedBorder(UIHelper.DARK_GREEN_COLOR, 2);
 
-    public static final Color VERY_LIGHT_GREY_COLOR = new Color(250, 252, 250);
+    public static final Color VERY_LIGHT_GREY_COLOR = new Color(236, 240, 241);
 
     //
 

src/main/java/org/isatools/isacreator/common/button/ButtonType.java

@@ -10,6 +10,7 @@ public enum ButtonType {
 
     BLUE(UIHelper.PETER_RIVER, UIHelper.BELIZE_HOLE),
     GREEN(UIHelper.LIGHT_GREEN_COLOR, UIHelper.DARK_GREEN_COLOR),
+    EMERALD(UIHelper.EMERALD, UIHelper.NEPHRITIS),
     RED(UIHelper.POMEGRANATE, UIHelper.ALIZARIN),
     GREY(new Color(236,240,241), new Color(230,230,230)),
     ORANGE(UIHelper.CARROT, UIHelper.PUMPKIN);

src/main/java/org/isatools/isacreator/effects/SimpleListCellRenderer.java

@@ -0,0 +1,84 @@
+/**
+ ISAcreator is a component of the ISA software suite (http://www.isa-tools.org)
+
+ License:
+ ISAcreator is licensed under the Common Public Attribution License version 1.0 (CPAL)
+
+ EXHIBIT A. CPAL version 1.0
+ The contents of this file are subject to the CPAL version 1.0 (the License);
+ you may not use this file except in compliance with the License. You may obtain a
+ copy of the License at http://isa-tools.org/licenses/ISAcreator-license.html.
+ The License is based on the Mozilla Public License version 1.1 but Sections
+ 14 and 15 have been added to cover use of software over a computer network and
+ provide for limited attribution for the Original Developer. In addition, Exhibit
+ A has been modified to be consistent with Exhibit B.
+
+ Software distributed under the License is distributed on an AS IS basis,
+ WITHOUT WARRANTY OF ANY KIND, either express or implied. See the License for
+ the specific language governing rights and limitations under the License.
+
+ The Original Code is ISAcreator.
+ The Original Developer is the Initial Developer. The Initial Developer of the
+ Original Code is the ISA Team (Eamonn Maguire, eamonnmag@gmail.com;
+ Philippe Rocca-Serra, proccaserra@gmail.com; Susanna-Assunta Sansone, sa.sanson@gmail.com;
+ http://www.isa-tools.org). All portions of the code written by the ISA Team are
+ Copyright (c) 2007-2011 ISA Team. All Rights Reserved.
+
+ EXHIBIT B. Attribution Information
+ Attribution Copyright Notice: Copyright (c) 2008-2011 ISA Team
+ Attribution Phrase: Developed by the ISA Team
+ Attribution URL: http://www.isa-tools.org
+ Graphic Image provided in the Covered Code as file: http://isa-tools.org/licenses/icons/poweredByISAtools.png
+ Display of Attribution Information is required in Larger Works which are defined in the CPAL as a work which combines Covered Code or portions thereof with code not governed by the terms of the CPAL.
+
+ Sponsors:
+ The ISA Team and the ISA software suite have been funded by the EU Carcinogenomics project (http://www.carcinogenomics.eu),
+ the UK BBSRC (http://www.bbsrc.ac.uk), the UK NERC-NEBC (http://nebc.nerc.ac.uk) and in part by the EU NuGO consortium (http://www.nugo.org/everyone).
+ */
+
+package org.isatools.isacreator.effects;
+
+import org.isatools.isacreator.common.UIHelper;
+import org.jdesktop.fuse.InjectedResource;
+import org.jdesktop.fuse.ResourceInjector;
+
+import javax.swing.*;
+import javax.swing.border.EmptyBorder;
+import java.awt.*;
+
+/**
+ * CustomListCellRenderer
+ *
+ * @author Eamonn Maguire
+ * @date Feb 9, 2010
+ */
+
+
+public class SimpleListCellRenderer implements ListCellRenderer {
+
+
+    private JPanel contents;
+    private JLabel text;
+
+    public SimpleListCellRenderer() {
+
+        contents = new JPanel(new BorderLayout());
+        contents.setOpaque(true);
+
+        text = UIHelper.createLabel("", UIHelper.VER_11_PLAIN, UIHelper.GREY_COLOR);
+
+        contents.add(text, BorderLayout.CENTER);
+        contents.setBorder(new EmptyBorder(2, 2, 2, 2));
+    }
+
+
+    public Component getListCellRendererComponent(JList list, Object value, int index, boolean selected, boolean cellGotFocus) {
+
+
+        text.setText(value.toString());
+        text.setFont(selected ? UIHelper.VER_11_BOLD : UIHelper.VER_11_PLAIN);
+
+        return contents;
+    }
+
+}