Merge pull request #259 from ISA-tools/development

Merging 1.7.5 in to master branch for release.
ISA-tools · Jan 20, 2014 · 877845a · 877845a
2 parents afc2c4a + 32db03f
commit 877845a
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diff --git a/ProgramData/field_templates/scidata.xml b/ProgramData/field_templates/scidata.xml
@@ -0,0 +1,141 @@
+<isatab-config-file xmlns="http://www.ebi.ac.uk/bii/isatab_configuration#">
+ <isatab-configuration table-name="SciData">
+ <measurement term-label="[investigation]" term-accession="" source-abbreviation=""/>
+ <technology term-label="" term-accession="" source-abbreviation=""/>
+
+ <field header="Comment [SciData Field 1]" data-type="String" is-file-field="false"
+ is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"
+ section="INVESTIGATION">
+ <description>
+ <![CDATA[A field indicating which ISA configuration was last used to open the ISAtab file.]]></description>
+ <default-value><![CDATA[]]></default-value>
+ </field>
+
+ <field header="Comment [SciData Field 2]" data-type="String" is-file-field="false"
+ is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"
+ section="INVESTIGATION">
+ <description>
+ <![CDATA[A field indicating which ISA configuration was last used to open the ISAtab file.]]></description>
+ <default-value><![CDATA[]]></default-value>
+ </field>
+ <field header="Comment [SciData Field 3]" data-type="String" is-file-field="false"
+ is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"
+ section="STUDY">
+ <description>
+ <![CDATA[A field indicating which ISA configuration was last used to open the ISAtab file.]]></description>
+ <default-value><![CDATA[]]></default-value>
+ </field>
+
+ <field header="Comment [SciData Field 4]" data-type="String" is-file-field="false"
+ is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"
+ section="STUDY DESIGN DESCRIPTORS">
+ <description>
+ <![CDATA[A field indicating which ISA configuration was last used to open the ISAtab file.]]></description>
+ <default-value><![CDATA[]]></default-value>
+ </field>
+ <field header="Comment [SciData Field 5]" data-type="String" is-file-field="false"
+ is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"
+ section="INVESTIGATION">
+ <description>
+ <![CDATA[A field indicating which ISA configuration was last used to open the ISAtab file.]]></description>
+ <default-value><![CDATA[]]></default-value>
+ </field>
+
+ <field header="Comment [SciData Field 6]" data-type="String" is-file-field="false"
+ is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"
+ section="INVESTIGATION">
+ <description>
+ <![CDATA[A field indicating which ISA configuration was last used to open the ISAtab file.]]></description>
+ <default-value><![CDATA[]]></default-value>
+ </field>
+ <field header="Comment [SciData Field 7]" data-type="String" is-file-field="false"
+ is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"
+ section="INVESTIGATION">
+ <description>
+ <![CDATA[A field indicating which ISA configuration was last used to open the ISAtab file.]]></description>
+ <default-value><![CDATA[]]></default-value>
+ </field>
+
+ <field header="Comment [SciData Field 8]" data-type="String" is-file-field="false"
+ is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"
+ section="INVESTIGATION">
+ <description>
+ <![CDATA[A field indicating which ISA configuration was last used to open the ISAtab file.]]></description>
+ <default-value><![CDATA[]]></default-value>
+ </field>
+ <field header="Comment [SciData Field 9]" data-type="String" is-file-field="false"
+ is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"
+ section="INVESTIGATION">
+ <description>
+ <![CDATA[A field indicating which ISA configuration was last used to open the ISAtab file.]]></description>
+ <default-value><![CDATA[]]></default-value>
+ </field>
+
+ <field header="Comment [SciData Field 10]" data-type="String" is-file-field="false"
+ is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"
+ section="INVESTIGATION">
+ <description>
+ <![CDATA[A field indicating which ISA configuration was last used to open the ISAtab file.]]></description>
+ <default-value><![CDATA[]]></default-value>
+ </field>
+ <field header="Comment [SciData Field 11]" data-type="String" is-file-field="false"
+ is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"
+ section="INVESTIGATION">
+ <description>
+ <![CDATA[A field indicating which ISA configuration was last used to open the ISAtab file.]]></description>
+ <default-value><![CDATA[]]></default-value>
+ </field>
+
+ <field header="Comment [SciData Field 12]" data-type="String" is-file-field="false"
+ is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"
+ section="INVESTIGATION">
+ <description>
+ <![CDATA[A field indicating which ISA configuration was last used to open the ISAtab file.]]></description>
+ <default-value><![CDATA[]]></default-value>
+ </field>
+ <field header="Comment [SciData Field 13]" data-type="String" is-file-field="false"
+ is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"
+ section="INVESTIGATION">
+ <description>
+ <![CDATA[A field indicating which ISA configuration was last used to open the ISAtab file.]]></description>
+ <default-value><![CDATA[]]></default-value>
+ </field>
+
+ <field header="Comment [SciData Field 14]" data-type="String" is-file-field="false"
+ is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"
+ section="INVESTIGATION">
+ <description>
+ <![CDATA[A field indicating which ISA configuration was last used to open the ISAtab file.]]></description>
+ <default-value><![CDATA[]]></default-value>
+ </field>
+ <field header="Comment [SciData Field 15]" data-type="String" is-file-field="false"
+ is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"
+ section="INVESTIGATION">
+ <description>
+ <![CDATA[A field indicating which ISA configuration was last used to open the ISAtab file.]]></description>
+ <default-value><![CDATA[]]></default-value>
+ </field>
+
+ <field header="Comment [SciData Field 16]" data-type="String" is-file-field="false"
+ is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"
+ section="INVESTIGATION">
+ <description>
+ <![CDATA[A field indicating which ISA configuration was last used to open the ISAtab file.]]></description>
+ <default-value><![CDATA[]]></default-value>
+ </field>
+ <field header="Comment [SciData Field 17]" data-type="String" is-file-field="false"
+ is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"
+ section="INVESTIGATION">
+ <description>
+ <![CDATA[A field indicating which ISA configuration was last used to open the ISAtab file.]]></description>
+ <default-value><![CDATA[]]></default-value>
+ </field>
+ <field header="Comment [SciData Field 18]" data-type="String" is-file-field="false"
+ is-multiple-value="false" is-required="false" is-hidden="false" is-forced-ontology="false"
+ section="INVESTIGATION">
+ <description>
+ <![CDATA[A field indicating which ISA configuration was last used to open the ISAtab file.]]></description>
+ <default-value><![CDATA[]]></default-value>
+ </field>
+ </isatab-configuration>
+</isatab-config-file>
diff --git a/README.md b/README.md
@@ -19,14 +19,17 @@
 ### Running ISAcreator
 
 To run ISAcreator locally:
+
 1. Clone the code to your machine. You may clone from the primary repository at ISA-tools/ISAcreator, or from your own fork.
 2. Compile the code (`mvn assembly:assembly -Dmaven.test.skip=true -Pbuild`) - the build profile automatically sets some system variables like version etc. from information held within the pom.
-3. Run the code (`java -cp target/ISAcreator-1.7.1-jar-with-dependencies.jar org.isatools.isacreator.launch.ISAcreatorApplication`)
+3. Run the code (`java -cp target/ISAcreator-<version number>-jar-with-dependencies.jar org.isatools.isacreator.launch.ISAcreatorApplication`)
 
 ### Contributing
 
 You should read this article about Github Flow: <http://scottchacon.com/2011/08/31/github-flow.html>. Although we don't strictly use Github flow, it's a really useful tutorial on how to use Git for collaborative development.
 
+Ensure you have maven 2.2.1 installed and enabled as well as git. If you have trouble with dependencies, and you are running behind a proxy, please ensure you set the proxy in both MAVEN_OPTS and settings.xml. See [here](https://answers.atlassian.com/questions/31384/plugin-sdk-proxy-setting-for-https-is-not-working-but-http-is) for more information.
+
 1. Fork it.
 2. Clone your forked repository to your machine
 3. Create a branch off of the development branch (`git checkout -b myisacreator`)
@@ -55,4 +58,4 @@ For a list of contributors, please see <http://github.com/ISA-tools/ISAcreator/c
 
 ## License
 
-CPAL License, available at <http://isatab.sourceforge.net/licenses/ISAcreator-license.html>
+CPAL License, available at <http://isatab.sourceforge.net/licenses/ISAcreator-license.html>