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Merge pull request #259 from ISA-tools/development
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Merging 1.7.5 in to master branch for release.
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@eamonnmag
eamonnmag committed Jan 20, 2014
2 parents afc2c4a + 32db03f commit 877845a
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141 changes: 141 additions & 0 deletions ProgramData/field_templates/scidata.xml
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<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>
7 changes: 5 additions & 2 deletions README.md
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Expand Up @@ -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`)
Expand Down Expand Up @@ -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>
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