Introduction

This is a comprehensive manual to show how the Research Data Submission Tool for the Plant Genomics & Phenomics Research Data Repository (PGP) works. The PGP repository is an instance of the e!DAL research data infrastructure.

Prerequisite

The Research Data Submission Tool for the PGP Repository ia available as Java Webstart Application. To run the tool a current Java Runtime (JRE) version 8 (or newer) and containig the JavaFX Library is necessary. We recommend to download the official Oracle JDK from the Oracle website.

If you are using a JRE/JDK without JavaFX Library (e.g. OpenJDK) you will receive an error message when try to launch the application.
You can easily check if you have already installed suitable JRE/JDK by run the java -version command. To test if your Java installation also contain the needed Java Webstart binary just run javaws which should pop-up a help menĂ¼ (see Figure 1).
$ java -version
java version "1.8.0_161"
Java(TM) SE Runtime Environment (build 1.8.0_161-b12)
Java HotSpot(TM) 64-Bit Server VM (build 25.161-b12, mixed mode)
javaws
Figure 1: Java Webstart Help Menu

Data Submission

1. Java Webstart Application

Please visit the project website of the PGP repository (see Figure 2) as entry point to initiate the data submission tool.

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Figure 2: Project-Website of the PGP Repository

Click one of the IPK or ELIXIR submission link and download the corresponding Java-Webstart file (eDAL-Publication_(IPK|ELIXIR).jnlp). You can start the application by just double-click on the downloaded *.jnlp file or execute it via terminal:

$ javaws e!DAL_Publication_(IPK|ELIXIR).jnlp
If you have already installed the correct JRE/JDK and configured your browser correct, you will usually asked if you want to execute the webstart application directly from your browser instead of download the *.jnlp file.

Before the Application will be initiated you have to allow that the system can execute it (see Figure 3).

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Figure 3: Java Webstart Application
Depending on your system security settings, it is possible that you will be asked to allow the Java application to connect to the internet through your firewall (see Figure 4). It is necessary to accept this request to login via the Elixir module and authenticate yourself.
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Figure 4: System Firewall Notification

2. Authentication & Login

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Figure 5: IPK Login Screen
It is only possible to login with your IPK account if you are within the local IPK network or if you are connected via VPN client.
Figure 6: ELIXIR Login Screen
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To start the actual data submision tool it is necessary to authenticate yourself using your prefered authentication provider. Beside using a third party authentication provider, it is also possible to authenticate yourself by using your existing institutional credentials. To check if your home organisation already has an ELIXIR AAI compatible identity provider, just enter the name in the search box below the buttons for the third-party login provider.

If run the authentication process via the ELIXIR AAI the first time you will be asked to create an ELIXIR account and connect it with you prefered login modules.

3. Data Deposition & License

Before you can start describing and uploading your data, please read the Data Deposition and License Agreement carefully. It can accessed directly within the application or downloaded as PDF document. Further the document will send to you as attachment in a confirmation e-Mail.

elixir
Figure 7: Publication Tool

After reading the document the form will be unlocked automatically.

4. Data Selection & Description

After selecting your datasets, which you want to upload, by clicking into the first field you can use additional fields to enter all necessary information to describe your data.

pub_tool_1
Figure 8: Publication Tool
You can select single files as well as comprehensive datasets containing subdirectories and files. It is not allowed to upload compressed files or directories, because this would prevent from navigating later through the dataset on the provided content pages for every DOI.

When all necessary metadata are filled, you can go to the next step.

5. Agreement & Data Upload

pub_tool_2
Figure 9: Upload Process

Before the actual upload process will be initiated, you finally need to accept the Deposition and License Agreement.

Depending on the volume of your dataset and your the network connection, the upload can take a while. Please do not interrupt the process.
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Figure 10: Upload successful
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Figure 11: Confirmation e-Mail

After finishing the upload process, you can submit another dataset or close the application. You will receive a confirmation if that your request is under review via e-Mail.

6. Data Review

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Figure 12: Acceptance Notification e-Mail

When the review of your submission was successful, you will receive an the acceptance notification with a temporal preview link to the content pages of your data as well as a link to assign the final DOI or to reject the request.

The linked preview content page is identical to the later final DOI content page. Please use this URL only for internal communication e.g. with the editors and reviewers of the research paper that should referring your data. At this point you can still makes changes. If you assigned the DOI, it is fixed and unchangeable! When it is necessary to change the uploaded data, then just reject the submission and initiate a new submission.
If your data is part of a research article, please do not forget to assign the final DOI at the end, when working on the pages proofs. Do not publish your article using the temporal preview link !

7. DOI Assigning

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Figure 13: DOI Assignment e-Mail

When you confirm the DOI assignment you will receive a final e-Mail with your DOI, which should be worldwide resolvable within the next five minutes.

If you were satisfied with our service, please give credit and cite e!DAL: Arend et al.: e!DAL-a framework to store, share and publish research data. BMC Bioinformatics 15(214), 2014.

Troubleshooting

Mac OS security settings

If you using Mac OS depending on your version it is possible that you will receive a warning that the app you try to start is not downloaded fromn the App Store. This is just becaue of the strict Mac system security settings. If you want to start the publication tool anyway, just allow the execution in your security settings
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First of all just confirm that the application was blocked. The Mac OS will in background add the possibility to ignore this to you security configuration.

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Just open the 'System Preferences'.

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Go the the 'Security & Privacy' menu and open the 'General' tab. Confirm that you want to open the apllication anyway by clicking on the 'Open Anyway' button at the end of the page.

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Then you can start the Java Webstart applicaiton again and now you allow to run the publication tool.

Proxy Settings

Publication tool for the PGP repository already provides an embedded and powerful function to automatically detect the correct network and proxy configuration to establish a connection to the embedded services like DataCite or ORCID.

If you have problem to load the Webstart application or if some functions of the publication tool (e.g. the ORCID search) are blocked or do not work correct, then please check you network connection and verify that your proxy settings are correct.

Additonally it is maybe necessary that you also define the proxy settings in the Java Control Panel, which can be found in your 'System Preferences' or startet via terminal:

$ javaws -viewer
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