Submitting a study
==================

There are two ways to submit a study to ENA:

1) Using the Webinterface
-----------------------
The Webinterface for the dev submission database can be found at: 

https://wwwdev.ebi.ac.uk/ena/submit/webin/login

You could follow this guide: 

https://ena-docs.readthedocs.io/en/latest/submit/study/interactive.html

First, create a directory for your submission files::

  mkdir /mnt/submission/

Register a study now via the webinterface! At the end of the process, you can download a file containing your submission details, you will need the project accession later on, so make sure to save the file, for example in::

  /mnt/submission/study.txt


The following description below is for reference only, if you want to create a study programmatically. Continue with the next step (register sample), when you have submitted a study.


2) Registering a study programmatically
-----------------------
... using the linux command line tool ``curl``
We will use this approach in this short course. 

First, create a work folder for submissions and a subfolder for the study files::

  mkdir -p /mnt/submission/study
  cd /mnt/submission/study

Create submission.xml
^^^^^^^^^^
The next thing you need to to is to create a file submission.xml with the following content::

  <SUBMISSION>
     <ACTIONS>
        <ACTION>
           <ADD/>
        </ACTION>
        <ACTION>
           <HOLD HoldUntilDate="TODO: release date"/>
        </ACTION>
     </ACTIONS>
  </SUBMISSION>

You can use an editor like ``gedit`` to do so. Fill in a valid date like "2022-11-25". You might as well delete the complete ACTION block containing HOLD if the data should be released immediately. 

Create study.xml
^^^^^^^^^^
Now create file study.xml with the following content::

  <PROJECT_SET>
     <PROJECT alias="Your course alias here! Be creative">
        <TITLE>Test dataset from the de.NBI NFDI4Microbiota course on metagenomics 2022</TITLE>
        <DESCRIPTION>This is an artificial dataset that should contain 12 organisms.</DESCRIPTION>
        <SUBMISSION_PROJECT>
           <SEQUENCING_PROJECT/>
        </SUBMISSION_PROJECT>
     </PROJECT>
  </PROJECT_SET>

Again, use ``gedit``, ``vi`` or any other editor to create the file. Change the alias to something unique! You can also change title and description to your likings. 

It is possible to submit multiple studies at once, just add additional PROJECTs in the PROJECT_SET.


Set credentials as environment variables
^^^^^^^^^^^^^^^^

To not type your username password every time you submit, you can store them as environment variables::

  export ENA_USER=Webin-xxxx
  export ENA_PWD=password

Submit the study
^^^^^^^^^^^^^^^^

Now, it is time to submit::

  curl -u $ENA_USER:$ENA_PWD -F "SUBMISSION=@submission.xml" -F "PROJECT=@study.xml" "https://wwwdev.ebi.ac.uk/ena/submit/drop-box/submit/" > receipt.xml

Make sure to use wwwdev to submit to the ENA test server.


Your study accession
^^^^^^^^^^^^^^^^

The response is stored in the file "receipt.xml". You can find the accession number for your study in this line::

  <PROJECT accession="PRJEB57247" alias="mgw2022test" status="PRIVATE" holdUntilDate="2024-11-03Z">
  
Also note, that this number is only valid for today, since it is discarded after 24 hours::

     <MESSAGES>
          <INFO>This submission is a TEST submission and will be discarded within 24 hours</INFO>
     </MESSAGES>

Note your accession number somewhere, you will need it for the next steps.

Now let's submit our environmental sample for this study.



References
^^^^^^^^^^
**ENA - Registering a Study** https://ena-docs.readthedocs.io/en/latest/submit/study.html