Programmatic XML submissions

Programmatic XML submissions are supported through the secure HTTPS protocol. Please note that data files must be uploaded before they can be submitted. A receipt XML with accessions is provided upon successful submission.

Production service: https://www.ebi.ac.uk/ena/submit/drop-box/submit/
Test service: https://www-test.ebi.ac.uk/ena/submit/drop-box/submit/

The test service is recreated from the content of the production service every day at 03.00 GMT/BST.

If you have any questions please contact datasubs@ebi.ac.uk.

How to submit

Submissions are made through the secure HTTPS protocol using POST multipart/form-data according to RFC1867.

Test service: https://www-test.ebi.ac.uk/ena/submit/drop-box/submit/

Production service: https://www.ebi.ac.uk/ena/submit/drop-box/submit/

When using curl each XML file is submitted using the '-F' option:

-F "FILETYPE=@FILENAME"

The list of supported file types is:

Type XML
SUBMISSION Submission XML
STUDY Study XML
SAMPLE Sample XML
EXPERIMENT Experiment XML
RUN Run XML
ANALYSIS Analysis XML
DAC EGA DAC XML
POLICY EGA Policy XML
DATASET EGA Dataset XML
PROJECT Project XML

Webin submission account name and password can be provided using basic HTTP authentication or using 'auth' URL parameter:

auth=ENA%20USERNAME%20PASSWORD

Data files must be uploaded before they can be submitted.

Each submission must contain a submission XML file and the submission XML file must have an ACTION element (ADD, MODIFY or VALIDATE) for each other type of XML file in the submission.

Below is an example of a read submission to the test service:

curl -F "SUBMISSION=@submission.xml" -F "STUDY=@study.xml" -F "SAMPLE=@sample.xml" -F "EXPERIMENT=@experiment.xml" -F "RUN=@run.xml" "https://www-test.ebi.ac.uk/ena/submit/drop-box/submit/?auth=ENA%20USERNAME%20PASSWORD" 

Submitting data files

Data files are first uploaded and then associated and submitted with run or analysis objects.

The uploaded data files are listed in the Run or Analysis XML or in a Manifest file. When a Manifest file is used then it must be defined in the Run or Analysis XML.

Manifest files are created using the md5sum command and they contain a list of files with their MD5 checksums to be associated with a run or analysis. Please note that it is not necessary to provide a checksum for the manifest file itself in the XML. Manifest file names are expected to end with '.all' suffix. 

Preparing XMLs

Programmatic submissions are made in XML format ... more information.

Updating XMLs

Updates can be made programmatically in XML format ... more information.

Validating XMLs

Submitted XMLs are validated both structurally and semantically .. more information.

Withdrawing XMLs

It is possible to withdraw submitted objects before and after they have become public .. more information.

Retrieving submitted XMLs

Submitted XMLs can be retrieved from the submission service using assigned accession numbers.

  • Projects: https://www.ebi.ac.uk/ena/submit/drop-box/projects/<accession>?format=html
  • Studies: https://www.ebi.ac.uk/ena/submit/drop-box/studies/<accession>?format=xml
  • Samples: https://www.ebi.ac.uk/ena/submit/drop-box/samples/<accession>?format=xml
  • Runs: https://www.ebi.ac.uk/ena/submit/drop-box/runs/<accession>?format=xml
  • Experiments: https://www.ebi.ac.uk/ena/submit/drop-box/experiments/<accession>?format=xml
  • Analyses://www.ebi.ac.uk/ena/submit/drop-box/analyses/<accession>?format=xml

Please provide your Webin credentials as the basic HTTP authentication username and password.

Receipt XML

Once a submission has been processed a receipt XML is returned that conforms to the SRA.receipt.xsd schema.

If the submission was successful then the returned XML contains /RECEIPT/@success="true".

If there were any errors then the XML contains /RECEIPT/@success="false".

An example of a successful sample submission:

<RECEIPT receiptDate="2014-12-02T16:06:20.871Z" submissionFile="sample_file_1.xml" success="true">
<SAMPLE accession="ERS049536" alias="sample_1" status="PRIVATE"/>
<SUBMISSION accession="ERA390457" alias="submission_1"/>
<MESSAGES>
<INFO>This is an info message.</INFO>
</MESSAGES>
<ACTIONS>ADD</ACTIONS>
</RECEIPT>

 

An example of a failed sample submission:

<RECEIPT receiptDate="2014-12-02T16:06:20.871Z" submissionFile="sample_file_1.xml" success="false">
<SAMPLE accession="ERS049536" alias="sample_1" status="PRIVATE"/>
<SUBMISSION accession="ERA390457" alias="submission_1"/>
<MESSAGES>
<ERROR>This is an error message.</ERROR>
</MESSAGES>
<ACTIONS>ADD</ACTIONS>
</RECEIPT>

If you cannot rectify the errors or do not understand the error message(s) please contact datasubs@ebi.ac.uk explaining the problem and attaching the submitted XMLs and errors.

The receipt XML can also be later requested using the RECEIPT action for all submission that contained ADD actions (see below). Please note that this receipt will only contains assigned accession numbers.

<SUBMISSION>
     <ACTIONS>
         <ACTION>
             <RECEIPT target="submission alias or accession"></RECEIPT>
         </ACTION>
    </ACTIONS>
</SUBMISSION>

 

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