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xmlimport

XML import procedure

Please note that this procedure is currently still in beta testing phase. We hope no problems are encountered when exporting and uploading your catalog. You are welcome to give any feedback on the process.

1. Export your catalog

Export your data according to the current StrainInfo XML schema for BRC catalogs.

A few reminders
  • XML has 5 control characters which should be translated to their respective rendering code when used in content fields.
<&lt;
>&gt;
'&apos;
&quot;
&&amp;
  • XML files use UTF-8 as default character encoding; Note that some tools or editors which you may use in processing or postprocessing your export, may default to ASCII encoding, and should be explicitly instructed to use UTF encoding.

2. Validate your exported XML

Ensure your export validates against the current StrainInfo XML schema. This can be done using popular XML editor tools containing XML Schema validation such as e.g. Oxygen XML.

  For using our vallidation:
  XMLLINT="/usr/bin/xmllint"
  SCHEMA="/opt/strainupload/siconfigfiles/straininfo/strainupload/si-catalog.xsd" 
  (is also online you can download it [[http://www.straininfo.net/schema/2.0/si-catalog.xsd]])
  File= "path to your file"
  $XMLLINT --nowarning --noout --schema "$SCHEMA" "$FILE"     

3. Optional: compress your XML file

In case of large collection exports, it can be desirable to compress the exported XML file to conserve bandwidth and to speed up the upload process. The StrainInfo server will automatically decompress compressed archives before validating and importing (ZIP, RAR, 'gzip' and BZIP2 are supported).

The archive should contain a single file only.

4. Request your upload account information

The upload account is different from your regular StrainInfo login
Currently, account creation requests can only be made via email to straininfo@UGent.be.

Please include the following information: (it might be a good idea to copy/paste this form…)

  Full culture collection/BRC name:
  Acronym:
  WDCM number:
  Official web site:

  Address:
  Country:

  General public e-mail:  

  Person responsible for XML export:
  E-mail of that person (status messages):

Note that the person responsible for the XML export will receive automatic emails of the integration status (succes, failure,…). If the feedback email address has some sort of spam filtering applied, there is a possibility of feedback mails getting blocked. Either check your spam folder after upload, or whitelist strainupload@straininfo.net

5. Upload the XML file to StrainInfo

File uploads to StrainInfo are handled via the Secure Copy (SCP) and Secure File Transfer (SFTP) protocol. You can use any SCP/SFTP-enabled file transfer client program. We noticed the best results with filezilla which is free. WinSCP generated partial uploads.

Use the following connection details:

  • Protocol: SCP or SFTP
  • Server: sync.straininfo.net
  • Port: 22 (default)
  • Username and password as provided upon registration.

Your XML file can be named arbitrarily.

Soon after the upload has been completed, an automated report with feedback will be sent to the status messages e-mail address. If your uploaded export validated successfully, we will initiate the semi-automatic synchronization procedure. After a successful integration, the XML file will be removed from the upload directory.

To facilitate automated transfers and provide enhanced security, we support passwordless public key SCP.

Note: The old FTP synchronization system has been deprecated; If you are holder of an account on the legacy FTP system, and you haven't received your new credentials yet, please contact us.

xmlimport.txt · Last modified: 2014/12/08 12:37 by admin