I have tried to remake this example by downloading DrugBank XML file on http://www.drugbank.ca/downloads. Your example WF doesn't work on the last version of DrugBank.
Therefore, I attempted to change there nodes settings in order to extract data as discribed in https://www.knime.org/files/nodedetails/_xml_XPath.html and http://www.w3schools.com/XPath/xpath_syntax.asp. Unfortunatly, my experiment is unconclusive.
I'm a newbie with regard to this KNIME utility. I would like to learn how to configure settings of XML reader and XPath properly. I don't understand the utility of namespace and how to configure that.
I have adapted the exising workflow to work with version 4.2 and attached. We are also working on multi XPath extractor node that will reduce the size and improve the speed of the data extraction step drastically. Once the node is available I will update the example workflow on the server to work with 4.2.
Please notice that you have to unzip the XML prior processing it with the XML Reader node.
Drugbank released a new version 5.0.0 a few days ago and I have the same problem as Baptiste had in the past: the xml reader node gives an empty table. Could you tell me what to change in Drugbank_Network_analysis to be able to read this new drugbank.xml file?
. Also gives an empty table. I therefore imported the workflow 01203001_drugBank_4_2 - but there are deprecated nodes (e.g. missing values) which stop it working. Is there a workflow available that is currently working? Many thanks, Shoumo
To get the Palladian nodes, you must now use a separate update site as described by @qqilihq in this post. Note that you should change the update site URL to match the version of KNIME you’re using (probably 4.1):
This should get you the required nodes, with the exception of the NekoHtmlParser. I wasn’t familar with this node, but I poked around on Nodepit and found that using the HtmlParser node is now recommended as a replacement:
Maybe Philipp can tell you more.
(On a side note, note that in most cases using deprecated nodes are fine - they should still work, it’s just they’ve been replaced by more up-to-date functionality. I think the main issue in the case of this workflow is not that the nodes are deprecated, but that the extension containing them moved to a different update site.)