SDTM 3.4 Define Generator using excel spec issue

Pinnacle 21 Support Define.xml
1

I think you should take a Define-XML course from CDISC …
What you see in the browser, is NOT the define.xml, it is a visualization of the XML contents of the define.xml through your stylesheet. We call that the “VIEW”.
In the old days, the link to the stylesheet was embedded within the define.xml itself. This is usually not the case anymore, as most browser do not accept that mechanism anymore for security reasons.

After you create your define.xml (several user-friendly, GUI based alternatives available on the market), you can open it e.g. in NotePad++ to see whether the link to the stylesheet is present.
You can then generate the VIEW (as define.html) using one of these modern tools, or using something as simple as Saxon.
See e.g. Sam Hume’s excellent explanation at Generating Html From Define.

This step is usually already included when you use one of the modern GUI based tools.

You learn all this, and much much more about define.xml more during the CDISC one-day course on define.xml: Define-XML | CDISC.

2

Hi Jozef,

I managed to solve the problem, the xsl file was corrupted somehow. When I replaced the 2.1 xsl file with one from the p21 downloads section, the xml view worked fine,

Thanks very much for your help!

3

Hi Ryan,
What do you mean with “replaced the 2.1 xsl file”?
Is that the one from CDISC?
If yes, it may mean that your P21-generated define-xml file is not compliant with the standard, as the xsl from CDISC should always work.
Or did you have your own 2.1 xsl file?

P.S. The XSL stylesheet is the RESPONSABILITY of the SPONSOR!

4

Hi Jozef,

I downloaded the define2-1-0.xsl file from P21, renamed it and referenced that in the xml.

I’m hoping you can help me with another issue I’m having. Everything looks fine in the stylesheet except the VLM collapse expand tabs are not showing. (I have tried both the CDISC and P21 xsl)

The xml doesn’t mention ValueListDef or the information (like the where clauses) I have stored in the ValueLevel tab of the excel specification.

Thanks in advance!

5

I forgot to add that P21 validator has flagged 4 issues

  1. DD021 “Invalid Standard Name Value”, although I have used the correct term of “SDTM-IG”

  2. DD0082. “Codelist is not referenced” for all codelists that I have under the ValueLevel tab

  3. DD0127 “Invalid use of NCI Code for codelist” although the “NCI Codelist Code” and “NCI Term code” are correct.

  4. DD01131 “Duplicate codelist name” Although the values mentioned have no duplicates.

6

Hi Ryan,

For the VLM buttons, are they not displaying, or when clicked no action is being done?

I recommend sending your validation report to community@pinnacle21.com so we can review each issue and provide feedback that way.

Kind regards,

Matt

7

Hi Matt,

They don’t appear. That would be great.

I’ll send a copy of the report,

Thanks very much!

8

You can always contact me per e-mail, the address is easy to find out.
Please take into account that I am NOT working for P21, I am an independant consultant, and major contributor to the development of define.xml versions 1.0, 2.0 and 2.1.
Jozef Aerts
XML4Pharma

9

Every time I heard about this issue, it had to do with the browser not allowing active content, such as Javascript.
And every time the browser was Internet Explorer (IE).
As jozef suggested, take a look at Generating Html From Define and generate HTML from the Define-XML file.
Then see if you can open this HTML in another browser.

Lex Jansen

10

Hi,

Thank you in advance for your help,

I’m using Community Version 4.0.2 to generate an excel spec based on our XPT files (UTF-8 and configuration SDTM-IG 3.4)

When I take this spec and import it using the define generator and select 2.0, P21 creates a define with no issue.

When using 2.1, the xml opens as plain text in the browser.

One issue could be that the spec is still in progress. Although the 2.0 generator creates a working define using both the shell spec or a partially filled spec.

Thank you!