Scripts created links not being indexed with Google
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Google had issues understanding links that were embedded in script. ... By linkingwith script it would appear that the link was reciprocated but the site would not pass ...So those old ad networks are now being indexed without much difficulty.
have look at the following link it may help you
http://www.searchenginejournal.com/17-ways-to-get-de-indexed/53537/
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It looks like you are correct - this link is difficult to detect on this page, because it sits in the widget. A quick look at the page source for this page reveals that the link www.sitegeek.com/webhostingpad is not visible in the page source, either - just the link to the javascript widget. So the reason these tools can't detect the link is that, to a tool's view, it is not present on the page at all: it lives somewhere else and is only displayed here via the widget.
As to how to fix this, it really depends on what kind of development resources you have available. Google is notorious for having difficulty crawling JavaScript and Ajax, and while they have gotten better at it, they're still not great at it. Ideally, you would change the way your page templates are created so that when the page is generated, it calls for the information, dynamically generates the table, but then publishes it directly on the page rather than calling it via a widget. This would probably be a fair amount of work and would require re-coding the pages that these tables appear on, so it may not be worth it to you to do, depending on how important you decide those external links are.
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There are few details are given on
http://searchengineland.com/tested-googlebot-crawls-javascript-heres-learned-220157and third test "Dynamically Inserted Content" is quite similar to our issue. Not sure how to implement this ?
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You're correct, the third test is similar to your situation. So it may be that Google is crawling the link just fine and is passing that link juice, and just that the tools you're using aren't sophisticated enough to detect it. The dynamically inserted text is present on Google's cached version of the page, so it may very well be fine and you might not need to do anything. I usually try not to rely on Google to figure things like this out, since they are inconsistent at best at correctly understanding JavaScript code, but like I said, if changing how this information is displayed on these pages is going to require a lot of time/expense/work on your part, it may not be worth doing.