Issue #452 and #355

Type(s) of Change(s)

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• API-specific change (fix or addition to an API function)
• Updates documentation (inline or markdown files)

Description

There were two problems with using tokens in URLs.

First, the tokens were not "deep" enough. For example, when setting the URL for a gene or mRNA content type you had available the [obi__organism] token but that was it! There was nothing for the genus and species. If you used it then it an empty string would be substituted for the token. This pull request fixes that problem. Now, the tokens reference the sub elements of a field so we now have tokens for genus and species. Tokens should exist for any field that has sub elements and those elements are defined in the elementInfo() function of the field.

Second, non alphanumeric characters were being rewritten as underscores. That causes problems with migrating from Tv2 aliases.

Finally, I fixed a typo in the TripalJob class that I discovered while testing this fix. It was preventing me from re-running jobs. Just take a look at the code below and you'll see the problem. The if statement tries to evaluate the $path but it is set in the line below:

Testing

The easiest test is to edit the gene content type and set the URL alias to this:
mRNA/[obi__organism,TAXRANK:0000005]/[obi__organism,TAXRANK:0000006]/[data__identifier]
Before using that URL string, check the 'Available Tokens' to make sure you see the tokens used in the string above.

It will take time to update your URLs if you have thousands of records. So, testing on a small site or different content type would go fastest.

Screenshots (if appropriate):

Additional Notes (if any):

• My code follows the code style of this project.
• My change requires a change to the documentation.
• I have updated the documentation accordingly.