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There are a couple of important things to take note of if you are trying to access a Custom Table via the Web Service.
Table Naming
If a custom table name has any of the following characters or contains spaces that table will not be included in the metadata for the WebService -''#@$^!%&(),;.[]{}`~+=
We recommend table names contain only alphanumeric characters and underscores.
Tables Indexes
For Custom Tables to work correctly in the Webservice there has to be a single field that uniquely defines each row.
That field should be indexed and marked as Primary. The index should only include that field.
When the web service is 'handling' a custom table it will determine the identifier Field as follows:
Inspect the indexes to find one marked Primary, if it finds one it will use the first field in the Primary index, if it does not find a primary index it will use the first field.