brsynth/rptools

Use `>>` instead of `>>` in `brsynth:smiles` SBML annotations

tduigou opened this issue · 2 comments

tduigou commented

Example:
[H]C(=C([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H].O=P(O)(O)OP(=O)(O)O.O=P(O)(O)OP(=O)(O)O>>[H]OP(=O)(O[H])OP(=O)(O[H])OC([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])C([H])([H])C([H])=C(C([H])([H])[H])C([H])([H])[H]

breakthewall commented

I think it is not possible since XML recognizes it as a special character. This is why there is conversion in rpSBML.py each time an XML annotation is read.

tduigou commented

OK I see.

For the record..

Links:

In particular this:

The ampersand character (&) and the left angle bracket (<) MUST NOT appear in their literal form, except when used as markup delimiters, or within a comment, a processing instruction, or a CDATA section. If they are needed elsewhere, they MUST be escaped using either numeric character references or the strings " & " and " < " respectively. The right angle bracket (>) may be represented using the string " > ", and MUST, for compatibility, be escaped using either " > " or a character reference when it appears in the string " ]]> " in content, when that string is not marking the end of a CDATA section.

=> It sounds the use of >> might be tolerate but not recommended.

Looking in the code, libsbml converts automatically from > to &gt; using libsbml.XMLNode.toXMLString at the insertion of the value. At the reading the reader needs to be make the translation back, which is done in rpSBML.py.

Since the present situation is the safest way, I close the ticket.