Rocoto XML regex fix

[maddenp-noaa]

Synopsis

Given rocoto.yaml:

workflow:
  entities:
    GREETING: hello
  attrs:
    realtime: false
    scheduler: slurm
  cycledef:
    - spec: 202410290000 202410300000 06:00:00
  log: logs/test.log
  tasks:
    task_greet:
      command: true && echo &GREETING;
      cores: 1
      walltime: 00:00:10

Current behavior:

$ uw rocoto realize --config-file rocoto.yaml 
[2024-11-01T23:10:42]     INFO 0 UW schema-validation errors found in Rocoto config
...
lxml.etree.XMLSyntaxError: xmlParseEntityRef: no name, line 11, column 20

The problematic line in the XML is:

<command>true &&amp; echo &GREETING;</command>

due to the regex corrected in this PR, which changed a correct && into &&. The regex is meant to correct mangled entities like &FOO;, which should appear as &FOO; in the XML.

With the change in this PR:

$ uw rocoto realize --config-file rocoto.yaml 
[2024-11-01T23:13:57]     INFO 0 UW schema-validation errors found in Rocoto config
[2024-11-01T23:13:57]     INFO 0 Rocoto XML validation errors found
<?xml version='1.0' encoding='utf-8'?>
<!DOCTYPE workflow [
  <!ENTITY GREETING "hello">
]>
<workflow realtime="False" scheduler="slurm">
  <cycledef>202410290000 202410300000 06:00:00</cycledef>
  <log>logs/test.log</log>
  <task name="greet">
    <cores>1</cores>
    <walltime>00:00:10</walltime>
    <command>true &amp;&amp; echo &GREETING;</command>
    <jobname>greet</jobname>
  </task>
</workflow>

I think this this command should be interpreted as true && echo hello at run time, but maybe someone with a Rocoto workflow could confirm by e.g. adding true && to the start of a <command> tag's text, which should have no effect (and, specifically, should cause no error).

Type

• Bug fix (corrects a known issue)

Impact

• This is a non-breaking change (existing functionality continues to work as expected)

Checklist

• I have added myself and any co-authors to the PR's Assignees list.
• I have reviewed the documentation and have made any updates necessitated by this change.

[christinaholtNOAA]

I'm not a huge fan of how the XML bash command no longer looks very bash-like, but I do appreciate the added resiliency it allows.