Escaped test run output before logging it, to avoid a rich MarkupError

[ewels]

Reported by @sateeshperi and @henningonsbring via nf-core/modules#1460

Errors in the test data gave this unhelpful Python traceback error:

MarkupError: closing tag '[/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/db/metamaps.tar.gz]' at position 589 doesn't match any open tag

This was due to the underlying nf-core/tools code logging the output from the test command to the terminal. This happened to include square brackets, which the Rich library was interpreting as formatting markup.

Properly escaping that text before logging it should fix the issue and properly log the error to the terminal.

Untested, as I can't easily replicate the testing error.

Full original log output

nextflow run tests/modules/metamaps/mapdirectly -entry test_metamaps_mapdirectly -c tests/config/nextflow.config --outdir /tmp/tmpxbjzlp64 -work-dir /tmp/tmpenszt8k7                                            
Picked up JAVA_TOOL_OPTIONS:  -Xmx3435m

╭───────────────────────────────────────────────────────────────────────────────── Traceback (most recent call last) ──────────────────────────────────────────────────────────────────────────────────╮
│                                                                                                                                                                                                      │
│ /opt/conda/bin/nf-core:8 in <module>                                                                                                                                                                 │
│                                                                                                                                                                                                      │
│   7 │   sys.argv[0] = re.sub(r'(-script\.pyw|\.exe)?$', '', sys.argv[0])                                                                                                                             │
│ ❱ 8 │   sys.exit(run_nf_core())                                                                                                                                                                      │
│   9                                                                                                                                                                                                  │
│ /opt/conda/lib/python3.9/site-packages/nf_core/__main__.py:90 in run_nf_core                                                                                                                         │
│                                                                                                                                                                                                      │
│    89 │   # Lanch the click cli                                                                                                                                                                      │
│ ❱  90 │   nf_core_cli()                                                                                                                                                                              │
│    91                                                                                                                                                                                                │
│                                                                                                                                                                                                      │
│ /opt/conda/lib/python3.9/site-packages/click/core.py:1128 in __call__                                                                                                                                │
│                                                                                                                                                                                                      │
│   1127 │   │   """Alias for :meth:`main`."""                                                                                                                                                         │
│ ❱ 1128 │   │   return self.main(*args, **kwargs)                                                                                                                                                     │
│   1129                                                                                                                                                                                               │
│                                                                                                                                                                                                      │
│ /opt/conda/lib/python3.9/site-packages/rich_click/rich_click.py:594 in main                                                                                                                          │
│                                                                                                                                                                                                      │
│   593 │   │   try:                                                                                                                                                                                   │
│ ❱ 594 │   │   │   return super().main(*args, standalone_mode=False, **kwargs)                                                                                                                        │
│   595 │   │   except click.ClickException as e:                                                                                                                                                      │
│                                                                                                                                                                                                      │
│ /opt/conda/lib/python3.9/site-packages/click/core.py:1053 in main                                                                                                                                    │
│                                                                                                                                                                                                      │
│   1052 │   │   │   │   with self.make_context(prog_name, args, **extra) as ctx:                                                                                                                      │
│ ❱ 1053 │   │   │   │   │   rv = self.invoke(ctx)                                                                                                                                                     │
│   1054 │   │   │   │   │   if not standalone_mode:                                                                                                                                                   │
│                                                                                                                                                                                                      │
│ /opt/conda/lib/python3.9/site-packages/click/core.py:1659 in invoke                                                                                                                                  │
│                                                                                                                                                                                                      │
│   1658 │   │   │   │   with sub_ctx:                                                                                                                                                                 │
│ ❱ 1659 │   │   │   │   │   return _process_result(sub_ctx.command.invoke(sub_ctx))                                                                                                                   │
│   1660                                                                                                                                                                                               │
│                                                                                                                                                                                                      │
│ /opt/conda/lib/python3.9/site-packages/click/core.py:1659 in invoke                                                                                                                                  │
│                                                                                                                                                                                                      │
│   1658 │   │   │   │   with sub_ctx:                                                                                                                                                                 │
│ ❱ 1659 │   │   │   │   │   return _process_result(sub_ctx.command.invoke(sub_ctx))                                                                                                                   │
│   1660                                                                                                                                                                                               │
│                                                                                                                                                                                                      │
│ /opt/conda/lib/python3.9/site-packages/click/core.py:1395 in invoke                                                                                                                                  │
│                                                                                                                                                                                                      │
│   1394 │   │   if self.callback is not None:                                                                                                                                                         │
│ ❱ 1395 │   │   │   return ctx.invoke(self.callback, **ctx.params)                                                                                                                                    │
│   1396                                                                                                                                                                                               │
│                                                                                                                                                                                                      │
│ /opt/conda/lib/python3.9/site-packages/click/core.py:754 in invoke                                                                                                                                   │
│                                                                                                                                                                                                      │
│    753 │   │   │   with ctx:                                                                                                                                                                         │
│ ❱  754 │   │   │   │   return __callback(*args, **kwargs)                                                                                                                                            │
│    755                                                                                                                                                                                               │
│                                                                                                                                                                                                      │
│ /opt/conda/lib/python3.9/site-packages/click/decorators.py:26 in new_func                                                                                                                            │
│                                                                                                                                                                                                      │
│    25 │   def new_func(*args, **kwargs):  # type: ignore                                                                                                                                             │
│ ❱  26 │   │   return f(get_current_context(), *args, **kwargs)                                                                                                                                       │
│    27                                                                                                                                                                                                │
│                                                                                                                                                                                                      │
│ /opt/conda/lib/python3.9/site-packages/nf_core/__main__.py:585 in create_test_yml                                                                                                                    │
│                                                                                                                                                                                                      │
│   584 │   except UserWarning as e:                                                                                                                                                                   │
│ ❱ 585 │   │   log.critical(e)                                                                                                                                                                        │
│   586 │   │   sys.exit(1)                                                                                                                                                                            │
│                                                                                                                                                                                                      │
│ /opt/conda/lib/python3.9/logging/__init__.py:1493 in critical                                                                                                                                        │
│                                                                                                                                                                                                      │
│   1492 │   │   if self.isEnabledFor(CRITICAL):                                                                                                                                                       │
│ ❱ 1493 │   │   │   self._log(CRITICAL, msg, args, **kwargs)                                                                                                                                          │
│   1494                                                                                                                                                                                               │
│                                                                                                                                                                                                      │
│ /opt/conda/lib/python3.9/logging/__init__.py:1589 in _log                                                                                                                                            │
│                                                                                                                                                                                                      │
│   1588 │   │   │   │   │   │   │   │    exc_info, func, extra, sinfo)                                                                                                                                │
│ ❱ 1589 │   │   self.handle(record)                                                                                                                                                                   │
│   1590                                                                                                                                                                                               │
│                                                                                                                                                                                                      │
│ /opt/conda/lib/python3.9/logging/__init__.py:1599 in handle                                                                                                                                          │
│                                                                                                                                                                                                      │
│   1598 │   │   if (not self.disabled) and self.filter(record):                                                                                                                                       │
│ �� 1599 │   │   │   self.callHandlers(record)                                                                                                                                                         │
│   1600                                                                                                                                                                                               │
│                                                                                                                                                                                                      │
│ /opt/conda/lib/python3.9/logging/__init__.py:1661 in callHandlers                                                                                                                                    │
│                                                                                                                                                                                                      │
│   1660 │   │   │   │   if record.levelno >= hdlr.level:                                                                                                                                              │
│ ❱ 1661 │   │   │   │   │   hdlr.handle(record)                                                                                                                                                       │
│   1662 │   │   │   if not c.propagate:                                                                                                                                                               │
│                                                                                                                                                                                                      │
│ /opt/conda/lib/python3.9/logging/__init__.py:952 in handle                                                                                                                                           │
│                                                                                                                                                                                                      │
│    951 │   │   │   try:                                                                                                                                                                              │
│ ❱  952 │   │   │   │   self.emit(record)                                                                                                                                                             │
│    953 │   │   │   finally:                                                                                                                                                                          │
│                                                                                                                                                                                                      │
│ /opt/conda/lib/python3.9/site-packages/rich/logging.py:157 in emit                                                                                                                                   │
│                                                                                                                                                                                                      │
│   156 │   │                                                                                                                                                                                          │
│ ❱ 157 │   │   message_renderable = self.render_message(record, message)                                                                                                                              │
│   158 │   │   log_renderable = self.render(                                                                                                                                                          │
│                                                                                                                                                                                                      │
│ /opt/conda/lib/python3.9/site-packages/rich/logging.py:176 in render_message                                                                                                                         │
│                                                                                                                                                                                                      │
│   175 │   │   use_markup = getattr(record, "markup", self.markup)                                                                                                                                    │
│ ❱ 176 │   │   message_text = Text.from_markup(message) if use_markup else Text(message)                                                                                                              │
│   177                                                                                                                                                                                                │
│                                                                                                                                                                                                      │
│ /opt/conda/lib/python3.9/site-packages/rich/text.py:270 in from_markup                                                                                                                               │
│                                                                                                                                                                                                      │
│    269 │   │                                                                                                                                                                                         │
│ ❱  270 │   │   rendered_text = render(text, style, emoji=emoji, emoji_variant=emoji_variant)                                                                                                         │
│    271 │   │   rendered_text.justify = justify                                                                                                                                                       │
│                                                                                                                                                                                                      │
│ /opt/conda/lib/python3.9/site-packages/rich/markup.py:160 in render                                                                                                                                  │
│                                                                                                                                                                                                      │
│   159 │   │   │   │   │   except KeyError:                                                                                                                                                           │
│ ❱ 160 │   │   │   │   │   │   raise MarkupError(                                                                                                                                                     │
│   161 │   │   │   │   │   │   │   f"closing tag '{tag.markup}' at position {position} doesn't                                                                                                        │
│       match any open tag"                                                                                                                                                                            │
╰──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
MarkupError: closing tag '[/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/db/metamaps.tar.gz]' at position 589 doesn't match any open tag

PR checklist

• This comment contains a description of changes (with reason)
• CHANGELOG.md is updated
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated

[henningonsbring]

Ran nf-core modules create-test-yml metamaps/mapdirectly

Got output:

                                          ,--./,-.
          ___     __   __   __   ___     /,-._.--~\
    |\ | |__  __ /  ` /  \ |__) |__         }  {
    | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                          `._,._,'

    nf-core/tools version 2.3.2 - https://nf-co.re


INFO     Press enter to use default values (shown in brackets) or type your own responses                                                                                                                                                                              test_yml_builder.py:55
Test YAML output path (- for stdout) (tests/modules/metamaps/mapdirectly/test.yml): 
File exists! 'tests/modules/metamaps/mapdirectly/test.yml' Overwrite? [y/n]: y
INFO     Looking for test workflow entry points: 'tests/modules/metamaps/mapdirectly/main.nf'                                                                                                                                                                         test_yml_builder.py:123
─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
INFO     Building test meta for entry point 'test_metamaps_mapdirectly'                                                                                                                                                                                               test_yml_builder.py:157
Test name (metamaps mapdirectly test_metamaps_mapdirectly): 
Test command (nextflow run tests/modules/metamaps/mapdirectly -entry test_metamaps_mapdirectly -c tests/config/nextflow.config): 
Test tags (comma separated) (metamaps,metamaps/mapdirectly): 
Test output folder with results (leave blank to run test): 
? Choose software profile Docker
INFO     Running 'metamaps/mapdirectly' test with command:                                                                                                                                                                                                            test_yml_builder.py:321
         nextflow run tests/modules/metamaps/mapdirectly -entry test_metamaps_mapdirectly -c tests/config/nextflow.config --outdir /var/folders/s6/m7vtlhl147bfm538q4cb_z694thzg_/T/tmp5pjokg12 -work-dir                                                                                    
         /var/folders/s6/m7vtlhl147bfm538q4cb_z694thzg_/T/tmp9_vgm1le                                                                                                                                                                                                                        
CRITICAL Error running test workflow (exit code 1)                                                                                                                                                                                                                            __main__.py:585
         N E X T F L O W  ~  version 21.10.6                                                                                                                                                                                                                                                 
         Launching `tests/modules/metamaps/mapdirectly/main.nf`  - revision: 388518e749                                                                                                                                                                                                      
         [-        ] process > test_metamaps_mapdirectly:UNTAR                -                                                                                                                                                                                                              
         [-        ] process > test_metamaps_mapdirectly:METAMAPS_MAPDIRECTLY -                                                                                                                                                                                                              
                                                                                                                                                                                                                                                                                             
         executor >  local (1)                                                                                                                                                                                                                                                               
         [1a/057a89] process > test_metamaps_mapdirectly:UNTAR (metamaps.tar.gz) [  0%] 0 of 1                                                                                                                                                                                               
         [-        ] process > test_metamaps_mapdirectly:METAMAPS_MAPDIRECTLY    -                                                                                                                                                                                                           
                                                                                                                                                                                                                                                                                             
         executor >  local (1)                                                                                                                                                                                                                                                               
         [1a/057a89] process > test_metamaps_mapdirectly:UNTAR (metamaps.tar.gz) [100%] 1 of 1 ✔                                                                                                                                                                                             
         [-        ] process > test_metamaps_mapdirectly:METAMAPS_MAPDIRECTLY    -                                                                                                                                                                                                           
                                                                                                                                                                                                                                                                                             
         executor >  local (1)                                                                                                                                                                                                                                                               
         [1a/057a89] process > test_metamaps_mapdirectly:UNTAR (metamaps.tar.gz) [100%] 1 of 1 ✔                                                                                                                                                                                             
         [-        ] process > test_metamaps_mapdirectly:METAMAPS_MAPDIRECTLY    -                                                                                                                                                                                                           
         Execution aborted due to an unexpected error                                                                                                                                                                                                                                        
                                                                                                                                                                                                                                                                                             
          -- Check script 'tests/modules/metamaps/mapdirectly/../../../../modules/metamaps/mapdirectly/main.nf' at line: 2 or see '.nextflow.log' file for more details                                                                                                                      
                                                                                                                                                                                                                                                                                             
         executor >  local (1)                                                                                                                                                                                                                                                               
         [1a/057a89] process > test_metamaps_mapdirectly:UNTAR (metamaps.tar.gz) [100%] 1 of 1 ✔                                                                                                                                                                                             
         [-        ] process > test_metamaps_mapdirectly:METAMAPS_MAPDIRECTLY    -                                                                                                                                                                                                           
         Execution aborted due to an unexpected error                                                                                                                                                                                                                                        
                                                                                                                                                                                                                                                                                             
          -- Check script 'tests/modules/metamaps/mapdirectly/../../../../modules/metamaps/mapdirectly/main.nf' at line: 2 or see '.nextflow.log' file for more details

[henningonsbring]

Great work