rm internal tools

[gsaudade99]

Now we have the conditions in tool_defautls I think we can remove this

[bgruening]

we don't have that in our internal destination definition, do we?

There is no reject: pulsar ?

[gsaudade99]

I think we added a condition to not add a pulsar tag to the expression tools under the id remote_resources

[domgz]

Hmm, I am not sure whether to proceed or not with this one.

There are internal tools, including __DATA_FETCH__, that do not define a tool_type.

On the other hand, I would expect such cases to be covered by tool.requires_galaxy_python_environment == True. But this 10-year old code doesn't look very trustworthy to me...

That should not be very hard to check if we set up the debug handler. Afaik Galaxy loads a registry of all installed tools in memory, so it would be a matter of inserting a breakpoint, looking into the registry a and making sure tool.requires_galaxy_python_environment == True for all these tools.

Ofc this could also be achieved without the debug handler, for example changing the code so that when a handler finishes loading it writes this information to a file.

[bgruening]

xref: https://github.com/usegalaxy-eu/galaxy/blob/697a55524bdfd94275f8bf0308846eaf6d017a30/lib/galaxy/tools/__init__.py#L266

[gsaudade99]

xref: https://github.com/usegalaxy-eu/galaxy/blob/697a55524bdfd94275f8bf0308846eaf6d017a30/lib/galaxy/tools/__init__.py#L266

Settles it no @kysrpex ?

[domgz]

xref: https://github.com/usegalaxy-eu/galaxy/blob/697a55524bdfd94275f8bf0308846eaf6d017a30/lib/galaxy/tools/__init__.py#L266

Settles it no @kysrpex ?

I can only say that I am not sure, I would have to check more carefully to be sure.

[gsaudade99]

So I have analyzed the piece of code and cross referenced with the tools that we have mentioned in tools.yml:

    @property
    def requires_galaxy_python_environment(self):
      ...
      else:
              unversioned_legacy_tool = self.old_id in GALAXY_LIB_TOOLS_UNVERSIONED
              versioned_legacy_tool = self.old_id in GALAXY_LIB_TOOLS_VERSIONED
              legacy_tool = unversioned_legacy_tool or (
                  versioned_legacy_tool and self.old_id and self.version_object < GALAXY_LIB_TOOLS_VERSIONED[self.old_id]
              )
              return legacy_tool

This means that any tool that is unversioned tool in the list GALAXY_LIB_TOOLS_UNVERSIONED will return true:

For our tools this is true in:

• export_remote
• DATA_FETCH
• upload1

For the other three tools, the tooltype is explicit in the tool datasouce:

• param_value_from_file - expression tool
• ucsc_table_direct1 - data_source
• toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/. - expression

This leaves the edge case of other tools that match the regex __.*__ that are not in the list above mentioned and are not type annotated in the tool source.

Where can I find more tools that would match that regex? If we can know this is safe to merge this PR.