Move galaxy.web.stack.database_heartbeat into galaxy.model - since it was the only thing in galaxy.web.stack that used galaxy.model at all and it didn't import anything else from galaxy.web.stack.
Once that was done, I refactored this whole package (galaxy.web.stack) into galaxy.web_stack. It doesn't use the framework setup or exported by the base galaxy.web package so it wouldn't seem to belong there. It also has very different dependencies than the rest of that. And finally and most importantly, this elimiantes almost all dependency from galaxy.jobs and galaxy.tools and galaxy.workflows to anything in galaxy.web.
PR #8118 - adding to_dict to the dependency manager and an embedded loading of dependency resolution options from galaxy.yml - was really quite poorly thought through.
Certain options could be embedded - but only the resolvers and the actual dictified representation of the DependencyManager couldn't be actually embedded properly in the app config - but this is exactly what I wanted to do on the Pulsar side and it would make no sense to have the exact same options in both apps and configured differently.
So now the actual dictified representation of the whole DependencyManager can be directly embedded in galaxy.yml as the ``dependency_resolution:`` parameter. All the parameters can still be configured at the top level of the YAML file but with 'dependency' in the config option name (some prefixes, some suffixes, etc... a hodgepodge that has grown organically). Give the messiness of the existing options might be better to encourage using ``dependency_resolution:`` in the future.
Fix the following traceback:
```
/usr/users/ga002/soranzon/software/galaxyproject_galaxy/scripts/db_shell.py in printquery(statement, bind)
60 if bind is None:
61 bind = statement.session.get_bind(
---> 62 statement._mapper_zero_or_none())
63 statement = statement.statement
64 elif bind is None:
AttributeError: 'Query' object has no attribute '_mapper_zero_or_none'
```
due to the removal of `_mapper_zero_or_none()` in SQLAlchemy commit
https://github.com/sqlalchemy/sqlalchemy/commit/234a5b9723fbbb9747c0f9e3917baf8500b73370
* include categories as keywords for repository index
* allow filtering on category/owner using github-like wildards "category:name"
* only log metadtaa like matched terms, do not return in http response
* refactoring
- Auto-bootstrap user announcements for datatypes, tools, and viz. (follow up on #7527)
- Many fixes for things broken in #7527
- Treat procedures as an enhancment for categorizing things.
- Speed up release note generation a bit by not considering really, really old PRs.
This is (so far a subset of) the tool utilities from galaxy-lib. galaxy-lib mocked out a fake galaxy.tools to allow these to all exist below the galaxy.tools - but this was a terrible hack - in order for the new packages to be true subsets of Galaxy they need to be refactored into a new package that doesn't depend on models, SA, galaxy.jobs, etc...
[x] galaxy.tools.deps -> galaxy.tool_util.deps
[x] galaxy.tools.loader -> galaxy.tool_util.loader
[x] galaxy.tools.cwl -> galaxy.tool_util.cwl
[x] galaxy.tools.loader -> galaxy.tool_util.loader
[x] galaxy.tools.fetcher -> galaxy.tool_util.fetcher
[x] galaxy.tools.locations -> galaxy.tool_util.locations
[x] galaxy.tools.parser -> galaxy.tool_util.parser
It's important to not set the DatabaseHeartbeat `server_name` prior to forking,
which we avoid be getting `server_name` from
`application_stack.app.config.server_name`.
`WorkerProcess.server_name` for uwsgi web processes will look like:
`main.web.1` and mules like `main.job-handlers.1` while webless workers
remain named `handler1`.
Daniel Blankenberg