Report if empty inputs were used or if the same input was used more than once, these were identified as common sources of potential errors across many tools. Neither of these are definite problems, but both could be depending on the tool and both happen frequently. Outline a few more ideas as TODOs in the code.
SQLite does not always update foreign key constraints when the target
table is renamed, so we start with the table rename in both `upgrade()`
and `downgrade()`.
xref. https://www.sqlite.org/lang_altertable.html
Reported by @curtisecombsjr
Fix the following traceback when installing https://toolshed.g2.bx.psu.edu/view/iuc/package_openssl_1_0/ :
```
File "lib/tool_shed/galaxy_install/install_manager.py", line 121, in install_and_build_package_via_fabric
tool_dependency = self.install_and_build_package(install_environment, tool_dependency, actions_dict)
File "lib/tool_shed/galaxy_install/install_manager.py", line 79, in install_and_build_package
initial_download=True)
File "lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 31, in execute_step
initial_download=initial_download)
File "lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 548, in execute_step
dir = self.url_download(work_dir, downloaded_filename, url, extract=True, checksums=checksums)
File "lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 77, in url_download
extraction_path = archive.extract(install_dir)
File "lib/galaxy/util/compression_utils.py", line 111, in extract
self.archive.extractall(extraction_path, members=self.safemembers())
File "/usr/lib64/python2.7/tarfile.py", line 2041, in extractall
for tarinfo in members:
File "lib/galaxy/util/compression_utils.py", line 135, in safemembers
raise Exception(finfo.name + " is blocked.")
openssl-1.0.2d/apps/md4.c is blocked.
```
Should fix https://github.com/galaxyproject/galaxy/issues/7700:
```
File "lib/galaxy/web/framework/middleware/batch.py", line 80, in __call__
return self.application(environ, start_response)
File "lib/galaxy/web/framework/middleware/request_id.py", line 15, in __call__
return self.app(environ, start_response)
File "lib/galaxy/web/framework/middleware/xforwardedhost.py", line 23, in __call__
return self.app(environ, start_response)
File "lib/galaxy/web/framework/middleware/translogger.py", line 71, in __call__
return self.application(environ, replacement_start_response)
File "lib/galaxy/web/framework/middleware/error.py", line 166, in __call__
response = self.exception_handler(exc_info, environ)
File "lib/galaxy/web/framework/middleware/error.py", line 181, in exception_handler
get_vars = wsgilib.parse_querystring(environ)
File "/gpfs1/data/galaxy_server/galaxy-dev/.venv/lib/python2.7/site-packages/paste/request.py", line 107, in parse_querystring
strict_parsing=False)
File "/global/apps/bioinf/galaxy/bin/Python-2.7.13/lib/python2.7/urlparse.py", line 409, in parse_qsl
pairs = [s2 for s1 in qs.split('&') for s2 in s1.split(';')]
File "lib/galaxy/web/framework/middleware/error.py", line 154, in __call__
app_iter = self.application(environ, sr_checker)
File "/gpfs1/data/galaxy_server/galaxy-dev/.venv/lib/python2.7/site-packages/paste/recursive.py", line 85, in __call__
return self.application(environ, start_response)
File "/gpfs1/data/galaxy_server/galaxy-dev/.venv/lib/python2.7/site-packages/paste/httpexceptions.py", line 640, in __call__
return self.application(environ, start_response)
File "lib/galaxy/web/framework/base.py", line 143, in __call__
return self.handle_request(environ, start_response)
File "lib/galaxy/web/framework/base.py", line 222, in handle_request
body = method(trans, **kwargs)
File "lib/galaxy/web/framework/decorators.py", line 101, in decorator
return func(self, trans, *args, **kwargs)
File "lib/galaxy/webapps/galaxy/controllers/admin.py", line 1736, in manage_tool_dependencies
viewkey=viewkey)
File "lib/galaxy/web/framework/webapp.py", line 917, in fill_template
return self.fill_template_mako(filename, **kwargs)
File "lib/galaxy/web/framework/webapp.py", line 930, in fill_template_mako
return template.render(**data)
File "/gpfs1/data/galaxy_server/galaxy-dev/.venv/lib/python2.7/site-packages/mako/template.py", line 462, in render
return runtime._render(self, self.callable_, args, data)
File "/gpfs1/data/galaxy_server/galaxy-dev/.venv/lib/python2.7/site-packages/mako/runtime.py", line 838, in _render
**_kwargs_for_callable(callable_, data))
File "/gpfs1/data/galaxy_server/galaxy-dev/.venv/lib/python2.7/site-packages/mako/runtime.py", line 873, in _render_context
_exec_template(inherit, lclcontext, args=args, kwargs=kwargs)
File "/gpfs1/data/galaxy_server/galaxy-dev/.venv/lib/python2.7/site-packages/mako/runtime.py", line 899, in _exec_template
callable_(context, *args, **kwargs)
File "/gpfs1/data/galaxy_server/galaxy-dev/database/compiled_templates/base.mako.py", line 69, in render_body
__M_writer(unicode(next.body()))
File "/gpfs1/data/galaxy_server/galaxy-dev/database/compiled_templates/webapps/galaxy/admin/manage_dependencies.mako.py", line 80, in render_body
__M_writer(unicode(render_dependencies_details(tools, requirements_status, tool_ids_by_requirements)))
File "/gpfs1/data/galaxy_server/galaxy-dev/database/compiled_templates/webapps/galaxy/admin/manage_dependencies.mako.py", line 50, in render_dependencies_details
return render_render_dependencies_details(context._locals(__M_locals),tools,requirements_status,tool_ids_by_requirements)
File "/gpfs1/data/galaxy_server/galaxy-dev/database/compiled_templates/webapps/galaxy/admin/manage_dependencies.mako.py", line 185, in render_render_dependencies_details
__M_writer(filters.html_escape(unicode( ", ".join([tools[tid].name for tid in tool_ids]) )))
KeyError: u'testtoolshed.g2.bx.psu.edu/repos/matthias/dada2_makesequencetable/dada2_makeSequenceTable/1.10.0+galaxy0'
```
I suppose this can happen if the toolbox reloads while gathering dependencies.
If the user is not an admin.
Fixes https://github.com/galaxyproject/galaxy/issues/7710
An alternative would be to skip Accessibility / Ownership
exceptions, but given that we can just restrict the query
this seems like the better approach to me.
Martin Cech