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.
```
The redirect_uri generated by requests-oauthlib (Custos) already
has its query parameters encoded, so calling `encodeURI` results
in those parameters being double encoded.
Follow-up on https://github.com/galaxyproject/galaxy/pull/7569
Fix the following exception at Galaxy startup:
```
galaxy.datatypes.registry ERROR 2019-04-10 19:07:33,159 [p:3319,w:0,m:0] [MainThread] Error calling method mtx from class <module 'galaxy.datatypes.tabular' from 'lib/galaxy/datatypes/tabular.pyc'>
Traceback (most recent call last):
File "lib/galaxy/datatypes/registry.py", line 485, in load_datatype_sniffers
aclass = getattr(module, datatype_class_name)()
AttributeError: 'module' object has no attribute 'mtx'
```
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.
Dannon Baker