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* wqflask/base/mrna_assay_tissue_data.py: Replace "flask.g" with database_connection.
(MrnaAssayTissueData.__init__): Use database_connection.
(MrnaAssayTissueData.get_symbol_values_pairs): Ditto.
* wqflask/base/species.py: Replace "Flask.g" imports with
"database_connection".
(Chromosomes.chromosomes): Use database_connection.
* wqflask/base/trait.py: Import database_connection.
(retrieve_trait_info): Use database_connection.
* wqflask/utility/authentication_tools.py: Replace "flask.g" with
database_connection.
(get_group_code): Use database_connection.
* wqflask/utility/helper_functions.py: Replace "flask.g" with
"database_connection".
(get_species_groups): Use database_connection.
* wqflask/wqflask/db_info.py: Replace "Flask" and "g" with
"database_connection".
(InfoPage.get_info): Use database_connection.
* wqflask/wqflask/do_search.py (DoSearch.execute): Use
database_connection().
* wqflask/wqflask/external_tools/send_to_geneweaver.py: Replace
"Flask" and "g" import with database_connection.
(test_chip): Use database_connection.
* wqflask/wqflask/external_tools/send_to_webgestalt.py: Replace
"Flask, g" imports with database_connection.
(test_chip): Use database_connection.
* wqflask/wqflask/gsearch.py: Replace "Flask" and "g" import with
database_connection.
(GSearch.__init__): Use database_connection.
* wqflask/wqflask/interval_analyst/GeneUtil.py (loadGenes):
Use database_connection().
* wqflask/wqflask/show_trait/SampleList.py: Replace "flask.g import"
with database_connection.
(SampleList.get_attributes): Use database_connection.
(SampleList.get_extra_attribute_values): Ditto.
* wqflask/wqflask/show_trait/show_trait.py: Replace "Flask" and "g"
import with database_connection.
(ShowTrait.__init__): Use database_connection.
(ShowTrait.get_external_links): Ditto.
(get_nearest_marker): Ditto.
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* wqflask/wqflask/update_search_results.py: Replace "Flask" and "g"
import with "database_connection".
(GSearch.__init__): Reformat SQL. Rename "re" to "results" since "re"
is part of the stdlib.
* wqflask/wqflask/marker_regression/rqtl_mapping.py: Replace flask.g
with database_connection.
(write_covarstruct_file): Replace g.db with database_connection().
* wqflask/wqflask/search_results.py: Replace "Flask" and "g" imports
with "database_connection" import.
(trait_info_str): Replace g.db with database_connection.
* wqflask/wqflask/docs.py (Docs): Use dababase_connection() context
manager.
(update_text): Ditto.
* wqflask/wqflask/marker_regression/display_mapping_results.py:
Replace "Flask" and "g" import with "database_connection".
(DisplayMappingResults.__init__): Use database_connection.
(DisplayMappingResults.drawSNPTrackNew): Ditto.
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This causes noisy logging.
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Use the new auth proxy tools instead.
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user_ids being stored as different encoding
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dealing with the permissions response either being a list or not a list (this should be temporary until I figure out what is going on here)
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* wqflask/base/trait.py: Apply pep8.
* wqflask/utility/authentication_tools.py: Ditto.
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* wqflask/utility/authentication_tools.py: Apply pep8 formatting to
file.
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* wqflask/utility/authentication_tools.py
(check_resource_availability): Combine if statements into one boolean
check in one if branch.
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* wqflask/utility/authentication_tools.py: Remove accidental char at beginning
of line.
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group didn't have an InbredSetCode set in the DB
* wqflask/utility/authentication_tools.py - Changed get_group_code to
return an empty string instead of None if InbredSetCode doesn't exist
for a dataset group
* wqflask/wqflask/views.py - Changed zipped export filename to
"export_(datetime)" instead of "collection_(datetime)" since this export
can occur from both the collection page and the global search page
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* wqflask/utility/authentication_tools.py(add_new_resource): If group_code is
"None", an error is thrown when you try to: `group_code + "_" + str(trait_id)`
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See: <https://docs.python.org/2/library/2to3.html#2to3fixer-future>
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Run `2to3-3.8 -f idioms -w .`
See: <https://docs.python.org/2/library/2to3.html#2to3fixer-idioms>
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* wqflask/utility/authentication_tools.py: the code forgot to get
resource_info when a resource wasn't in Redis yet, causing an error when
it was referenced, so I added a line getting the resource info (and also
a couple comments for other lines related to authentication)
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something that automatically inserts resources with default privileges
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and also simplified the check_owner_or_admin function a little
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