Age | Commit message (Collapse) | Author |
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* Commit 49580eb9cd47bb2ce15fd44be11bb9580d85efef removed the use of
the gn-proxy, but left some code that was used expressly for use
with the gn-proxy. This commit removes that code.
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doesn't have a position in the DB
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faster
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Bug/fix broken correlations
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* wqflask/base/trait.py: Import utility.hmac
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"%s" should only be used outside table names and column names
otherwise a string literal will be inserted thereby leading to errors
in the sql statements.
* wqflask/base/data_set.py (geno_mrna_confidentiality): Use f-strings
for table/columns/clause.
* wqflask/base/trait.py (retrieve_trait_info): Ditto.
* wqflask/wqflask/gsearch.py (GSearch.__init__): Ditto.
* wqflask/wqflask/interval_analyst/GeneUtil.py (loadGenes): Ditto.
* wqflask/wqflask/snp_browser/snp_browser.py
(SnpBrowser.get_browser_results): Ditto.
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* wqflask/base/data_set.py: Remove un-used imports.
* wqflask/base/trait.py: Ditto.
wqflask/tests/wqflask/show_trait/test_show_trait.py: Ditto.
* wqflask/wqflask/show_trait/show_trait.py: Ditto.
* wqflask/wqflask/views: Ditto.
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* wqflask/base/trait.py: Remove utility.logger
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* wqflask/base/trait.py (retrieve_trait_info): Wrap error message in
ValueError.
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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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information
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It's originally a boolean, which causes an error when passed to the JS
code as JSON
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Some of this was caused by heatmaps supporting code; that code should probably pass the traits differently than the way it does in the "trait_info_str" function
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was passed that wasn't Temp
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take dataset as an optional argument (to avoid having to pointlessly create it)
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See: https://is.gd/pL7IJF
Ran:
find . \( -type d -name .git -prune \) -o -type f -print0 | xargs -0 sed -i 's/(object)//g'
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* wqflask/base/trait.py (jsonable_table_row): Delete it.
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necessary for them to show up correctly when selecting traits from collections in pop-up windows, like when selecting cofactors for mapping)
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resulting from a trait missing both pre_publication_description and pubmed ID
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and added an assert that 'name' is passed instead of using if/else, since it should always be passed
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Feature/corr table changes
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for genotype/snp cofactors (the code previously only accounted for
probeset/phenotype cofactors, so it was treating genotypes/snps like
phenotype traits)
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cofactors were genotypes (because it tried to get the
"description_display" which doesn't exist for genotype traits)
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ID for the purposes of showing pre-publication abbreviation/description
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* wqflask/wqflask/wgcna/wgcna_analysis.py: Apply pep8
* wqflask/wqflask/collect.py: Ditto
* wqflask/base/trait.py: Ditto
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* wqflask/base/trait.py (retrieve_trait_info): Add extra param to
ignore errors such as: "utf-8 codec can't decode byte 0xb5 in position
0: invalid start byte" thrown in Python3.
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github.com:BonfaceKilz/genenetwork2 into build/python3-migration
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* wqflask/base/trait.py (retrieve_trait_info): If the
description_string or discription_display value return a None object,
evaluate to an empty string. Fixes errors related to *len(None)*.
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* wqflask/base/trait.py (retrieve_trait_info): If the
description_string or discription_display value return a None object,
evaluate to an empty string. Fixes errors related to *len(None)*.
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* wqflask/base/trait.py: Fixes error parsing error: "(GeneNetwork
error: float argument required, not NoneType)"
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* wqflask/base/trait.py (retrieve_trait_info): Convert "target_string"
to a str, otherwise an exception will be thrown if it's None.
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* wqflask/base/trait.py: Apply pep8.
* wqflask/utility/authentication_tools.py: Ditto.
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* wqflask/base/trait.py: Remove python2 codecs.BOM_UTF8 methods.
* wqflask/wqflask/search_results.py: Remove utf-8 decode method on string.
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Mysqldb's escape returns a binary string. Use utils.db_tools which adds an extra
step of converting the binary string to a string.
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