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2020-10-09Merge pull request #458 from BonfaceKilz/tests/add-extra-tests-for-collectionsBonfaceKilz
Tests/add extra tests for collections
2020-10-09Apply PEP 8 to bufferBonfaceKilz
* wqflask/wqflask/wgcna/wgcna_analysis.py: Apply pep8 * wqflask/wqflask/collect.py: Ditto * wqflask/base/trait.py: Ditto
2020-10-09Add test for process_traits from collections.pyBonfaceKilz
* wqflask/tests/wqflask/test_collect.py: Add it.
2020-10-08Fixed remaining issue that applies to all dataset typeszsloan
* wqflask/base/data_set.py - Fixed issue where there was an error when trying to take the len of the query results when there were no results
2020-10-08Fixed issue where new phenotype groups wouldn't be saved to the ↵zsloan
self.datasets property because the group name was used as the key (instead of the group name + "Publish", which is the full dataset name for phenotypes) * wqflask/base/data_set.py - Set "group_name" as a separate variable from "name" to avoid it being used as the key in self.datasets
2020-10-08Merge pull request #452 from zsloan/authentication_bug_fixzsloan
Checked if owner_id is "none" to avoid an error when trying to access…
2020-10-08Merge pull request #455 from zsloan/temp_trait_scatterplot_fixzsloan
Temp Trait Scatterplot Error Fix
2020-10-08When generating links to correlation scatterplots (in corr results and corr ↵zsloan
matrix), append the group name to Temp dataset names so temp traits can be used in scatterplot * wqflask/wqflask/correlation/corr_scatter_plot.py - Create the dataset object using the group name included with Temp dataset names (which take the form "Temp_(group_name)") * wqflask/wqflask/templates/correlation_matrix.html - Change scatterplot links to include the group name if the dataset name is "Temp" * wqflask/wqflask/templates/correlation_page.html - Change scatterplot links to include the group name if the dataset name is "Temp" + a couple minor style changes
2020-10-06Merge pull request #454 from zsloan/update_docs_fixzsloan
Made change that should fix error when trying to change page text usi…
2020-10-06Made change that should fix error when trying to change page text using ckeditorzsloan
* wqflask/wqflask/docs.py - Changed query to include casting as binary to deal with certain unicode characters in ckeditor pages * wqflask/wqflask/views.py - Imported update_text from Docs since it previously wasn't updated, causing an error when attempting to update text
2020-10-06Merge pull request #453 from zsloan/index_page_textarea_fixzsloan
Index page dropdown/textarea fix
2020-10-06Fixed issue where drop-down arrows and textarea corners couldn't be clicked ↵zsloan
with certain window widths * wqflask/wqflask/templates/index_page_orig.html - Changed the left/right div's padding to prevent them from overlapping and changed the textareas' styles to make them only expandable vertically
2020-10-02Checked if owner_id is "none" to avoid an error when trying to access the ↵zsloan
resource manager page with newly added datasets * wqflask/wqflask/resource_manager.py - Only get owner user info conditional on owner_id not being "none" (which it will be by default for newly added datasets). Previously it would throw an error due to "owner_info" being None
2020-10-01Merge branch 'testing' of github.com:genenetwork/genenetwork2 into ↵zsloan
corr_matrix_error_fix
2020-09-30Changed the logic for adding 0 to the PCA results to do so when thezsloan
shared samples are < 2 instead of 0; this fixed the error when running the correlation matrix, but results in the PCA traits having no values * wqflask/wqflask/correlation_matrx/show_corr_matrix.py - changed "if num_overlap == 0" to "if num_overlap < 2" because correlations can't be run if there are fewer than 2 shared samples (and previously would throw an error if there was exactly 1 shared sample)
2020-09-30Added "natural-minus-na" sorting for relevant columns in the correlationzsloan
page * wqflask/wqflask/templates/correlation_page.html - Added natural-minus-na type to columns that can contain N/A values, since I apparently forgot to add it to this table before
2020-09-30Fixed issue where columns sorted by inner text (text inside link tags)zsloan
didn't sort all rows when a table is paginated and has more than one page * wqflask/wqflask/static/new/javascript/search_results.js - Added "extract_inner_text" function for getting the inner text from a string containing HTML in order to avoid using DataTables' orderDataType (which can only fetch values directly from the DOM, which is why sorting wasn't working with multiple pages), and also included this function in the "natural-minus-na" data type (so columns can be sorted that contain both HTML/links and N/A values) * wqflask/wqflask/templates/collections/view.html - Changed record column to use "natural-minus-na" sort method in order to fix the inner-text sorting issue + added sorting to the checkbox column (in the same way as it already works in the search result page) * wqflask/wqflask/templates/search_results_page.html - Replaced the columns that used orderDataType with using the updated "natural-minus-na" data type * wqflask/wqflask/templates/correlation_page.html - Fixed issue where N/As in the Year column (for phenotype correlations) were still displayed as links
2020-09-30Removed unused code from TempDataSet classzsloan
* wqflask/base/data_set.py - TempDataSet class contained some code referring to the SQL DB, but temp traits aren't stored in the SQL DB anymore
2020-09-29Trait page link-out buttons were previously inside <a> tags, but thiszsloan
caused there to be a small line between buttons when hovering over them (because the <a> tags were wider than the button itself); this was changed to instead just be an "onclick" on the button (which is also a bit more concise) * wqflask/wqflask/templates/show_trait_details.html - Replaced <a> tags with onclick for trait page link-out buttons
2020-09-29Removed "Color By Trait" button from the Bar Chart, because it was meantzsloan
to work with the figure we used before switching to Plotly. This feature will need to be redone to work with Plotly * wqflask/wqflask/templates/show_trait_statistics.html - commented out Color By Trait button until it's reimplemented
2020-09-29Made a variety of changes to table pageszsloan
* wqflask/wqflask/static/new/css/show_trait.css - Adding position relative and a 2px offset for glyphicons to make them better align with button text * wqflask/wqflask/templates/collections/view.html - Added glyphicon to Download button, changed a couple head names (Peak Location and Effect Size), made Location and Peak Location columns the same width, and made the "?" glossary links a little larger and red * wqflask/wqflask/templates/search_result_page.html - same as above * wqflask/wqflask/templates/show_trait_edit_data.html - Added glyphicon to Export button
2020-09-29Fixed issue where negative additive effect values weren't beingzsloan
displayed in the "view collection" page * wqflask/wqflask/templates/collections/view.html - Apparently the correct way to check if a value can be cast to a float in Jinja2 is to say "value != 0"; it previous said "value > 0" which exlcuded all negative values
2020-09-29Changed Add (to collection) button color to match other Add buttons andzsloan
changed the text for the GN1 link button * wqflask/wqflask/templates/show_trait_details.html - Changed Add button class to btn-success (to make it green like the other Add buttons) and changed text from "View in GN1" to "Go to GN1"
2020-09-29Changed the DataTables column sort arrows to a different color byzsloan
changing the image they're referencing * wqflask/wqflask/templates/base.html - Added CSS changing the table sort arrow image directly into base.html because it requires using url_for to reference the images in the GUIX profile (so it needs to be in the template and can't just be added to a CSS file)
2020-09-28Changed add to collection to open the collection in a new tab/page sozsloan
the results on the initial page aren't lost * wqflask/wqflask/static/new/javascript/search_results.js - Changed the add to collection method name to "add_to_collection" because it was previously "add" which is a terrible method name * wqflask/wqflask/templates/collections/add.html - Added target="_blank" to the add to collection form so it will open in a new tab/window
2020-09-28Fix casting errorBonfaceKilz
* 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)*.
2020-09-28Convert None to "" in if statementBonfaceKilz
* wqflask/base/trait.py: Fixes error parsing error: "(GeneNetwork error: float argument required, not NoneType)"
2020-09-28Update trait testsBonfaceKilz
* wqflask/tests/base/test_trait.py (test_retrieve_trait_info_with_non_empty_lrs): Check trait.LRS_score_repr is set correctly if trait.lrs is None. (test_retrieve_trait_info_with_empty_lrs_field): Check trait.LRS_score_repr and test_trait.LRS_location_repr is set correctly if trait.lrs is None. (test_retrieve_trait_info_with_empty_chr_field): Check test_trait.LRS_score_repr and test_trait.LRS_location_repr is set correctly if trait.locus is None.
2020-09-23Fix failing buildsBonfaceKilz
* wqflask/wqflask/__init__.py: Move imports from views.py to "__init__.py". Fixes failing build. * wqflask/wqflask/views.py: Ditto.
2020-09-23Fix failing testsBonfaceKilz
* wqflask/tests/base/test_trait.py: In python2 it's necessary to decode the utf-8 string.
2020-09-22Merge branch 'testing' of github.com:genenetwork/genenetwork2 into testingzsloan
2020-09-22Fixed a pretty big mistake where user accounts would be saved even whenzsloan
there was some mistake/error during registration * wqflask/wqflask/user_login.py - Previously it would still save a user even if there was some problem like their e-mail already being associated with an account. It would display the error, but still run save_user. I fixed this so that it no longer saves the user if there are any errors
2020-09-22Added something to the mapping result page CSS to change the highlightzsloan
color to match the high color in other tables * wqflask/wqflask/static/new/css/marker_regression.css - changed background color when selecting a row (i.e. "highlight color")
2020-09-22Fixed a couple mistakes in the previous commit and changed the positionzsloan
header on the mapping results page to include the mapping scale * wqflask/wqflask/marker_regression/run_mapping.py - changed how "display_pos" is defined for marker obs * wqflask/wqflask/templates/mapping_results.html - Fixed issues with last commit and changed position header name to include mapping scale
2020-09-22Replaced Chr and Mb/cM columns with a single position column in mappingzsloan
results and also changes the -log(p) to use an endash instead * wqflask/wqflask/marker_regression/run_mapping.py - added "display_pos" to each marker object that is a combination of Chr and Mb/cM * wqflask/wqflask/templates/mapping_results.html - Included "display_pos" in results table and replaced -log(p) with using an endash
2020-09-18Apply pep8 formattingBonfaceKilz
2020-09-17Mock "SECRET_HMAC_CODE"BonfaceKilz
* wqflask/tests/utility/test_hmac.py: Mock app.config's "SECRET_HMAC_CODE" value.
2020-09-17Apply pep8BonfaceKilz
* wqflask/utility/hmac.py: Apply pep8 and fix typo.
2020-09-17Add tests for hmac utilityBonfaceKilz
* wqflask/tests/utility/test_hmac.py: New tests.
2020-09-16Add new tests for "base/trait.py"BonfaceKilz
* wqflask/tests/base/test_trait.py: New tests.
2020-09-16Apply pep8BonfaceKilz
* wqflask/utility/authentication_tools.py: Apply pep8 formatting to file.
2020-09-16Add tests for "add_new_resource" methodBonfaceKilz
* wqflask/tests/utility/test_authentication_tools.py: Add them.
2020-09-16Remove unnecessary if branchBonfaceKilz
* wqflask/utility/authentication_tools.py (check_resource_availability): Combine if statements into one boolean check in one if branch.
2020-09-16Add tests for authentication toolsBonfaceKilz
Catches bugs in: - https://github.com/genenetwork/genenetwork2/pull/422/commits/70dbeeb5832711ed5271434e482c18bc7ea095b8 * wqflask/tests/utility/test_authentication_tools.py: New file. Add tests for "check_resource_availability".
2020-09-15Fix failing testsBonfaceKilz
* wqflask/tests/base/test_data_set.py: Update failing tests introduced by the change in 301bdd2f4.
2020-09-14Merge branch 'scroller_testing' of github.com:zsloan/genenetwork2 into testingzsloan
2020-09-13Added in-progress info-page to views.py as well as in-progresszsloan
authorization/security guide * wqflask/wqflask/views.py - Added endpoint for info page and authorization/security tutorial
2020-09-11Wrote code and template for reproducing GN1's Info Page (page thatzsloan
displays info about a dataset + download links for its data) * wqflask/wqflask/db_info.py - Python that pulls the info out of the DB and parses the download links from the ipfs response * wqflask/wqflask/templates/info_page.html - template for displaying db info; need to make a lot of changes to its format/aesthetics
2020-09-10Modified "natural-minus-na" sort function to treat an array of valueszsloan
as equivalent to "N/A" (since different tables sometimes include other values that imply there's no value) and applied it to some extra columns in the Interval Analyst table * wqflask/wqflask/static/new/javascript/search_results.js - Modified sort_NAs function to take an array of "N/A"-equivalent values instead of just comparing against the string "N/A" * wqflask/wqflask/templates/mapping_results.html - Applied "natural-minus-na" sort method to several columns that include "--" in the Interval Analyst table
2020-09-10Fixed several sorting issues and moved orderDataType definitions intozsloan
search_results.js since all the tables that use them import that file (that file's name needs to be changed, though) * wqflask/wqflask/static/new/javascript/search_results.js - Added the dom-checkbox and dom-inner-text order types into this file; they were previously duplicated across several template files * wqflask/wqflask/templates/gsearch_gene.html - Added dom-inner-text order type to relevant columns with hyperlink contents and disabled deferRender since it conflicted with use of both pagination and orderDataType for sorting * wqflask/wqflask/templates/gsearch_pheno.html - Same as above * wqflask/wqflask/templates/mapping_results.html - Added dom-inner-text for a few columns that have hyperlink values - still need to modify natural-minus-na to also include other "N/A"-equivalent values like "--" * wqflask/wqflask/templates/search_result_page.html Removed the dom-checkbox and dom-inner-text order types from this file since they were moved to search_results.js
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