| Age | Commit message (Expand) | Author |
|---|
| 2022-02-09 | pep8 formatting | Alexander Kabui |
| 2022-02-09 | fetch pheno input data | Alexander Kabui |
| 2022-02-09 | parse geno input data | Alexander Kabui |
| 2022-02-09 | parse input data | Alexander Kabui |
| 2022-02-09 | init py file:call gn3 ctl api | Alexander Kabui |
| 2022-02-09 | add ui template for ctl | Alexander Kabui |
| 2022-02-07 | Double quote shell variables to prevent globbing and word splitting | Frederick Muriuki Muriithi |
| 2022-02-07 | Add 'api' to root of partial correlations URL...Add api to the root of the partial correlations URL, making it:
/api/correlations/partial
rather than:
/correlations/partial
| Frederick Muriuki Muriithi |
| 2022-02-05 | Update live jupyter notebooks | jgart |
| 2022-02-02 | Add covarstruct for rqtl mapping...Added a function for generating a covarstruct file required for R/qtl
mapping
This file contains info on whether each covariate is categorical or
numerical and is generated by querying the TraitMetadata table in the DB
| zsloan |
| 2022-01-31 | wqflask: Use a more semantic name when downloading samples...* wqflask/wqflask/metadata_edits.py (get_sample_data_as_csv): Save csv
file to be downloaded as "sample-name-<dataset_id>.csv" instead of
"myplot.csv"
| BonfaceKilz |
| 2022-01-29 | Fix bug: rho/r not set appropriately...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* The column heading, and the "data-column-heading" values depend on
the correlation method. The initial idea had been to set these
values up from the server.
With the use of Javascript, however, the system defaults to using
`r`, which is a bug when the method is any of the Spearman's
methods.
| Frederick Muriuki Muriithi |
| 2022-01-29 | Include the "Locus" in the display...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
| Frederick Muriuki Muriithi |
| 2022-01-29 | Provide missing argument...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
| Frederick Muriuki Muriithi |
| 2022-01-29 | Fix check for non-existent values | Frederick Muriuki Muriithi |
| 2022-01-29 | Hide template row instead of deleting it | Frederick Muriuki Muriithi |
| 2022-01-29 | Add more items to trait string...Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
| Frederick Muriuki Muriithi |
| 2022-01-29 | Update styling: Display traits in a tabular-like form...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Display the trait details in a tabular-life form without using a table.
| Frederick Muriuki Muriithi |
| 2022-01-29 | Include template to get rid of repetitive template code...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* The generation of input elements that relate to the traits is very
similar, therefore this commit pulls it out into a separate template
that can be included where needed.
| Frederick Muriuki Muriithi |
| 2022-01-29 | Display results for Geno and ProbeSet tables...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Add function to display the results for the **Geno**
and **ProbeSet** tables.
| Frederick Muriuki Muriithi |
| 2022-01-29 | Improve UI elements...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Force results area to use up the entire width of the page
* Set background colour and line-height of header row
* Add some padding to the cells
* Reorganise layout
* Set up appropriate classes for .with-trait items
| Frederick Muriuki Muriithi |
| 2022-01-29 | Format numbers for display...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Format the numbers for display, to reduce the number of columns
needed for display.
| Frederick Muriuki Muriithi |
| 2022-01-29 | Display data for "Publish" datasets...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Display the correlations results for "Publish" datasets.
| Frederick Muriuki Muriithi |
| 2022-01-29 | Add templates for the results tables...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Add templates for the tables that will display the results.
| Frederick Muriuki Muriithi |
| 2022-01-29 | Add elements to display results. Provide PoC JS...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Add some html elements to be used to display the results of running
the partial correlations
* Provide some initial proof-of-concept javascript code to animate the
various elements and to use for displaying both successful and error
results.
| Frederick Muriuki Muriithi |
| 2022-01-29 | Use list rather than tuple...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Using a tuple, rather than a list for the HTTP methods in the route
definition causes an error. This fixes that by using a list.
| Frederick Muriuki Muriithi |
| 2022-01-29 | Skip the target traits selection step...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Skip the target traits selection step, and only allow running the
partial correlations against one of the available databases.
| Frederick Muriuki Muriithi |
| 2022-01-29 | Implement better styling...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Separate the form elements that allow selection from the elements
that display previous selections.
This allows styling of the "active" area of the form in a different
way from the "display" area of the form, allowing the user to see
information on their previous choices, even while making further
selections for the partial correlations.
| Frederick Muriuki Muriithi |
| 2022-01-29 | Automate setting of the development GN3 repo...* When developing the GN2 code, there are times we need to use the
latest code in GN3, and rather than manually editing the
`bin/genenetwork` file every time we need that, this commit enables
the use of an environment variable.
In this case, launching the application with something like:
$ env GN3_DEV_REPO_PATH="$HOME/genenetwork3" ...\
./bin/genenetwork2 ./the_settings.py -gunicorn-dev
will add the path to the development version to the PYTHONPATH. If
the GN3_DEV_REPO_PATH variable is not set, then the PYTHONPATH is
not altered, and would be as if there is no development version of
GN3 in use.
| Frederick Muriuki Muriithi |
| 2022-01-29 | Add "Partial Correlations" UI elements on collections page...Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
* Add UI elements to trigger the partial correlations feature
* Connect partial correlation view to the application
* Point to correct application element for gunicorn
| Frederick Muriuki Muriithi |
| 2022-01-28 | Update PYTHONPATH...The PYTHONPATH apparently needs to be updated to 3.9, because 3.8 throws an error (at least on production). | zsloan |
| 2022-01-28 | Revert 'bin: Set shebang to sh instead of bash'...It seems that this also needed to be reverted, because I was getting the error below (which was prevented by reverting to #! /bin/bash):
./bin/genenetwork2: 135: ./bin/genenetwork2: Syntax error: redirection unexpected | zsloan |
| 2022-01-28 | Revert "bin: Set GN2_PROFILE from GUIX_ENVIRONMENT."...This reverts commit f4e336eb1ea526156e112cff97a3ec8137a2bc90.
| Arun Isaac |
| 2022-01-28 | Revert "bin: Do not set environment variables set by guix shell."...This reverts commit 344e428126b60932bff4c62c5ded8c36519155e8.
| Arun Isaac |
| 2022-01-28 | Revert "README: Document `guix shell' development process."...This reverts commit e0a260b0de55fbea0c507eb0ca5fbdc3c1a825c0.
| Arun Isaac |
| 2022-01-27 | Highlight rows selected by filterByIndex...This adds the "selected" class to rows selected by filterByIndex, which adds highlighting to them
I also made the variables in this part of the code camel cased
| zsloan |
| 2022-01-27 | Changed var to let | zsloan |
| 2022-01-27 | Removed unused variables code | zsloan |
| 2022-01-27 | Added the div for showing the error when the Select Rows text has wrong syntax | zsloan |
| 2022-01-27 | Replaced the try/catch with something checking for the correct pattern with r... | zsloan |
| 2022-01-27 | Added a comment explaining what the parseIndexString function does | zsloan |
| 2022-01-27 | Replaced a confusing for loop with something that is (hopefully) easier to re... | zsloan |
| 2022-01-27 | Changed functions in search_results.js to be camelCased, except for change_bu... | zsloan |
| 2022-01-27 | Removed unnecessary variable from for-loop in parse_index_string | zsloan |
| 2022-01-27 | Changed the placeholder text for the table search to Search For | zsloan |
| 2022-01-27 | Added some JS disabling form submission on hitting Enter, so that users can h... | zsloan |
| 2022-01-27 | Moved the Show/Hide Columns text onto the same line as the buttons, to save a... | zsloan |
| 2022-01-27 | Changed the glossary question mark to appear at the very end of the colum tex... | zsloan |
| 2022-01-27 | Changed search result index column to be static (so it doesn't change when th... | zsloan |
| 2022-01-27 | Replaced the Select Top feature with one that functions more like the Block B... | zsloan |
