Age | Commit message (Collapse) | Author |
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Add api to the root of the partial correlations URL, making it:
/api/correlations/partial
rather than:
/correlations/partial
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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
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* 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"
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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.
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Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
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Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
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Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi
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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.
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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.
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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.
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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
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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* 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.
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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
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The PYTHONPATH apparently needs to be updated to 3.9, because 3.8 throws an error (at least on production).
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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
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This reverts commit f4e336eb1ea526156e112cff97a3ec8137a2bc90.
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This reverts commit 344e428126b60932bff4c62c5ded8c36519155e8.
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This reverts commit e0a260b0de55fbea0c507eb0ca5fbdc3c1a825c0.
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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
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regex, for validating the Select Rows input
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read and explicitly inverts start_index and end_index when the former is greater than the latter
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change_buttons because it's referenced in many other files
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