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Prototype for storing single-cell data #1020

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arteymix wants to merge 298 commits into development from feature-single-cell

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arteymix commented Feb 5, 2024 •

edited

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TODO

add a CLI for loading/reloading single cell data and cell type assignments
extend the GEO loader to detect MEX and other supported formats and apply the appropriate strategy for loading vectors
Add support for HDF5-based single-cell data formats #1039
support saving single cell data to disk (I already added a SingleCellExpresionDataMatrix, we need to finish the work and write it to file). I think MEX is a pretty decent output format for this.

REST API

review which fields should be exposed on the REST API for filtering purposes
add aliases in the REST API to refer to the preferred single cell dimension and cell assignment

arteymix force-pushed the feature-single-cell branch 6 times, most recently from 9222a95 to 788a61b Compare

February 7, 2024 20:13

arteymix commented

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gemma-core/src/test/java/ubic/gemma/persistence/util/ListUtilsTest.java Outdated Show resolved Hide resolved

arteymix force-pushed the feature-single-cell branch 2 times, most recently from f04ae2f to d791771 Compare

February 7, 2024 20:23

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arteymix force-pushed the feature-single-cell branch from b60a8de to 0ce142a Compare

February 8, 2024 00:23

This was linked to issues Feb 10, 2024

Store original cell-by-gene matrix #1012

Closed

Identify the input formats for single-cell data we want to support in Gemma #1028

Closed

arteymix force-pushed the feature-single-cell branch from 80c6409 to e804d92 Compare

February 13, 2024 03:40

This was linked to issues Feb 16, 2024

Import additional characteristics from Seurat Disk and AnnData formats #1037

Closed

Use "cell type assignment" instead of "cell type labelling" #1038

Closed

arteymix force-pushed the feature-single-cell branch 4 times, most recently from b2c8a8b to 6a993b7 Compare

February 19, 2024 20:47

arteymix added the single cell label

arteymix self-assigned this

arteymix force-pushed the feature-single-cell branch from b7d4810 to 7c29995 Compare

February 21, 2024 23:26

arteymix linked an issue

that may be closed by this pull request

Load single-cell data from GEO #1029

Closed

3 tasks

arteymix added 3 commits

February 29, 2024 10:26


          Make environment profies mutually exclusive

454128e


          cli: Make batch tasks simple Runnable

c81d8ef


          cli: Fix parsing and declaration of numerical parameters

b2085c7

arteymix added 29 commits

November 6, 2024 13:58


          Fix MatrixConversionTest using setDataAsDoubles() before setting a QT

06c5a33


          More cleanups

53a82d0

Remove Serializable and serialVersionUID to classes that we never
serialize or put on disk caches.

Relocate some utility methods from the models into utility classes.

Replace LocalFile by java.io.File.


          Re-enable incremental compilation

29b2ea2


          Improve elements mapping (fix #1234)

Provide multiple strategies for mapping gene IDs and pick the one with
the greatest overlap.

Include mapping statistics in the audit event for the created
single-cell vectors.


          Fix lazy initialization error when checking a dataset accession

24277fd


          Remove empty RestEntityUrl file

fedf83a


          Don't execute deployment script in a terminal

9ae8892


          Fix more tests

c729d0e


          Fix exceeding packet size for MySQL by streaming cell IDs

1b2470e

Remove usage of LobHandler.


          Replace the pipe with a pair if piped streams

8f6f50b


          Consider the scale type when computing sparsity metrics

cc9f32e


          Improve handling of layered AnnData files

076e6e1


          Numerious cleanups for Gemma Web [WIP]

9d4b947

Display the biomaterial and bioassay hierarchy.


          Replace JAWR with Webpack

e3e85c4

Remove JAWR and any mention of it in the code and comments.

Add support for Webpack development server for serving continuously
built static assets.


          Merge branch 'feature-single-cell-webpack' into feature-single-cell-u…

f087c19

…i-work


          Set the JSP trim whitespace directive in web.xml

1e38dee


          Few improvements for the static assets server

89aa08b

Add resolveUrl and use that in the tags to generate link to resources.

Add a list of allowed directories to serves assets from. It does not
really do much security-wise, but it will catch unintended usages of the
JSP tags.

Add a useful message when the development profile is active and the
server is not running.


          Add IntelliJ scripts for building and serving static assets

de6bff5

Ensure that the appropriate assets are built when deploying to staging
or dev servers.


          Few more improvements for the subset page

7bf620e

Include annotations applicable at the subset-level.

Handle case where there might be more than one dimension for a given
subset.


          Fix source mappings in web.xml

5461ae6


          Fix EE set page

266dd4d


          Fix visibility of sprintf and visualizeDiffExpressionHandler

39fe57c


          Merge pull request #1288 from PavlidisLab/feature-single-cell-ui-work

f45ef66

UI work for single-cell


          Fix the lineplot and flotr2

016f899


          Move the JavascriptLogger into the gemma-lib bundle since it requires…

490771a

… dwrServices.js to be loaded


          Fix incorrect assertion in ExperimentalDesignWriter

99e6320


          Generate DWR client code

5f8e207

Generate all the DWR scripts and controllers with appropriate binding to
the window object.

Separate models from controllers.

Add overrides such as adding GA4 tracking and defining inheritance
structure in a separate file.


          More frontend cleanups

96fdd61

Ensure that all declared function are properly namespaced.


          Allow edition of single-cell QTs

85485be

Rewrite the edit page with Spring form tags.

Enable HTML escaping by default for Spring tags.

Allow for dynamic JSP attributes to be used for various tags.

arteymix linked an issue

that may be closed by this pull request

User interface requirements for single-cell #1270

Open

8 tasks

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