eef3ac987538affd38eb38ccddf6ce6721f4c6f4
jcasper
  Sun Nov 23 22:03:29 2025 -0800
Removing bigCompositeUpdate CGI (folded into cartDump), and some kent-ifying of
the remaining code.  refs #36320

diff --git src/hg/bigCompositeUpdate/README.md src/hg/bigCompositeUpdate/README.md
deleted file mode 100644
index 5beaee04ded..00000000000
--- src/hg/bigCompositeUpdate/README.md
+++ /dev/null
@@ -1,81 +0,0 @@
-# About bigComposite
-
-*(UPDATE 2025-09-14 at bottom)*
-
-For whomever is testing.
-
-- `bigComposite` should be in the `src/hg/makefile` among targets, and in my
-  mirror it gets installed to `apache/cgi-bin-${USER}` as expected.
-
-- For the bigComposite controls page to work, the `src/hg/js/bigComposite.js`
-  needs to be in the `apache/htdocs/js` dir, and the
-  `src/hg/htdocs/style/bigComposite.css` needs to be in
-  `apache/htdocs/style`. I don't know how to modify the build process for that
-  to be automatic.
-
-- Testing data for the trackDb entries can be found at:
-  ```console
-  https://smithlabresearch.org/data/mb2_trackDb.txt
-  ```
-
-  This is for hg38. It can be entered into a `hg38.trackDb` table like this:
-  ```console
-  mysql hg38 --local-infile=1 -e "
-      LOAD DATA LOCAL INFILE 'mb2_trackDb.txt'
-      REPLACE
-      INTO TABLE trackDb
-      FIELDS TERMINATED BY '\t'
-      LINES TERMINATED BY '\n';
-  "
-  ```
-
-- This file has one entry (the first) named `mb2`, which is the parent and has
-  type bigComposite. Then it has many entries named like
-  `mb2_dataElement_dataType`, where the `dataElement` is an SRA experiment
-  accession (for a WGBS methylome), and `dataType` is in
-  `{hmr,levels,reads}`. The bigBed/bigWig files are hosted on
-  smithlab.usc.edu.
-
-- The corresponding metadata can be found at:
-  ```console
-  https://smithlabresearch.org/data/mb2_metadata.json
-  ```
-
-- The metadata file includes some "settings" near the top, and a sub-dict
-  named `metadata` which has entries for all the dataElements (SRA
-  accessions). Note that not every dataElement from the `mb2_trackDb.txt` file
-  has an entry in the metadata: some were poorly annotated.
-
-- The files are large. For testing purposes you can use the script in this dir
-  that downsamples these to at most a specified number of dataElements.
-
-- In order to test the checkbox sets, and the paging of the data table, make
-  sure to get enough data to populate those.
-
-- The metadata in principle can be hosted anywhere, but CORS restrictions
-  currently block all but the local server. So putting the `mb2_metadata.json`
-  in the local `apache/htdocs` dir, and assigning
-  ```console
-  metaDataUrl /mb2_metadata.json\
-  ```
-  in the "settings" field of the trackDb entry for the mb2 bigComposite track
-  works.
-
-# Update (2025-09-14)
- - `bigComposite.js` has been updated to use TSV for the metadata table.
- - All config info is in the `trackDb.settings` field and parsed within `hgTrackUi.c`
- - Correspondingly, `hgTrackUi.c` has been updated.
- - Colors can be used or completely ignored. If used, they need a separate
-   JSON file, and checkbox filters for multiple columns can have associated
-   colors.
- - The updated data files (corresponding to those above and the new ones):
-   ```console
-   https://smithlabresearch.org/data/mb2_trackDb_updated.txt
-   https://smithlabresearch.org/data/mb2_metadata.tsv
-   https://smithlabresearch.org/data/mb2_color.json
-   ```
-   The `_trackDb_updated.txt` is used to fill the trackDb entries, and only
-   differs by specific lines in the `settings` field. The other two files go
-   in `htdocs` or can be put anywhere if the `metaDataUrl` and
-   `colorSettingsUrl` are changed in the first logical line of
-   `mb2_trackDb_updated.txt`.