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| author | Terry Truong <terry06890@gmail.com> | 2022-09-11 14:55:42 +1000 |
|---|---|---|
| committer | Terry Truong <terry06890@gmail.com> | 2022-09-11 15:04:14 +1000 |
| commit | 5de5fb93e50fe9006221b30ac4a66f1be0db82e7 (patch) | |
| tree | 2567c25c902dbb40d44419805cebb38171df47fa /backend/tol_data/otol | |
| parent | daccbbd9c73a5292ea9d6746560d7009e5aa666d (diff) | |
Add backend unit tests
- Add unit testing code in backend/tests/
- Change to snake-case for script/file/directory names
- Use os.path.join() instead of '/'
- Refactor script code into function defs and a main-guard
- Make global vars all-caps
Some fixes:
- For getting descriptions, some wiki redirects weren't properly resolved
- Linked images were sub-optimally propagated
- Generation of reduced trees assumed a wiki-id association implied a description
- Tilo.py had potential null dereferences by not always using a reduced node set
- EOL image downloading didn't properly wait for all threads to end when finishing
Diffstat (limited to 'backend/tol_data/otol')
| -rw-r--r-- | backend/tol_data/otol/README.md | 19 |
1 files changed, 19 insertions, 0 deletions
diff --git a/backend/tol_data/otol/README.md b/backend/tol_data/otol/README.md new file mode 100644 index 0000000..e018369 --- /dev/null +++ b/backend/tol_data/otol/README.md @@ -0,0 +1,19 @@ +This directory holds files obtained via the +[Open Tree of Life](https://tree.opentreeoflife.org/about/open-tree-of-life). + +# Tree Data Files +- `opentree13.4tree.tgz` <br> + Obtained from <https://tree.opentreeoflife.org/about/synthesis-release/v13.4>. + Contains tree data from the [Open Tree of Life](https://tree.opentreeoflife.org/about/open-tree-of-life). +- `labelled_supertree_ottnames.tre` <br> + Extracted from the .tgz file. Describes the structure of the tree. +- `annotations.json` <br> + Extracted from the .tgz file. Contains additional attributes of tree + nodes. Used for finding out which nodes have 'phylogenetic support'. + +# Taxonomy Data Files +- `ott3.3.tgz` <br> + Obtained from <https://tree.opentreeoflife.org/about/taxonomy-version/ott3.3>. + Contains taxonomy data from the Open Tree of Life. +- `otol/taxonomy.tsv` <br> + Extracted from the .tgz file. Holds taxon IDs from sources like NCBI, used to map between datasets. |