From 5de5fb93e50fe9006221b30ac4a66f1be0db82e7 Mon Sep 17 00:00:00 2001 From: Terry Truong Date: Sun, 11 Sep 2022 14:55:42 +1000 Subject: 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 --- backend/tol_data/otol/README.md | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 backend/tol_data/otol/README.md (limited to 'backend/tol_data/otol/README.md') 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`
+ Obtained from . + Contains tree data from the [Open Tree of Life](https://tree.opentreeoflife.org/about/open-tree-of-life). +- `labelled_supertree_ottnames.tre`
+ Extracted from the .tgz file. Describes the structure of the tree. +- `annotations.json`
+ 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`
+ Obtained from . + Contains taxonomy data from the Open Tree of Life. +- `otol/taxonomy.tsv`
+ Extracted from the .tgz file. Holds taxon IDs from sources like NCBI, used to map between datasets. -- cgit v1.2.3