update constants and toml file

Knowledge-Graph-Hub · Feb 7, 2024 · 6a4545b · 6a4545b
1 parent ea889dc
commit 6a4545b
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Showing 3 changed files with 14 additions and 13 deletions.
diff --git a/kg_microbe/transform_utils/constants.py b/kg_microbe/transform_utils/constants.py
@@ -241,6 +241,7 @@
 UNIPROT_KEYWORDS = ["Reference+proteome"]
 UNIPROT_DESIRED_FORMAT = "tsv"
 UNIPROT_SIZE = 500
-UNIPROT_BATCH_SIZE = 1
-ORGANISM_ID = "Organism_ID"
+ORGANISM_ID_MIXED_CASE = "Organism_ID"
 UNIPROT_ORG_ID_COLUMN_NAME = "Organism (ID)"
+TAXONOMY_ID_UNIPROT_PREFIX = "taxonomy_id:"
+UNIPROT_REVIEWED_FLAG = "reviewed:true+"
diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -27,7 +27,7 @@ notebook = "^7.0.6"
 jupyter-contrib-nbextensions = "^0.7.0"
 python-sql = "^1.4.2"
 ipython-sql = "^0.5.0"
-ruff = "^0.2.1"
+ruff = ">=0.2.1"
 
 [tool.poetry.group.docs]
 optional = true