refactor: split out utlities into their modules and change api to use metadata

1 files changed, 38 insertions, 0 deletions

diff --git a/gn3/db/wiki.py b/gn3/db/wiki.py
new file mode 100644
index 0000000..a56f26c
--- /dev/null
+++ b/gn3/db/wiki.py
@@ -0,0 +1,38 @@
+from typing import List
+
+
+class MissingDBDataException(Exception):
+    pass
+
+
+def get_species_id(cursor, species_name: str) -> int:
+    cursor.execute("SELECT SpeciesID from Species  WHERE Name = %s", (species_name,))
+    species_ids = cursor.fetchall()
+    if len(species_ids) != 1:
+        raise MissingDBDataException(
+            f"expected 1 species with Name={species_name} but found {len(species_ids)}!"
+        )
+    return species_ids[0][0]
+
+
+def get_next_comment_version(cursor, comment_id: int) -> int:
+    cursor.execute(
+        "SELECT MAX(versionId) as version_id from GeneRIF WHERE Id = %s", (comment_id,)
+    )
+    latest_version = cursor.fetchone()[0]
+    if latest_version is None:
+        raise MissingDBDataException(f"No comment found with comment_id={comment_id}")
+    return latest_version + 1
+
+
+def get_categories_ids(cursor, categories: List[str]) -> List[int]:
+    cursor.execute("SELECT Name, Id from GeneCategory")
+    raw_categories = cursor.fetchall()
+    dict_cats = dict(raw_categories)
+    category_ids = []
+    for category in set(categories):
+        cat_id = dict_cats.get(category.strip())
+        if cat_id is None:
+            raise MissingDBDataException(f"Category with Name={category} not found")
+        category_ids.append(cat_id)
+    return category_ids