feat(taxonomy): Indexed, case-insensitive scientific_name queries of NCBI taxonomy DB (#6170)

Updating the index on scientific_name in the NCBI taxonomy database to
allow for indexed, case-insensitive queries using user-supplied
scientific host names. This will be a slightly nicer user-experience
once we implement host name validation in prepro.

Current implementation: 
-> user gives us `hostNameScientific: aedes aegypti` 
-> DB stores `scientific_name: Aesdes aegypti` 
-> error: hostNameScienitific not found

New implementation allows for: 
-> user gives us `hostNameScientific: aedes aegypti` 
-> DB stores `scientific_name: Aesdes aegypti` 
-> {"tax_id":7159,"common_name":"yellow fever
mosquito","scientific_name":"Aedes
aegypti","parent_id":53541,"depth":28}

## Manual tests:
I reran the DB creation script, connected using `sqlite3`, and ran:
```sql
sqlite> SELECT * FROM taxonomy WHERE scientific_name = 'aedes aegypti' COLLATE NOCASE;
tax_id|common_name|scientific_name|parent_id|depth
7159|yellow fever mosquito|Aedes aegypti|53541|28
```

### PR Checklist
- [x] All necessary documentation has been adapted.
- [x] The implemented feature is covered by appropriate, automated
tests.
- [x] Any manual testing that has been done is documented (i.e. what
exactly was tested?)

🚀 Preview: Add `preview` label to enable

Author: maverbiest

ncbi_tax_download/README.md

@@ -36,7 +36,7 @@ CREATE TABLE IF NOT EXISTS "taxonomy" (
 );
 CREATE UNIQUE INDEX idx_tax_id ON taxonomy(tax_id);
 CREATE INDEX idx_parent_id ON taxonomy(parent_id);
-CREATE INDEX idx_scientific_name ON taxonomy(scientific_name);
+CREATE INDEX idx_scientific_name ON taxonomy(scientific_name COLLATE NOCASE);
 CREATE TABLE sqlite_stat1(tbl,idx,stat);
 CREATE TABLE sqlite_stat4(tbl,idx,neq,nlt,ndlt,sample);
 ```

ncbi_tax_download/src/ncbi_tax_download/ncbi.py

@@ -139,7 +139,9 @@ def write_to_sqlite(df: pd.DataFrame, output_db: Path) -> None:
 
         conn.execute("CREATE UNIQUE INDEX IF NOT EXISTS idx_tax_id ON taxonomy(tax_id);")
         conn.execute("CREATE INDEX IF NOT EXISTS idx_parent_id ON taxonomy(parent_id);")
-        conn.execute("CREATE INDEX IF NOT EXISTS idx_scientific_name ON taxonomy(scientific_name);")
+        conn.execute(
+            "CREATE INDEX IF NOT EXISTS idx_scientific_name ON taxonomy(scientific_name COLLATE NOCASE);"
+        )
 
         conn.execute("ANALYZE;")
 

ncbi_tax_download/tests/test_db_creation.py

@@ -1,4 +1,3 @@
-import os
 import shutil
 from io import BytesIO
 from pathlib import Path