From f0dc54dc6d6fd66a49496b6896d1158f3acfdbbb Mon Sep 17 00:00:00 2001
From: Kiyoon Kim <kiyoon@users.noreply.github.com>
Date: Wed, 17 Jul 2024 11:27:54 +0900
Subject: [PATCH] refactor: remove tools

---
 tools/create_uniprot_accession_to_pk_id.py | 82 ----------------------
 tools/create_uniprot_empty_table.py        | 55 ---------------
 tools/uniprot_xml_to_postgresql.py         |  8 ---
 3 files changed, 145 deletions(-)
 delete mode 100644 tools/create_uniprot_accession_to_pk_id.py
 delete mode 100644 tools/create_uniprot_empty_table.py
 delete mode 100644 tools/uniprot_xml_to_postgresql.py

diff --git a/tools/create_uniprot_accession_to_pk_id.py b/tools/create_uniprot_accession_to_pk_id.py
deleted file mode 100644
index f5c2202..0000000
--- a/tools/create_uniprot_accession_to_pk_id.py
+++ /dev/null
@@ -1,82 +0,0 @@
-import logging
-
-import psycopg
-
-from bio_data_to_db.utils.postgresql import (
-    create_db_if_not_exists,
-    create_schema_if_not_exists,
-    make_columns_unique,
-    polars_write_database,
-    set_column_as_primary_key,
-)
-
-logger = logging.getLogger(__name__)
-
-
-def main():
-    uri_wo_db = "postgresql://kiyoon@localhost:5432"
-    db_name = "uniprot"
-    uri = f"{uri_wo_db}/{db_name}"
-
-    create_db_if_not_exists(uri_wo_db, db_name)
-    create_schema_if_not_exists(uri, "public")
-
-    with psycopg.connect(
-        conninfo=uri,
-    ) as conn:
-        try:
-            cursor = conn.cursor()
-            conn.autocommit = True
-            cursor.execute(
-                query="""
-                CREATE TABLE public.accession_to_pk_id (
-                  accession TEXT,
-                  uniprot_pk_id BIGINT
-                )
-            """
-            )
-            logger.info(
-                "Table structure 'uniprot.public.accession_to_pk_id' created successfully"
-            )
-
-            cursor.execute(
-                query="""
-                INSERT INTO public.accession_to_pk_id (accession, uniprot_pk_id)
-                SELECT UNNEST(accessions), uniprot_pk_id
-                FROM public.uniprot_info
-            """
-            )
-            logger.info(
-                "Table 'uniprot.public.accession_to_pk_id' insert content successfully"
-            )
-
-            cursor.execute(
-                query="""
-                CREATE TABLE public.accession_to_pk_id_list (
-                  accession TEXT PRIMARY KEY,
-                  uniprot_pk_ids BIGINT[]
-                )
-            """
-            )
-            logger.info(
-                "Table structure 'uniprot.public.accession_to_pk_id_list' created successfully"
-            )
-
-            cursor.execute(
-                query="""
-                INSERT INTO public.accession_to_pk_id_list (accession, uniprot_pk_ids)
-                SELECT accession, ARRAY_AGG(uniprot_pk_id) AS uniprot_pk_ids
-                FROM public.accession_to_pk_id
-                GROUP BY accession;
-            """
-            )
-            logger.info(
-                "Table 'uniprot.public.accession_to_pk_id_list' content added successfully"
-            )
-
-        except psycopg.Error:
-            logger.exception("Error creating table 'uniprot.public.accession_to_pk_id'")
-
-
-if __name__ == "__main__":
-    main()
diff --git a/tools/create_uniprot_empty_table.py b/tools/create_uniprot_empty_table.py
deleted file mode 100644
index 8e84a69..0000000
--- a/tools/create_uniprot_empty_table.py
+++ /dev/null
@@ -1,55 +0,0 @@
-import logging
-
-import psycopg
-
-from bio_data_to_db.utils.postgresql import (
-    create_db_if_not_exists,
-    create_schema_if_not_exists,
-    make_columns_unique,
-    polars_write_database,
-    set_column_as_primary_key,
-)
-
-logger = logging.getLogger(__name__)
-
-
-def main():
-    create_db_if_not_exists("postgresql://kiyoon@localhost:5432", "uniprot")
-    create_schema_if_not_exists("postgresql://kiyoon@localhost:5432/uniprot", "public")
-
-    with psycopg.connect(
-        conninfo="postgresql://kiyoon@localhost:5432/uniprot",
-    ) as conn:
-        try:
-            cursor = conn.cursor()
-            conn.autocommit = True
-            cursor.execute(
-                query="""
-                CREATE TABLE public.uniprot_info (
-                  uniprot_pk_id BIGINT GENERATED BY DEFAULT AS IDENTITY PRIMARY KEY,
-                  accessions TEXT[],
-                  names TEXT[],
-                  protein_names TEXT[],
-                  gene_names TEXT[],
-                  organism_scientific TEXT,
-                  organism_commons TEXT[],
-                  organism_synonyms TEXT[],
-                  ncbi_taxonomy_id INT,
-                  deargen_ncbi_taxonomy_id INT,
-                  lineage TEXT[],
-                  keywords TEXT[],
-                  geneontology_ids TEXT[],
-                  geneontology_names TEXT[],
-                  sequence TEXT,
-                  deargen_molecular_functions TEXT[]
-                )
-            """
-            )
-            logger.info("Database 'uniprot' created successfully")
-
-        except psycopg.Error:
-            logger.exception("Error creating database 'uniprot'")
-
-
-if __name__ == "__main__":
-    main()
diff --git a/tools/uniprot_xml_to_postgresql.py b/tools/uniprot_xml_to_postgresql.py
deleted file mode 100644
index e57f353..0000000
--- a/tools/uniprot_xml_to_postgresql.py
+++ /dev/null
@@ -1,8 +0,0 @@
-from __future__ import annotations
-
-from bio_data_to_db import uniprot_xml_to_postgresql
-
-uniprot_xml_to_postgresql(
-    uniprot_xml_path="~/Downloads/uniprot_sprot.xml",
-    uri="postgresql://kiyoon@localhost:5432/uniprot",
-)