diff --git a/src/db_utils/db_creation.py b/src/db_utils/db_creation.py index 0a8ba1b661ad9b6ab0f861cc1df2e92de50118f7..ccfed76ee3fd0616cf19ad91ab26ba31d9caa572 100755 --- a/src/db_utils/db_creation.py +++ b/src/db_utils/db_creation.py @@ -61,8 +61,7 @@ def create_cin_projects_table(conn: sqlite3.Connection) -> None: """ c = conn.cursor() c.execute('''CREATE TABLE IF NOT EXISTS cin_projects - ([id] INT NOT NULL, - [id_sample] VARCHAR(60) NOT NULL, + ([id_sample] VARCHAR(60) NOT NULL, [id_project] VARCHAR(45) NOT NULL, [database] VARCHAR(45) NOT NULL, [name] VARCHAR(60) NULL, @@ -71,7 +70,7 @@ def create_cin_projects_table(conn: sqlite3.Connection) -> None: [cell_line] VARCHAR(45) NOT NULL, [institute] VARCHAR(45) NULL, [citation] VARCHAR(20) NULL, - PRIMARY KEY ([id]))''') + PRIMARY KEY ([id_sample]))''') conn.commit() @@ -128,7 +127,8 @@ def create_cin_exon_interaction_table(conn: sqlite3.Connection) -> None: PRIMARY KEY ([id]), FOREIGN KEY ([exon1]) REFERENCES cin_exon([id]), FOREIGN KEY ([exon2]) REFERENCES cin_exon([id]), - FOREIGN KEY ([id_project]) REFERENCES cin_projects([id]))''') + FOREIGN KEY ([id_project]) + REFERENCES cin_projects([id_sample]))''') conn.commit() @@ -149,7 +149,8 @@ def create_cin_gene_interaction_table(conn: sqlite3.Connection) -> None: PRIMARY KEY ([id]), FOREIGN KEY ([gene1]) REFERENCES cin_gene([id]), FOREIGN KEY ([gene2]) REFERENCES cin_gene([id]), - FOREIGN KEY ([id_project]) REFERENCES cin_projects([id]))''') + FOREIGN KEY ([id_project]) + REFERENCES cin_projects([id_sample]))''') conn.commit() diff --git a/src/db_utils/projects_metadata/get_fill_metadata.py b/src/db_utils/projects_metadata/get_fill_metadata.py index 537e479d699005ab2c80cd3b65677de5888f44e2..a63bed61ff07fc291a83e8077bee88298315900c 100644 --- a/src/db_utils/projects_metadata/get_fill_metadata.py +++ b/src/db_utils/projects_metadata/get_fill_metadata.py @@ -77,7 +77,7 @@ def merge_metadata() -> pd.DataFrame: "Real source": "database", "Kept GSM": "id_sample", "Antibody": "antibody"}, inplace=True) - projects = projects.reset_index().rename(columns={"index": "id"}) + # projects = projects.reset_index().rename(columns={"index": "id"}) logging.debug(projects.head()) return projects