changed polars library code to fit its updated version

just_prs.py

@@ -12,17 +12,17 @@
 INVERS = "invers"
 
 class CravatPostAggregator (BasePostAggregator):
-    prs:dict = {}
-    prs_names:list = []
+    prs: dict = {}
+    prs_names: list = []
     # prs5_rsids = []
-    sql_get_prs:str = """SELECT name, title, total, invers FROM prs;"""
+    sql_get_prs: str = """SELECT name, title, total, invers FROM prs;"""
 
 
-    def check(self):
+    def check(self) -> bool:
         return True
 
 
-    def setup (self):
+    def setup(self) -> None:
         self.sql_file:str = str(Path(__file__).parent) + "/data/prs.sqlite"
         if Path(self.sql_file).exists():
             self.prsconn:sqlite3.Connection = sqlite3.connect(self.sql_file)
@@ -53,20 +53,20 @@ def setup (self):
         self.result_cursor.execute("DELETE FROM prs;")
 
 
-    def get_prs_dataframe(self, name):
+    def get_prs_dataframe(self, name: str) -> pl.DataFrame:
         import platform
         sql:str = f"SELECT pos, chrom, effect_allele, weight FROM prs, position, weights WHERE prs.name = '{name}' AND prs.id = weights.prsid AND weights.posid = position.id"
         ol_pl = platform.platform()
         if ol_pl.startswith("Windows"):
             conn_url = f"sqlite://{urllib.parse.quote(self.sql_file)}"
         else:
             conn_url = f"sqlite://{self.sql_file}"
-        return pl.read_sql(sql, conn_url)
+        return pl.read_database(sql, conn_url)
 
 
-    def calculate_prs(self, data_df, name):
+    def calculate_prs(self, data_df: pl.DataFrame, name: str) -> tuple:
         prs_df:pl.DataFrame = self.get_prs_dataframe(name)
-        prs_df = prs_df.with_column((pl.col('chrom') + pl.col('pos').cast(pl.datatypes.Utf8)).alias("key"))
+        prs_df = prs_df.with_columns((pl.col('chrom') + pl.col('pos').cast(pl.datatypes.Utf8)).alias("key"))
         unite:pl.DataFrame = data_df.join(prs_df, left_on='key', right_on="key")
         unite1 = unite.filter(pl.col("A") == pl.col("effect_allele"))
         unite2 = unite.filter(pl.col("B") == pl.col("effect_allele"))
@@ -79,12 +79,12 @@ def calculate_prs(self, data_df, name):
         return float(res1.item()) + float(res2.item()), unite.shape[0]
 
 
-    def process_file(self):
+    def process_file(self) -> None:
         self._close_db_connection()
         data_df = self.get_df("variant", None, 0)
         data_df = data_df.select(['base__pos', 'vcfinfo__zygosity', 'base__ref_base', 'base__alt_base', 'base__chrom'])
-        data_df = data_df.with_column(pl.col('vcfinfo__zygosity').fill_null("het"))
-        data_df = data_df.with_column((pl.col('base__chrom') + pl.col('base__pos').cast(pl.datatypes.Utf8)).alias("key"))
+        data_df = data_df.with_columns(pl.col('vcfinfo__zygosity').fill_null("het"))
+        data_df = data_df.with_columns((pl.col('base__chrom') + pl.col('base__pos').cast(pl.datatypes.Utf8)).alias("key"))
 
         het_zygot = data_df.filter(pl.col('vcfinfo__zygosity') == 'het')
         het_zygot = het_zygot.with_columns([pl.col('base__ref_base').alias("A"), pl.col('base__alt_base').alias("B")])
@@ -100,7 +100,7 @@ def process_file(self):
         self._open_db_connection()
 
 
-    def cleanup (self):
+    def cleanup(self) -> None:
         if self.result_cursor is not None:
             self.result_cursor.close()
         if self.result_conn is not None:
@@ -169,7 +169,7 @@ def get_percent(self, name:str, value:float) -> float:
             return min_percent
 
 
-    def postprocess(self):
+    def postprocess(self) -> None:
         sql:str = """ INSERT INTO prs (name, sum, avg, count, title, total, percent, fraction, invers) VALUES (?,?,?,?,?,?,?,?,?);"""
         for name in self.prs_names:
             avg:float = 0

just_prs.yml

@@ -1,5 +1,5 @@
 title: Prs postagregator
-version: 0.1.1
+version: 0.1.2
 data_version: 0.1.1
 requires_opencravat: '>=1.8.1'
 type: postaggregator
@@ -16,6 +16,8 @@ input_columns:
   - base__ref_base
   - base__chrom
   - vcfinfo__zygosity
+pypi_dependency:
+  - polars>=0.19.0
 tags:
 - prs
 - longevity
@@ -36,3 +38,4 @@ developer:
 release_note:
   0.1.0: initial commit
   0.1.1: updated database, added new prs
+  0.1.2: updated dependencies and changed polars code according to its new version