print method

src/gene/etl/base.py

@@ -79,13 +79,13 @@ def perform_etl(self, use_existing: bool = False) -> List[str]:
             uploaded.
         """
         self._extract_data(use_existing)
-        _logger.info(f"Transforming and loading {self._src_name} data to DB...")
-        if not self._silent:
-            click.echo("Transforming and loading data to DB...")
+        self._print_info(
+            f"Transforming and loading {self._src_name.value} data to DB..."
+        )
         self._add_meta()
         self._transform_data()
         self._database.complete_write_transaction()
-        _logger.info(f"Data load complete for {self._src_name}.")
+        self._print_info(f"Data load complete for {self._src_name.value}.")
         return self._processed_ids
 
     def _extract_data(self, use_existing: bool) -> None:
@@ -248,3 +248,12 @@ def _get_seq_id_aliases(self, seq_id: str) -> List[str]:
         except KeyError as e:
             _logger.warning(f"SeqRepo raised KeyError: {e}")
         return aliases
+
+    def _print_info(self, msg: str) -> None:
+        """Log information and print to console if not on silent mode.
+
+        :param msg: message to print
+        """
+        if not self._silent:
+            click.echo(msg)
+        _logger.info(msg)

src/gene/etl/ensembl.py

@@ -4,7 +4,6 @@
 from typing import Dict, Optional
 from urllib.parse import unquote
 
-import click
 import gffpandas.gffpandas as gffpd
 import pandas as pd
 from tqdm import tqdm
@@ -54,8 +53,7 @@ def _transform_data(self) -> None:
 
         gene_df = df[df["ID"].str.startswith("gene", na=False)]
 
-        if not self._silent:
-            click.echo(f"Loading rows from {self._data_file}:")
+        self._print_info(f"Loading rows from {self._data_file}:")
         for _, row in tqdm(
             gene_df.iterrows(), total=gene_df.shape[0], disable=self._silent, ncols=80
         ):

src/gene/etl/hgnc.py

@@ -4,7 +4,6 @@
 import re
 from typing import Dict, List
 
-import click
 from tqdm import tqdm
 
 from gene.etl.base import Base, GeneNormalizerEtlError
@@ -32,8 +31,7 @@ def _transform_data(self) -> None:
 
         records = data["response"]["docs"]
 
-        if not self._silent:
-            click.echo(f"Loading rows from {self._data_file}:")
+        self._print_info(f"Loading rows from {self._data_file}:")
         for r in tqdm(records, total=len(records), disable=self._silent, ncols=80):
             gene = {
                 "concept_id": r["hgnc_id"].lower(),

src/gene/etl/ncbi.py

@@ -6,7 +6,6 @@
 from typing import Any, Dict, List, Optional
 from urllib.parse import unquote
 
-import click
 import gffpandas.gffpandas as gffpd
 import pandas as pd
 from tqdm import tqdm
@@ -83,8 +82,7 @@ def _get_prev_symbols(self) -> Dict[str, str]:
             history = csv.reader(history_file, delimiter="\t")
             next(history)
             prev_symbols = {}
-            if not self._silent:
-                click.echo(f"Gathering previous symbols from {self._history_src}")
+            self._print_info(f"Gathering previous symbols from {self._history_src}")
             for row in tqdm(history, total=length, ncols=80, disable=self._silent):
                 if row[0] != "9606":
                     continue  # humans only
@@ -150,8 +148,7 @@ def _get_gene_info(self, prev_symbols: Dict[str, str]) -> Dict[str, Dict]:
             info = csv.reader(info_file, delimiter="\t")
             next(info)
 
-            if not self._silent:
-                click.echo(f"Extracting genes from {self._info_src}")
+            self._print_info(f"Extracting genes from {self._info_src}")
             for row in tqdm(info, total=length, ncols=80, disable=self._silent):
                 params: Dict[str, Any] = {
                     "concept_id": f"{NamespacePrefix.NCBI.value}:{row[1]}",
@@ -196,8 +193,7 @@ def _get_gene_gff(self, df: pd.DataFrame, info_genes: Dict) -> None:
         :param info_genes: A dictionary of gene's from the NCBI info file.
         """
         genes_df = df[df["ID"].str.startswith("gene", na=False)]
-        if not self._silent:
-            click.echo(f"Extracting genes from {self._info_src}")
+        self._print_info(f"Extracting genes from {self._info_src}")
         for _, row in tqdm(
             genes_df.iterrows(), total=genes_df.shape[0], ncols=80, disable=self._silent
         ):
@@ -440,8 +436,7 @@ def _transform_data(self) -> None:
         df = gffpd.read_gff3(self._gff_src).attributes_to_columns()
         self._get_gene_gff(df, info_genes)
 
-        if not self._silent:
-            click.echo("Loading completed gene objects...")
+        self._print_info("Loading completed gene objects...")
         for gene in tqdm(
             info_genes.values(), total=len(info_genes), disable=self._silent, ncols=80
         ):