Merge pull request #37 from cancervariants/cli

Add cli class back
cancervariants · Mar 29, 2021 · bb4cee4 · bb4cee4
2 parents e8e21d2 + e94eb99
commit bb4cee4
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Showing 2 changed files with 133 additions and 134 deletions.
diff --git a/gene/__init__.py b/gene/__init__.py
@@ -10,7 +10,7 @@
 logger.setLevel(logging.DEBUG)
 
 
-__version__ = "0.1.2"
+__version__ = "0.1.3"
 
 
 class DownloadException(Exception):

diff --git a/gene/cli.py b/gene/cli.py
@@ -9,141 +9,140 @@
 from os import environ
 
 
-@click.command()
-@click.option(
-    '--normalizer',
-    help="The normalizer(s) you wish to update separated by spaces."
-)
-@click.option(
-    '--prod',
-    is_flag=True,
-    help="Working in production environment."
-)
-@click.option(
-    '--db_url',
-    help="URL endpoint for the application database."
-)
-@click.option(
-    '--update_all',
-    is_flag=True,
-    help='Update all normalizer sources.'
-)
-def update_normalizer_db(normalizer, prod, db_url, update_all):
-    """Update selected normalizer source(s) in the gene database."""
-    sources = {
-        'hgnc': HGNC,
-        'ensembl': Ensembl,
-        'ncbi': NCBI
-    }
-    if prod:
-        environ['GENE_NORM_PROD'] = "TRUE"
-        db: Database = Database()
-    else:
-        if db_url:
-            endpoint_url = db_url
-        elif 'GENE_NORM_DB_URL' in environ.keys():
-            endpoint_url = environ['GENE_NORM_DB_URL']
+class CLI:
+    """Class for updating the normalizer database via Click"""
+
+    @staticmethod
+    @click.command()
+    @click.option(
+        '--normalizer',
+        help="The normalizer(s) you wish to update separated by spaces."
+    )
+    @click.option(
+        '--prod',
+        is_flag=True,
+        help="Working in production environment."
+    )
+    @click.option(
+        '--db_url',
+        help="URL endpoint for the application database."
+    )
+    @click.option(
+        '--update_all',
+        is_flag=True,
+        help='Update all normalizer sources.'
+    )
+    def update_normalizer_db(normalizer, prod, db_url, update_all):
+        """Update selected normalizer source(s) in the gene database."""
+        sources = {
+            'hgnc': HGNC,
+            'ensembl': Ensembl,
+            'ncbi': NCBI
+        }
+        if prod:
+            environ['GENE_NORM_PROD'] = "TRUE"
+            db: Database = Database()
         else:
-            endpoint_url = 'http://localhost:8000'
-        db: Database = Database(db_url=endpoint_url)
-
-    if update_all:
-        normalizers = [src for src in sources]
-        _update_normalizers(normalizers, sources, db)
-    elif not normalizer:
-        _help_msg()
-    else:
-        normalizers = normalizer.lower().split()
-
-        if len(normalizers) == 0:
-            raise Exception("Must enter a normalizer")
-
-        non_sources = _check_norm_srcs_match(sources, normalizers)
-
-        if len(non_sources) != 0:
-            raise Exception(f"Not valid source(s): {non_sources}")
-
-        _update_normalizers(normalizers, sources, db)
-
-
-def _help_msg():
-    """Display help message."""
-    ctx = click.get_current_context()
-    click.echo(
-        "Must either enter 1 or more sources, or use `--update_all` parameter")  # noqa: E501
-    click.echo(ctx.get_help())
-    ctx.exit()
-
-
-def _check_norm_srcs_match(sources, normalizers):
-    """Check that entered normalizers are actual sources."""
-    return set(normalizers) - {src for src in sources}
-
-
-def _update_normalizers(normalizers, sources, db):
-    """Update selected normalizer sources."""
-    for n in normalizers:
-        click.echo(f"\nDeleting {n}...")
-        start_delete = timer()
-        _delete_data(n, db)
-        end_delete = timer()
-        delete_time = end_delete - start_delete
-        click.echo(f"Deleted {n} in "
-                   f"{delete_time:.5f} seconds.\n")
-        click.echo(f"Loading {n}...")
-        start_load = timer()
-        sources[n](database=db)
-        end_load = timer()
-        load_time = end_load - start_load
-        click.echo(f"Loaded {n} in {load_time:.5f} seconds.")
-        click.echo(f"Total time for {n}: "
-                   f"{(delete_time + load_time):.5f} seconds.")
-
-
-def _delete_data(source, database):
-    # Delete source's metadata
-    try:
-        metadata = database.metadata.query(
-            KeyConditionExpression=Key(
-                'src_name').eq(SourceName[f"{source.upper()}"].value)
-        )
-        if metadata['Items']:
-            database.metadata.delete_item(
-                Key={'src_name': metadata['Items'][0]['src_name']},
-                ConditionExpression="src_name = :src",
-                ExpressionAttributeValues={
-                    ':src': SourceName[f"{source.upper()}"].value}
-            )
-    except ClientError as e:
-        click.echo(e.response['Error']['Message'])
-
-    # Delete source's data from genes table
-    try:
-        while True:
-            response = database.genes.query(
-                IndexName='src_index',
-                KeyConditionExpression=Key('src_name').eq(
-                    SourceName[f"{source.upper()}"].value)
+            if db_url:
+                endpoint_url = db_url
+            elif 'GENE_NORM_DB_URL' in environ.keys():
+                endpoint_url = environ['GENE_NORM_DB_URL']
+            else:
+                endpoint_url = 'http://localhost:8000'
+            db: Database = Database(db_url=endpoint_url)
+
+        if update_all:
+            normalizers = [src for src in sources]
+            CLI()._update_normalizers(normalizers, sources, db)
+        elif not normalizer:
+            CLI()._help_msg()
+        else:
+            normalizers = normalizer.lower().split()
+
+            if len(normalizers) == 0:
+                raise Exception("Must enter a normalizer")
+
+            non_sources = set(normalizers) - {src for src in sources}
+
+            if len(non_sources) != 0:
+                raise Exception(f"Not valid source(s): {non_sources}")
+
+            CLI()._update_normalizers(normalizers, sources, db)
+
+    @staticmethod
+    def _help_msg():
+        """Display help message."""
+        ctx = click.get_current_context()
+        click.echo(
+            "Must either enter 1 or more sources, or use `--update_all` parameter")  # noqa: E501
+        click.echo(ctx.get_help())
+        ctx.exit()
+
+    @staticmethod
+    def _update_normalizers(normalizers, sources, db):
+        """Update selected normalizer sources."""
+        for n in normalizers:
+            click.echo(f"\nDeleting {n}...")
+            start_delete = timer()
+            CLI()._delete_data(n, db)
+            end_delete = timer()
+            delete_time = end_delete - start_delete
+            click.echo(f"Deleted {n} in "
+                       f"{delete_time:.5f} seconds.\n")
+            click.echo(f"Loading {n}...")
+            start_load = timer()
+            sources[n](database=db)
+            end_load = timer()
+            load_time = end_load - start_load
+            click.echo(f"Loaded {n} in {load_time:.5f} seconds.")
+            click.echo(f"Total time for {n}: "
+                       f"{(delete_time + load_time):.5f} seconds.")
+
+    @staticmethod
+    def _delete_data(source, database):
+        # Delete source's metadata
+        try:
+            metadata = database.metadata.query(
+                KeyConditionExpression=Key(
+                    'src_name').eq(SourceName[f"{source.upper()}"].value)
             )
-
-            records = response['Items']
-            if not records:
-                break
-
-            with database.genes.batch_writer(
-                    overwrite_by_pkeys=['label_and_type', 'concept_id']) \
-                    as batch:
-
-                for record in records:
-                    batch.delete_item(
-                        Key={
-                            'label_and_type': record['label_and_type'],
-                            'concept_id': record['concept_id']
-                        }
-                    )
-    except ClientError as e:
-        click.echo(e.response['Error']['Message'])
+            if metadata['Items']:
+                database.metadata.delete_item(
+                    Key={'src_name': metadata['Items'][0]['src_name']},
+                    ConditionExpression="src_name = :src",
+                    ExpressionAttributeValues={
+                        ':src': SourceName[f"{source.upper()}"].value}
+                )
+        except ClientError as e:
+            click.echo(e.response['Error']['Message'])
+
+        # Delete source's data from genes table
+        try:
+            while True:
+                response = database.genes.query(
+                    IndexName='src_index',
+                    KeyConditionExpression=Key('src_name').eq(
+                        SourceName[f"{source.upper()}"].value)
+                )
+
+                records = response['Items']
+                if not records:
+                    break
+
+                with database.genes.batch_writer(
+                        overwrite_by_pkeys=['label_and_type', 'concept_id']) \
+                        as batch:
+
+                    for record in records:
+                        batch.delete_item(
+                            Key={
+                                'label_and_type': record['label_and_type'],
+                                'concept_id': record['concept_id']
+                            }
+                        )
+        except ClientError as e:
+            click.echo(e.response['Error']['Message'])
 
 
 if __name__ == '__main__':
-    update_normalizer_db()
+    CLI().update_normalizer_db()