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From maximebeauche...@apache.org
Subject [incubator-superset] branch master updated: Add csv upload support for BigQuery (#7756)
Date Sun, 23 Jun 2019 21:20:26 GMT
This is an automated email from the ASF dual-hosted git repository.

maximebeauchemin pushed a commit to branch master
in repository https://gitbox.apache.org/repos/asf/incubator-superset.git


The following commit(s) were added to refs/heads/master by this push:
     new 1c4092c  Add csv upload support for BigQuery (#7756)
1c4092c is described below

commit 1c4092c61cc8aeb3f3c0dabb7831813e514dfbdd
Author: Ville Brofeldt <33317356+villebro@users.noreply.github.com>
AuthorDate: Mon Jun 24 00:20:09 2019 +0300

    Add csv upload support for BigQuery (#7756)
    
    * Add extra_require for bigquery to setup.py
    
    * Refactor df_to_db and add df upload capability for BigQuery
    
    * Fix unit tests and clarify kwarg logic
    
    * Fix flake8 errors
    
    * Add minimum versions for bigquery dependencies
    
    * wrap to_gbq in try-catch block and raise error if pandas-gbq is missing
    
    * Fix linting error and make error more generic
---
 setup.py                             |  4 +++
 superset/db_engine_specs/base.py     | 49 +++++++++++++++++++++++-------------
 superset/db_engine_specs/bigquery.py | 37 ++++++++++++++++++++++++---
 superset/db_engine_specs/hive.py     |  4 +--
 tests/db_engine_specs_test.py        |  6 ++---
 5 files changed, 74 insertions(+), 26 deletions(-)

diff --git a/setup.py b/setup.py
index 420375b..28c6bbd 100644
--- a/setup.py
+++ b/setup.py
@@ -108,6 +108,10 @@ setup(
         'wtforms-json',
     ],
     extras_require={
+        'bigquery': [
+            'pybigquery>=0.4.10',
+            'pandas_gbq>=0.10.0',
+        ],
         'cors': ['flask-cors>=2.0.0'],
         'hive': [
             'pyhive[hive]>=0.6.1',
diff --git a/superset/db_engine_specs/base.py b/superset/db_engine_specs/base.py
index da80d86..5254bae 100644
--- a/superset/db_engine_specs/base.py
+++ b/superset/db_engine_specs/base.py
@@ -230,36 +230,45 @@ class BaseEngineSpec(object):
         return parsed_query.get_query_with_new_limit(limit)
 
     @staticmethod
-    def csv_to_df(**kwargs):
+    def csv_to_df(**kwargs) -> pd.DataFrame:
+        """ Read csv into Pandas DataFrame
+        :param kwargs: params to be passed to DataFrame.read_csv
+        :return: Pandas DataFrame containing data from csv
+        """
         kwargs['filepath_or_buffer'] = \
             config['UPLOAD_FOLDER'] + kwargs['filepath_or_buffer']
         kwargs['encoding'] = 'utf-8'
         kwargs['iterator'] = True
         chunks = pd.read_csv(**kwargs)
-        df = pd.DataFrame()
         df = pd.concat(chunk for chunk in chunks)
         return df
 
-    @staticmethod
-    def df_to_db(df, table, **kwargs):
+    @classmethod
+    def df_to_sql(cls, df: pd.DataFrame, **kwargs):
+        """ Upload data from a Pandas DataFrame to a database. For
+        regular engines this calls the DataFrame.to_sql() method. Can be
+        overridden for engines that don't work well with to_sql(), e.g.
+        BigQuery.
+        :param df: Dataframe with data to be uploaded
+        :param kwargs: kwargs to be passed to to_sql() method
+        """
         df.to_sql(**kwargs)
-        table.user_id = g.user.id
-        table.schema = kwargs['schema']
-        table.fetch_metadata()
-        db.session.add(table)
-        db.session.commit()
 
-    @staticmethod
-    def create_table_from_csv(form, table):
-        def _allowed_file(filename):
+    @classmethod
+    def create_table_from_csv(cls, form, table):
+        """ Create table (including metadata in backend) from contents of a csv.
+        :param form: Parameters defining how to process data
+        :param table: Metadata of new table to be created
+        """
+        def _allowed_file(filename: str) -> bool:
             # Only allow specific file extensions as specified in the config
             extension = os.path.splitext(filename)[1]
-            return extension and extension[1:] in config['ALLOWED_EXTENSIONS']
+            return extension is not None and extension[1:] in config['ALLOWED_EXTENSIONS']
 
         filename = secure_filename(form.csv_file.data.filename)
         if not _allowed_file(filename):
             raise Exception('Invalid file type selected')
-        kwargs = {
+        csv_to_df_kwargs = {
             'filepath_or_buffer': filename,
             'sep': form.sep.data,
             'header': form.header.data if form.header.data else 0,
@@ -273,10 +282,9 @@ class BaseEngineSpec(object):
             'infer_datetime_format': form.infer_datetime_format.data,
             'chunksize': 10000,
         }
-        df = BaseEngineSpec.csv_to_df(**kwargs)
+        df = cls.csv_to_df(**csv_to_df_kwargs)
 
-        df_to_db_kwargs = {
-            'table': table,
+        df_to_sql_kwargs = {
             'df': df,
             'name': form.name.data,
             'con': create_engine(form.con.data.sqlalchemy_uri_decrypted, echo=False),
@@ -286,8 +294,13 @@ class BaseEngineSpec(object):
             'index_label': form.index_label.data,
             'chunksize': 10000,
         }
+        cls.df_to_sql(**df_to_sql_kwargs)
 
-        BaseEngineSpec.df_to_db(**df_to_db_kwargs)
+        table.user_id = g.user.id
+        table.schema = form.schema.data
+        table.fetch_metadata()
+        db.session.add(table)
+        db.session.commit()
 
     @classmethod
     def convert_dttm(cls, target_type, dttm):
diff --git a/superset/db_engine_specs/bigquery.py b/superset/db_engine_specs/bigquery.py
index af6e066..954966f 100644
--- a/superset/db_engine_specs/bigquery.py
+++ b/superset/db_engine_specs/bigquery.py
@@ -14,10 +14,10 @@
 # KIND, either express or implied.  See the License for the
 # specific language governing permissions and limitations
 # under the License.
-# pylint: disable=C,R,W
 import hashlib
 import re
 
+import pandas as pd
 from sqlalchemy import literal_column
 
 from superset.db_engine_specs.base import BaseEngineSpec
@@ -86,8 +86,8 @@ class BigQueryEngineSpec(BaseEngineSpec):
         # replace non-alphanumeric characters with underscores
         label_mutated = re.sub(r'[^\w]+', '_', label_mutated)
         if label_mutated != label:
-            # add md5 hash to label to avoid possible collisions
-            label_mutated += label_hashed
+            # add first 5 chars from md5 hash to label to avoid possible collisions
+            label_mutated += label_hashed[:6]
 
         return label_mutated
 
@@ -141,3 +141,34 @@ class BigQueryEngineSpec(BaseEngineSpec):
     @classmethod
     def epoch_ms_to_dttm(cls):
         return 'TIMESTAMP_MILLIS({col})'
+
+    @classmethod
+    def df_to_sql(cls, df: pd.DataFrame, **kwargs):
+        """
+        Upload data from a Pandas DataFrame to BigQuery. Calls
+        `DataFrame.to_gbq()` which requires `pandas_gbq` to be installed.
+
+        :param df: Dataframe with data to be uploaded
+        :param kwargs: kwargs to be passed to to_gbq() method. Requires both `schema
+        and ``name` to be present in kwargs, which are combined and passed to
+        `to_gbq()` as `destination_table`.
+        """
+        try:
+            import pandas_gbq
+        except ImportError:
+            raise Exception('Could not import the library `pandas_gbq`, which is '
+                            'required to be installed in your environment in order '
+                            'to upload data to BigQuery')
+
+        if not ('name' in kwargs and 'schema' in kwargs):
+            raise Exception('name and schema need to be defined in kwargs')
+        gbq_kwargs = {}
+        gbq_kwargs['project_id'] = kwargs['con'].engine.url.host
+        gbq_kwargs['destination_table'] = f"{kwargs.pop('schema')}.{kwargs.pop('name')}"
+
+        # Only pass through supported kwargs
+        supported_kwarg_keys = {'if_exists'}
+        for key in supported_kwarg_keys:
+            if key in kwargs:
+                gbq_kwargs[key] = kwargs[key]
+        pandas_gbq.to_gbq(df, **gbq_kwargs)
diff --git a/superset/db_engine_specs/hive.py b/superset/db_engine_specs/hive.py
index 301b132..4142745 100644
--- a/superset/db_engine_specs/hive.py
+++ b/superset/db_engine_specs/hive.py
@@ -94,8 +94,8 @@ class HiveEngineSpec(PrestoEngineSpec):
         except pyhive.exc.ProgrammingError:
             return []
 
-    @staticmethod
-    def create_table_from_csv(form, table):
+    @classmethod
+    def create_table_from_csv(cls, form, table):
         """Uploads a csv file and creates a superset datasource in Hive."""
         def convert_to_hive_type(col_type):
             """maps tableschema's types to hive types"""
diff --git a/tests/db_engine_specs_test.py b/tests/db_engine_specs_test.py
index cdc08cd..6acc8ba 100644
--- a/tests/db_engine_specs_test.py
+++ b/tests/db_engine_specs_test.py
@@ -702,15 +702,15 @@ class DbEngineSpecsTestCase(SupersetTestCase):
         self.assertEqual(label, label_expected)
 
         label = BigQueryEngineSpec.make_label_compatible(column('SUM(x)').name)
-        label_expected = 'SUM_x__5f110b965a993675bc4953bb3e03c4a5'
+        label_expected = 'SUM_x__5f110'
         self.assertEqual(label, label_expected)
 
         label = BigQueryEngineSpec.make_label_compatible(column('SUM[x]').name)
-        label_expected = 'SUM_x__7ebe14a3f9534aeee125449b0bc083a8'
+        label_expected = 'SUM_x__7ebe1'
         self.assertEqual(label, label_expected)
 
         label = BigQueryEngineSpec.make_label_compatible(column('12345_col').name)
-        label_expected = '_12345_col_8d3906e2ea99332eb185f7f8ecb2ffd6'
+        label_expected = '_12345_col_8d390'
         self.assertEqual(label, label_expected)
 
     def test_oracle_sqla_column_name_length_exceeded(self):


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