diff --git a/lib/python/.gitignore b/lib/python/.gitignore
index 1f4bb524a1c7dfe8ec62be60b755993e13f7dedc..b11bfe061cb8fd2c97c9195211a8ba08ed1ae0ee 100644
--- a/lib/python/.gitignore
+++ b/lib/python/.gitignore
@@ -7,6 +7,7 @@ dbrepo.egg-info/
build/
htmlcov/
tmp-*
+report.xml
# debug
debug.py
@@ -15,9 +16,8 @@ debug.py
.pypirc
# coverage
-coverage.txt
+coverage.*
.coverage
-report.xml
# environment
.env
diff --git a/lib/python/README.md b/lib/python/README.md
index 443787cbb4cdcb13d0e3ec522d0d9762262000e8..11506a7bf059630b65ed703d4674cde8cf3642e9 100644
--- a/lib/python/README.md
+++ b/lib/python/README.md
@@ -2,7 +2,7 @@
Official client library for [DBRepo](https://www.ifs.tuwien.ac.at/infrastructures/dbrepo/1.4.3/), a database
repository to support research based
-on [requests](https://pypi.org/project/requests/), [pydantic](https://pypi.org/project/pydantic/), [tuspy](https://pypi.org/project/tuspy/)
+on [requests](https://pypi.org/project/requests/), [pydantic](https://pypi.org/project/pydantic/)
and [pika](https://pypi.org/project/pika/).
## Installing
@@ -20,9 +20,11 @@ Get public data from a table as pandas `DataFrame`:
```python
from dbrepo.RestClient import RestClient
-client = RestClient(endpoint="https://dbrepo1.ec.tuwien.ac.at")
+client = RestClient(endpoint="https://test.dbrepo.tuwien.ac.at")
# Get a small data slice of just three rows
-df = client.get_table_data(database_id=7, table_id=13, page=0, size=3, df=True)
+df = client.get_table_data(database_id="e0d82287-9099-4077-8f69-3c19fc3bc145",
+ table_id="71f8c746-ea26-4651-b3f2-ce46830f1af4",
+ page=0, size=3)
print(df)
# x_coord component unit ... value stationid meantype
# 0 16.52617 Feinstaub (PM10) µg/m³ ... 21.0 01:0001 HMW
@@ -32,19 +34,23 @@ print(df)
# [3 rows x 12 columns]
```
-Import data into a table:
+Create table and import `DataFrame` into a table:
```python
import pandas as pd
from dbrepo.RestClient import RestClient
-client = RestClient(endpoint="https://dbrepo1.ec.tuwien.ac.at", username="foo",
+client = RestClient(endpoint="https://test.dbrepo.tuwien.ac.at", username="foo",
password="bar")
df = pd.DataFrame(data={'x_coord': 16.52617, 'component': 'Feinstaub (PM10)',
'unit': 'µg/m³', ...})
-client.import_table_data(database_id=7, table_id=13, file_name_or_data_frame=df)
+client.create_table(database_id="e0d82287-9099-4077-8f69-3c19fc3bc145",
+ name="Sensor", is_public=True, is_schema_public=True,
+ dataframe=df)
```
+... or just create the table schema by setting `create_table(..., withData=False)`.
+
## Supported Features & Best-Practices
- Manage user
@@ -76,7 +82,6 @@ AMQP_API_PORT="5672"
AMQP_API_USERNAME="foo"
AMQP_API_PASSWORD="bar"
AMQP_API_VIRTUAL_HOST="dbrepo"
-REST_UPLOAD_ENDPOINT="https://dbrepo1.ec.tuwien.ac.at/api/upload/files"
```
You can disable logging by setting the log level to e.g. `INFO`:
diff --git a/lib/python/coverage.xml b/lib/python/coverage.xml
deleted file mode 100644
index ac21b0bc1ed6b9f659ba578333c89e481c34ca8f..0000000000000000000000000000000000000000
--- a/lib/python/coverage.xml
+++ /dev/null
@@ -1,1866 +0,0 @@
-<?xml version="1.0" ?>
-<coverage version="7.6.10" timestamp="1740478405603" lines-valid="1820" lines-covered="1743" line-rate="0.9577" branches-covered="0" branches-valid="0" branch-rate="0" complexity="0">
- <!-- Generated by coverage.py: https://coverage.readthedocs.io/en/7.6.10 -->
- <!-- Based on https://raw.githubusercontent.com/cobertura/web/master/htdocs/xml/coverage-04.dtd -->
- <sources>
- <source>/home/mweise/Projects/fda-services/lib/python</source>
- </sources>
- <packages>
- <package name="dbrepo" line-rate="0.9134" branch-rate="0" complexity="0">
- <classes>
- <class name="RestClient.py" filename="dbrepo/RestClient.py" complexity="0" line-rate="0.9248" branch-rate="0">
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- </lines>
- </class>
- <class name="exceptions.py" filename="dbrepo/api/exceptions.py" complexity="0" line-rate="1" branch-rate="0">
- <methods/>
- <lines>
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- </lines>
- </class>
- </classes>
- </package>
- </packages>
-</coverage>
diff --git a/lib/python/dbrepo/RestClient.py b/lib/python/dbrepo/RestClient.py
index 9b043bd32faa64783d02406a78d4a81b57716711..f2a93151ecff15ece92618ddf30d9d7bfa0f1dcd 100644
--- a/lib/python/dbrepo/RestClient.py
+++ b/lib/python/dbrepo/RestClient.py
@@ -11,7 +11,7 @@ from dbrepo.api.dto import *
from dbrepo.api.exceptions import ResponseCodeError, NotExistsError, \
ForbiddenError, MalformedError, NameExistsError, QueryStoreError, ExternalSystemError, \
AuthenticationError, FormatNotAvailable, RequestError, ServiceError, ServiceConnectionError
-from dbrepo.api.mapper import query_to_subset
+from dbrepo.api.mapper import query_to_subset, dataframe_to_table_definition
logging.basicConfig(format='%(asctime)s %(name)-12s %(levelname)-6s %(message)s', level=logging.INFO,
stream=sys.stdout)
@@ -463,9 +463,8 @@ class RestClient:
raise ResponseCodeError(
f'Failed to update database schema: response code: {response.status_code} is not 200 (OK)')
- def create_table(self, database_id: str, name: str, is_public: bool, is_schema_public: bool,
- columns: List[CreateTableColumn], constraints: CreateTableConstraints,
- description: str = None) -> TableBrief:
+ def create_table(self, database_id: str, name: str, is_public: bool, is_schema_public: bool, dataframe: DataFrame,
+ description: str = None, with_data: bool = True) -> TableBrief:
"""
Updates the database owner of a database with given database id.
@@ -473,9 +472,9 @@ class RestClient:
:param name: The name of the created table.
:param is_public: The visibility of the data. If set to true the data will be publicly visible.
:param is_schema_public: The visibility of the schema metadata. If set to true the schema metadata will be publicly visible.
- :param constraints: The constraints of the created table.
- :param columns: The columns of the created table.
+ :param dataframe: The `pandas` dataframe.
:param description: The description of the created table. Optional.
+ :param with_data: If set to `True`, the data will be included in the new table. Optional. Default: `True`.
:returns: The table, if successful.
@@ -488,12 +487,18 @@ class RestClient:
:raises ResponseCodeError: If something went wrong with the creation.
"""
url = f'/api/database/{database_id}/table'
+ columns, constraints = dataframe_to_table_definition(dataframe)
response = self._wrapper(method="post", url=url, force_auth=True,
payload=CreateTable(name=name, is_public=is_public, is_schema_public=is_schema_public,
description=description, columns=columns, constraints=constraints))
if response.status_code == 201:
body = response.json()
- return TableBrief.model_validate(body)
+ table = TableBrief.model_validate(body)
+ if with_data:
+ self.import_table_data(database_id=database_id,
+ table_id=table.id,
+ dataframe=dataframe.reset_index())
+ return table
if response.status_code == 400:
raise MalformedError(f'Failed to create table: {response.text}')
if response.status_code == 403:
@@ -919,9 +924,9 @@ class RestClient:
:raises ResponseCodeError: If something went wrong with the insert.
"""
- url = f'/api/upload'
buffer = BytesIO()
- dataframe.to_csv(path_or_buf=buffer, header=False, index=False)
+ dataframe.to_csv(path_or_buf=buffer, header=True, index=False)
+ url = f'/api/upload'
response = self._wrapper(method="post", url=url, force_auth=True,
files={'file': ('dataframe.csv', buffer.getvalue())})
if response.status_code == 201:
@@ -949,8 +954,8 @@ class RestClient:
url = f'/api/database/{database_id}/table/{table_id}/data/import'
response = self._wrapper(method="post", url=url, force_auth=True,
- payload=Import(location=self._upload(dataframe), separator=',', quote='"',
- header=True, line_termination='\n'))
+ payload=Import(location=self._upload(dataframe), separator=',', quote='"', header=True,
+ line_termination='\n'))
if response.status_code == 202:
return
if response.status_code == 400:
@@ -1354,7 +1359,7 @@ class RestClient:
payload=subset)
if response.status_code == 201:
logging.info(f'Created subset with id: {response.headers["X-Id"]}')
- return DataFrame.from_records(response.json())
+ return DataFrame.from_records(response.json(), columns=query.columns)
if response.status_code == 400:
raise MalformedError(f'Failed to create subset: {response.text}')
if response.status_code == 403:
diff --git a/lib/python/dbrepo/api/mapper.py b/lib/python/dbrepo/api/mapper.py
index c062b29923f17f18f8a9d21f5c1913df2b3bb3d4..bede7b38384dae549fed119c9794b96c6aa0c921 100644
--- a/lib/python/dbrepo/api/mapper.py
+++ b/lib/python/dbrepo/api/mapper.py
@@ -1,4 +1,11 @@
-from dbrepo.api.dto import Subset, QueryDefinition, Database, Table, Image, Filter, Order
+import logging
+
+import pandas
+from numpy import dtype
+from pandas import DataFrame, Series
+
+from dbrepo.api.dto import Subset, QueryDefinition, Database, Table, Image, Filter, Order, CreateTableColumn, \
+ CreateTableConstraints, ColumnType
from dbrepo.api.exceptions import MalformedError
@@ -28,7 +35,7 @@ def query_to_subset(database: Database, image: Image, query: QueryDefinition) ->
column_id=filter_column_ids[0],
operator_id=filter_ops_ids[0],
value=filter.value))
- order = None
+ orders = []
if query.order is not None:
for order in query.order:
# column_id
@@ -36,5 +43,80 @@ def query_to_subset(database: Database, image: Image, query: QueryDefinition) ->
column.internal_name == order.column]
if len(order_column_ids) != 1:
raise MalformedError(f'Failed to create view: order column name not found in database')
- order.append(Order(column_id=order_column_ids[0].id, direction=order.direction))
- return Subset(table_id=tables[0].id, columns=filtered_column_ids, filter=filters, order=order)
+ orders.append(Order(column_id=order_column_ids[0], direction=order.direction))
+ return Subset(table_id=tables[0].id, columns=filtered_column_ids, filter=filters, order=orders)
+
+
+def dataframe_to_table_definition(dataframe: DataFrame) -> ([CreateTableColumn], CreateTableConstraints):
+ if dataframe.index.name is None:
+ raise MalformedError(f'Failed to map dataframe: index not set')
+ constraints = CreateTableConstraints(uniques=[],
+ checks=[],
+ foreign_keys=[],
+ primary_key=dataframe.index.names)
+ dataframe = dataframe.reset_index()
+ columns = []
+ for name, series in dataframe.items():
+ column = CreateTableColumn(name=str(name),
+ type=ColumnType.TEXT,
+ null_allowed=contains_null(dataframe[name]))
+ if series.dtype == dtype('float64'):
+ if pandas.to_numeric(dataframe[name], errors='coerce').notnull().all():
+ logging.debug(f"mapped column {name} from float64 to decimal")
+ column.type = ColumnType.DECIMAL
+ column.size = 40
+ column.d = 20
+ else:
+ logging.debug(f"mapped column {name} from float64 to text")
+ column.type = ColumnType.TEXT
+ elif series.dtype == dtype('int64'):
+ min_val = min(dataframe[name])
+ max_val = max(dataframe[name])
+ if 0 <= min_val <= 1 and 0 <= max_val <= 1 and 'id' not in name:
+ logging.debug(f"mapped column {name} from int64 to bool")
+ column.type = ColumnType.BOOL
+ columns.append(column)
+ continue
+ logging.debug(f"mapped column {name} from int64 to bigint")
+ column.type = ColumnType.BIGINT
+ elif series.dtype == dtype('O'):
+ try:
+ pandas.to_datetime(dataframe[name], format='mixed')
+ if dataframe[name].str.contains(':').any():
+ logging.debug(f"mapped column {name} from O to timestamp")
+ column.type = ColumnType.TIMESTAMP
+ columns.append(column)
+ continue
+ logging.debug(f"mapped column {name} from O to date")
+ column.type = ColumnType.DATE
+ columns.append(column)
+ continue
+ except ValueError:
+ pass
+ max_size = max(dataframe[name].astype(str).map(len))
+ if max_size <= 1:
+ logging.debug(f"mapped column {name} from O to char")
+ column.type = ColumnType.CHAR
+ column.size = 1
+ if 0 <= max_size <= 255:
+ logging.debug(f"mapped column {name} from O to varchar")
+ column.type = ColumnType.VARCHAR
+ column.size = 255
+ else:
+ logging.debug(f"mapped column {name} from O to text")
+ column.type = ColumnType.TEXT
+ elif series.dtype == dtype('bool'):
+ logging.debug(f"mapped column {name} from bool to bool")
+ column.type = ColumnType.BOOL
+ elif series.dtype == dtype('datetime64'):
+ logging.debug(f"mapped column {name} from datetime64 to datetime")
+ column.type = ColumnType.DATETIME
+ else:
+ logging.warning(f'default to \'text\' for column {name} and type {dtype}')
+ columns.append(column)
+ return columns, constraints
+
+def contains_null(dataframe: DataFrame) -> bool:
+ if '\\N' in dataframe.values:
+ return True
+ return dataframe.isnull().values.any()
diff --git a/lib/python/tests/test_unit_query.py b/lib/python/tests/test_unit_query.py
index 44f165b9b0ba36ab2375ddcd78c6c50cd363c7d9..528d6775a7e3b84a3afdceb68344518d234ba21d 100644
--- a/lib/python/tests/test_unit_query.py
+++ b/lib/python/tests/test_unit_query.py
@@ -93,14 +93,14 @@ class QueryUnitTest(unittest.TestCase):
def test_create_subset_succeeds(self):
with requests_mock.Mocker() as mock:
exp = [{'id': 1, 'username': 'foo'}, {'id': 2, 'username': 'bar'}]
- df = DataFrame.from_records(json.dumps(exp))
+ df = DataFrame.from_records(exp)
# mock
mock.get(f'/api/image/{self.image.id}', json=self.image.model_dump(),
status_code=200)
mock.get(f'/api/database/{self.database.id}', json=self.database.model_dump(),
status_code=200)
- mock.post(f'/api/database/{self.database.id}/subset', json=json.dumps(exp),
- headers={'X-Id': '1'}, status_code=201)
+ mock.post(f'/api/database/{self.database.id}/subset', json=exp,
+ headers={'X-Id': '85bc1217-29ab-4c09-9f98-8c019238a9c8'}, status_code=201)
# test
client = RestClient(username="a", password="b")
response = client.create_subset(database_id="6bd39359-b154-456d-b9c2-caa516a45732", page=0, size=10,
@@ -263,14 +263,14 @@ class QueryUnitTest(unittest.TestCase):
def test_create_subset_anonymous_succeeds(self):
with requests_mock.Mocker() as mock:
exp = [{'id': 1, 'username': 'foo'}, {'id': 2, 'username': 'bar'}]
- df = DataFrame.from_records(json.dumps(exp))
+ df = DataFrame.from_records(exp)
# mock
mock.get(f'/api/image/{self.image.id}', json=self.image.model_dump(),
status_code=200)
mock.get(f'/api/database/{self.database.id}', json=self.database.model_dump(),
status_code=200)
- mock.post(f'/api/database/{self.database.id}/subset', json=json.dumps(exp),
- headers={'X-Id': '1'}, status_code=201)
+ mock.post(f'/api/database/{self.database.id}/subset', json=exp,
+ headers={'X-Id': '85bc1217-29ab-4c09-9f98-8c019238a9c8'}, status_code=201)
# test
client = RestClient()
diff --git a/lib/python/tests/test_unit_table.py b/lib/python/tests/test_unit_table.py
index a5632f4237f2ab9a34b111e5168cebe7fc084ef6..c67b54c6144016df23a85fc6bb8fe8c46b9a0565 100644
--- a/lib/python/tests/test_unit_table.py
+++ b/lib/python/tests/test_unit_table.py
@@ -6,7 +6,7 @@ import requests_mock
from pandas import DataFrame
from dbrepo.RestClient import RestClient
-from dbrepo.api.dto import Table, CreateTableConstraints, Column, Constraints, ColumnType, ConceptBrief, UnitBrief, \
+from dbrepo.api.dto import Table, Column, Constraints, ColumnType, ConceptBrief, UnitBrief, \
TableStatistics, ColumnStatistic, PrimaryKey, ColumnBrief, TableBrief, UserBrief, History, HistoryEventType
from dbrepo.api.exceptions import MalformedError, ForbiddenError, NotExistsError, NameExistsError, \
AuthenticationError, ExternalSystemError, ServiceError, ServiceConnectionError, ResponseCodeError
@@ -25,125 +25,137 @@ class TableUnitTest(unittest.TestCase):
is_public=True,
is_schema_public=True)
with requests_mock.Mocker() as mock:
+ dataframe = DataFrame.from_records([{'id': 1, 'name': 'foobar'}], index=['id'])
# mock
mock.post('/api/database/6bd39359-b154-456d-b9c2-caa516a45732/table', json=exp.model_dump(),
status_code=201)
# test
client = RestClient(username="a", password="b")
response = client.create_table(database_id="6bd39359-b154-456d-b9c2-caa516a45732", name="Test",
- description="Test Table", columns=[],
- is_public=True, is_schema_public=True,
- constraints=CreateTableConstraints())
+ description="Test Table", dataframe=dataframe, with_data=False,
+ is_public=True, is_schema_public=True)
self.assertEqual(exp, response)
+ def test_create_table_index_missing_fails(self):
+ with requests_mock.Mocker() as mock:
+ dataframe = DataFrame.from_records([{'id': 1, 'name': 'foobar'}])
+ # test
+ client = RestClient(username="a", password="b")
+ try:
+ client.create_table(database_id="6bd39359-b154-456d-b9c2-caa516a45732", name="Test",
+ description="Test Table", dataframe=dataframe, with_data=False,
+ is_public=True, is_schema_public=True)
+ except MalformedError:
+ pass
+
def test_create_table_400_fails(self):
with requests_mock.Mocker() as mock:
+ dataframe = DataFrame.from_records([{'id': 1, 'name': 'foobar'}], index=['id'])
# mock
mock.post('/api/database/6bd39359-b154-456d-b9c2-caa516a45732/table', status_code=400)
# test
try:
client = RestClient(username="a", password="b")
response = client.create_table(database_id="6bd39359-b154-456d-b9c2-caa516a45732", name="Test",
- description="Test Table", columns=[],
- is_public=True, is_schema_public=True,
- constraints=CreateTableConstraints())
+ description="Test Table", dataframe=dataframe,
+ is_public=True, is_schema_public=True)
except MalformedError:
pass
def test_create_table_403_fails(self):
with requests_mock.Mocker() as mock:
+ dataframe = DataFrame.from_records([{'id': 1, 'name': 'foobar'}], index=['id'])
# mock
mock.post('/api/database/6bd39359-b154-456d-b9c2-caa516a45732/table', status_code=403)
# test
try:
RestClient(username="a", password="b").create_table(database_id="6bd39359-b154-456d-b9c2-caa516a45732",
name="Test",
- description="Test Table", columns=[],
- is_public=True, is_schema_public=True,
- constraints=CreateTableConstraints())
+ description="Test Table", dataframe=dataframe,
+ is_public=True, is_schema_public=True)
except ForbiddenError:
pass
def test_create_table_404_fails(self):
with requests_mock.Mocker() as mock:
+ dataframe = DataFrame.from_records([{'id': 1, 'name': 'foobar'}], index=['id'])
# mock
mock.post('/api/database/6bd39359-b154-456d-b9c2-caa516a45732/table', status_code=404)
# test
try:
client = RestClient(username="a", password="b")
response = client.create_table(database_id="6bd39359-b154-456d-b9c2-caa516a45732", name="Test",
- description="Test Table", columns=[],
- is_public=True, is_schema_public=True,
- constraints=CreateTableConstraints())
+ description="Test Table", dataframe=dataframe,
+ is_public=True, is_schema_public=True)
except NotExistsError:
pass
def test_create_table_409_fails(self):
with requests_mock.Mocker() as mock:
+ dataframe = DataFrame.from_records([{'id': 1, 'name': 'foobar'}], index=['id'])
# mock
mock.post('/api/database/6bd39359-b154-456d-b9c2-caa516a45732/table', status_code=409)
# test
try:
client = RestClient(username="a", password="b")
response = client.create_table(database_id="6bd39359-b154-456d-b9c2-caa516a45732", name="Test",
- description="Test Table", columns=[],
- is_public=True, is_schema_public=True,
- constraints=CreateTableConstraints())
+ description="Test Table", dataframe=dataframe,
+ is_public=True, is_schema_public=True)
except NameExistsError:
pass
def test_create_table_502_fails(self):
with requests_mock.Mocker() as mock:
+ dataframe = DataFrame.from_records([{'id': 1, 'name': 'foobar'}], index=['id'])
# mock
mock.post('/api/database/6bd39359-b154-456d-b9c2-caa516a45732/table', status_code=502)
# test
try:
client = RestClient(username="a", password="b")
response = client.create_table(database_id="6bd39359-b154-456d-b9c2-caa516a45732", name="Test",
- description="Test Table", columns=[],
- is_public=True, is_schema_public=True,
- constraints=CreateTableConstraints())
+ description="Test Table", dataframe=dataframe,
+ is_public=True, is_schema_public=True)
except ServiceConnectionError:
pass
def test_create_table_503_fails(self):
with requests_mock.Mocker() as mock:
+ dataframe = DataFrame.from_records([{'id': 1, 'name': 'foobar'}], index=['id'])
# mock
mock.post('/api/database/6bd39359-b154-456d-b9c2-caa516a45732/table', status_code=503)
# test
try:
client = RestClient(username="a", password="b")
response = client.create_table(database_id="6bd39359-b154-456d-b9c2-caa516a45732", name="Test",
- description="Test Table", columns=[],
- is_public=True, is_schema_public=True,
- constraints=CreateTableConstraints())
+ description="Test Table", dataframe=dataframe,
+ is_public=True, is_schema_public=True)
except ServiceError:
pass
def test_create_table_unknown_fails(self):
with requests_mock.Mocker() as mock:
+ dataframe = DataFrame.from_records([{'id': 1, 'name': 'foobar'}], index=['id'])
# mock
mock.post('/api/database/6bd39359-b154-456d-b9c2-caa516a45732/table', status_code=200)
# test
try:
client = RestClient(username="a", password="b")
response = client.create_table(database_id="6bd39359-b154-456d-b9c2-caa516a45732", name="Test",
- description="Test Table", columns=[],
- is_public=True, is_schema_public=True,
- constraints=CreateTableConstraints())
+ description="Test Table", dataframe=dataframe,
+ is_public=True, is_schema_public=True)
except ResponseCodeError:
pass
def test_create_table_anonymous_fails(self):
with requests_mock.Mocker() as mock:
+ dataframe = DataFrame.from_records([{'id': 1, 'name': 'foobar'}], index=['id'])
# mock
mock.post('/api/database/6bd39359-b154-456d-b9c2-caa516a45732/table', status_code=409)
# test
try:
response = RestClient().create_table(database_id="6bd39359-b154-456d-b9c2-caa516a45732", name="Test",
- description="Test Table", columns=[],
- is_public=True, is_schema_public=True,
- constraints=CreateTableConstraints())
+ description="Test Table", dataframe=dataframe,
+ is_public=True, is_schema_public=True)
except AuthenticationError:
pass