Compare commits

...
22 Commits
Author SHA1 Message Date
Ruslan Kuprieiev e18fd34b2c testing: bench: use --dataset instead of --size (#10134)
This is no longer just about size (e.g. we have mnist/openorca/used-cars),
so the --dataset makes more sense.
2023-12-04 14:43:37 +02:00
Ruslan Kuprieiev c0b64b0a10 testing: bench: add openorca (#10133)
Need to move the data into dvc at some point.
2023-12-04 12:43:50 +02:00
Ruslan Kuprieievandpre-commit-ci[bot] 3927e75ef1 testing: bench: add pytest_report_header (#10132)
* testing: bench: add pytest_report_header

Useful for sanity checks in logs.

* Update dvc/testing/benchmarks/plugin.py

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2023-12-04 11:23:12 +02:00
skshetry e5ae5ef24b add security-extend to codeql queries (#10131) 2023-12-04 13:29:29 +05:45
skshetry e187508f40 database: fix ui issues (#10129) 2023-12-04 13:27:05 +05:45
skshetry 8768b50aed experimental: support connection strings for databases (#10125)
* experimental: support connection strings for databases using connectorx

This adds an experimental support for connector strings using connectorx.

User has to provide config for the connection strings with:

Example:
```console
dvc config --local db_connection.pg postgres://user:pass@localhost:5432/database
```

And then, they can import using:
```console
dvc import-db --sql 'query' --conn pg
```

Check supported databases and how to configure in https://sfu-db.github.io/connector-x/databases.html.
This `db_connection` config is subject to change.

connectorx still has the same problem with dbt as before: no support for streaming,
but it'll be a bit more simpler to configure with the connection strings.

* add pandas to deps

* sqlalchemy

* dbt streaming sql

* fix test

* remove connectorx

* remove check in set

* use mode='wb' for serialization
2023-12-03 19:23:09 +05:45
skshetry 7c61463d2d tests: do not setup pytest plugin entrypoint (#10121)
We should not register a pytest plugin automaticallly, as we may
have fixtures that might override user's fixtures. Also, it might
raise import errors as in https://github.com/iterative/dvc/issues/10118.

We can still use this as a plugin ourselves by setting the following
in `conftest.py` file.
```python
pytest_plugins = ['dvc.testing.plugin']
```
2023-11-29 12:05:46 +05:45
Peter Rowlands b0d0315689 import/get: support pre-fetching LFS objects from Git-LFS repos 2023-11-29 14:39:54 +09:00
Peter Rowlands 7edcb6b1e5 deps: bump scmrepo minver to 1.5.0 2023-11-29 14:39:54 +09:00
Ruslan Kuprieiev b6d231f9cf testing: import virtualenv lazily
Fixes https://github.com/iterative/dvc/issues/10118
2023-11-28 22:20:34 +02:00
Ruslan Kuprieiev 322fcec5ca bench: test_sharing: use fetch instead of pull 2023-11-28 19:31:32 +02:00
Ruslan Kuprieiev 1e5b3603cc bench: test fetch instead of pull
`pull` is literally `fetch` + `checkout` and our main interest there is downloading, so let's just test fetch instead.
2023-11-28 19:31:32 +02:00
Ruslan Kuprieiev ffa630e8d5 push: handle missing/failed version_aware file
Previously we used recorded index which had stub entries
for missing/failed outputs, but now we actually collect
everything ourselves and those are missing.
2023-11-28 18:52:46 +02:00
Ruslan Kuprieiev 1e9b60dc48 deps: bump dvc-data to >=2.22.1 2023-11-27 16:17:42 +02:00
skshetry 83dd2b2a7b test: import-db: test for external model (#10112)
* test: import-db: test for external model

* close repo
2023-11-27 16:13:44 +05:45
Ivan Shcheklein d238350a2d fix(config): respect global config env variable 2023-11-23 20:51:52 +02:00
skshetry 06b9196371 pytest.ini_options: add --benchmark-skip to suppress pytest-benchmark warning with xdist (#10106)
We don't run benchmarks here, and benchmarking should always be a separate command than regular test run.
2023-11-23 19:55:23 +05:45
skshetry b4f42242c9 tmp_dir: fix object initialization for Python 3.12 (#10105) 2023-11-23 16:00:30 +05:45
skshetryandpre-commit-ci[bot] fbdb566079 remove pytest-virtualenv (#10103)
* remove pytest-virtualenv

It does not look like it's being actively maintained.

* force virtualenv

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
2023-11-23 14:53:39 +05:45
skshetry 3d7bbb8492 tests: add functional test for db (#10101)
* tests: add functional test for db

* fix test
2023-11-22 16:15:07 +05:45
skshetry fd7c891217 implement import-db command (#10040)
* implement import-db command

* generate .dvc file

* update

* fix tests

* pin dbt-fal

* try to run on ci

* use os.chdir

* fix

* revert

* require dbt-core>=1.5

* add db config schema

* remove platformdirs constraints

* use logger.getChild

* improve error messaging

* rename cli flag --export-format to --output-format

* use feature flag for db config

* hide command from dvc commands list

* refactor dependency._get

* remove todo

* refactor dependency._get

* fix dbt installation check
2023-11-21 19:38:50 +05:45
Ruslan Kuprieiev 2b3b15f767 deps: bump dvc-data to 2.22.0
Related https://github.com/iterative/dvc/issues/10059
2023-11-17 20:01:57 +02:00
44 changed files with 1593 additions and 96 deletions
+1
View File
@@ -34,6 +34,7 @@ jobs:
uses: github/codeql-action/init@v2
with:
languages: ${{ matrix.language }}
queries: security-extended
- name: Perform CodeQL Analysis
uses: github/codeql-action/analyze@v2
+2
View File
@@ -26,6 +26,7 @@ from dvc.commands import (
get_url,
git_hook,
imp,
imp_db,
imp_url,
init,
install,
@@ -65,6 +66,7 @@ COMMANDS = [
data_sync,
gc,
imp,
imp_db,
imp_url,
config,
checkout,
+21 -19
View File
@@ -1,6 +1,8 @@
import argparse
import os
from funcy import set_in
from dvc.cli.command import CmdBaseNoRepo
from dvc.cli.utils import append_doc_link
from dvc.log import logger
@@ -8,7 +10,7 @@ from dvc.ui import ui
logger = logger.getChild(__name__)
NAME_REGEX = r"^(?P<remote>remote\.)?(?P<section>[^\.]*)\.(?P<option>[^\.]*)$"
NAME_REGEX = r"^(?P<top>(remote|db)\.)?(?P<section>[^\.]*)\.(?P<option>[^\.]*)$"
def _name_type(value):
@@ -17,10 +19,12 @@ def _name_type(value):
match = re.match(NAME_REGEX, value)
if not match:
raise argparse.ArgumentTypeError(
"name argument should look like remote.name.option or section.option"
"name argument should look like remote.name.option or "
"db.name.option or section.option"
)
top = match.group("top")
return (
bool(match.group("remote")),
top.strip(".") if top else None,
match.group("section").lower(),
match.group("option").lower(),
)
@@ -49,12 +53,11 @@ class CmdConfig(CmdBaseNoRepo):
logger.error("name argument is required")
return 1
remote, section, opt = self.args.name
remote_or_db, section, opt = self.args.name
if self.args.value is None and not self.args.unset:
return self._get(remote, section, opt)
return self._set(remote, section, opt)
return self._get(remote_or_db, section, opt)
return self._set(remote_or_db, section, opt)
def _list(self):
if any((self.args.name, self.args.value, self.args.unset)):
@@ -75,18 +78,18 @@ class CmdConfig(CmdBaseNoRepo):
return 0
def _get(self, remote, section, opt):
def _get(self, remote_or_db, section, opt):
from dvc.config import ConfigError
levels = self._get_appropriate_levels(self.args.level)[::-1]
for level in levels:
conf = self.config.read(level)
if remote:
conf = conf["remote"]
if remote_or_db:
conf = conf[remote_or_db]
try:
self._check(conf, remote, section, opt)
self._check(conf, remote_or_db, section, opt)
except ConfigError:
if self.args.level:
raise
@@ -99,16 +102,15 @@ class CmdConfig(CmdBaseNoRepo):
return 0
def _set(self, remote, section, opt):
def _set(self, remote_or_db, section, opt):
with self.config.edit(self.args.level) as conf:
if remote:
conf = conf["remote"]
if remote_or_db:
conf = conf[remote_or_db]
if self.args.unset:
self._check(conf, remote, section, opt)
self._check(conf, remote_or_db, section, opt)
del conf[section][opt]
else:
self._check(conf, remote, section)
conf[section][opt] = self.args.value
conf.update(set_in(conf, [section, opt], self.args.value))
if self.args.name == "cache.type":
logger.warning(
@@ -119,10 +121,10 @@ class CmdConfig(CmdBaseNoRepo):
return 0
def _check(self, conf, remote, section, opt=None):
def _check(self, conf, remote_or_db, section, opt=None):
from dvc.config import ConfigError
name = "remote" if remote else "section"
name = remote_or_db or "section"
if section not in conf:
raise ConfigError(f"{name} '{section}' doesn't exist")
+167
View File
@@ -0,0 +1,167 @@
import argparse
from funcy import compact, merge
from dvc.cli import completion
from dvc.cli.command import CmdBase
from dvc.cli.utils import append_doc_link
from dvc.log import logger
from dvc.ui import ui
logger = logger.getChild(__name__)
class CmdTestDb(CmdBase):
def run(self):
from dvc.database import get_adapter
from dvc.database.dbt_utils import DBT_PROJECT_FILE, is_dbt_project
from dvc.dependency.db import _get_dbt_config
from dvc.exceptions import DvcException
connection = self.args.connection
db_config = self.repo.config.get("db", {})
config = db_config.get(connection, {})
if connection and not config:
raise DvcException(f"connection {connection} not found in config")
cli_config = compact(
{
"url": self.args.url,
"username": self.args.username,
"password": self.args.password,
}
)
conn_config = merge(config, cli_config)
cli_dbt_config = {"profile": self.args.profile, "target": self.args.target}
dbt_config = merge(_get_dbt_config(self.repo.config), cli_dbt_config)
project_dir = self.repo.root_dir
if not (conn_config or dbt_config):
if is_dbt_project(project_dir):
ui.write("Using", DBT_PROJECT_FILE, "for testing", styled=True)
else:
raise DvcException(
f"no config set and {DBT_PROJECT_FILE} is missing; "
"provide arguments or set a configuration"
)
adapter = get_adapter(conn_config, project_dir=project_dir, **dbt_config)
with adapter as db:
ui.write(f"Testing with {db}", styled=True)
creds = getattr(db, "creds", {})
for k, v in creds.items():
ui.write("\t", f"{k}:", v, styled=True)
if creds:
ui.write()
db.test_connection()
ui.write("Connection successful", styled=True)
class CmdImportDb(CmdBase):
def run(self):
if not (self.args.sql or self.args.model):
raise argparse.ArgumentTypeError("Either of --sql or --model is required.")
self.repo.imp_db(
url=self.args.url,
rev=self.args.rev,
project_dir=self.args.project_dir,
sql=self.args.sql,
model=self.args.model,
profile=self.args.profile,
target=self.args.target,
output_format=self.args.output_format,
out=self.args.out,
force=self.args.force,
connection=self.args.connection,
)
return 0
def add_parser(subparsers, parent_parser):
IMPORT_HELP = (
"Download file or directory tracked by DVC or by Git "
"into the workspace, and track it."
)
import_parser = subparsers.add_parser(
"import-db",
parents=[parent_parser],
description=append_doc_link(IMPORT_HELP, "import"),
add_help=False,
)
import_parser.add_argument(
"--url", help="Location of DVC or Git repository to download from"
)
import_parser.add_argument(
"--rev",
nargs="?",
help="Git revision (e.g. SHA, branch, tag)",
metavar="<commit>",
)
import_parser.add_argument(
"--project-dir", nargs="?", help="Subdirectory to the dbt project location"
)
group = import_parser.add_mutually_exclusive_group()
group.add_argument(
"--sql",
help="SQL query",
)
group.add_argument(
"--model",
help="Model name to download",
)
import_parser.add_argument("--profile", help="Profile to use")
import_parser.add_argument("--target", help="Target to use")
import_parser.add_argument(
"--output-format",
default="csv",
const="csv",
nargs="?",
choices=["csv", "json"],
help="Export format",
)
import_parser.add_argument(
"-o",
"--out",
nargs="?",
help="Destination path to download files to",
metavar="<path>",
).complete = completion.FILE
import_parser.add_argument(
"-f",
"--force",
action="store_true",
default=False,
help="Override destination file or folder if exists.",
)
import_parser.add_argument(
"--conn",
dest="connection",
nargs="?",
help="Database connection to use, needs to be set in config",
)
import_parser.set_defaults(func=CmdImportDb)
TEST_DB_HELP = "Test the database connection"
test_db_parser = subparsers.add_parser(
"test-db",
parents=[parent_parser],
description=append_doc_link(TEST_DB_HELP, "test-db"),
add_help=False,
)
test_db_parser.add_argument("--conn", dest="connection")
test_db_parser.add_argument("--url")
test_db_parser.add_argument("--password")
test_db_parser.add_argument("--username")
test_db_parser.add_argument("--profile")
test_db_parser.add_argument("--target")
test_db_parser.set_defaults(func=CmdTestDb)
+3 -3
View File
@@ -390,10 +390,10 @@ class Config(dict):
def _parse_named(conf):
result: Dict[str, Dict] = {"remote": {}, "machine": {}}
result: Dict[str, Dict] = {"remote": {}, "machine": {}, "db": {}}
for section, val in conf.items():
match = re_find(r'^\s*(remote|machine)\s*"(.*)"\s*$', section)
match = re_find(r'^\s*(remote|machine|db)\s*"(.*)"\s*$', section)
if match:
key, name = match
result[key][name] = val
@@ -408,7 +408,7 @@ def _pack_named(conf):
result = compact(conf)
# Transform remote.name -> 'remote "name"'
for key in ("remote", "machine"):
for key in ("remote", "machine", "db"):
for name, val in conf[key].items():
result[f'{key} "{name}"'] = val
result.pop(key, None)
+9
View File
@@ -318,6 +318,8 @@ SCHEMA = {
"feature": FeatureSchema(
{
Optional("machine", default=False): Bool,
"dbt_profile": str,
"dbt_target": str,
},
),
"plots": {
@@ -350,4 +352,11 @@ SCHEMA = {
"repo_url": str,
Optional("offline", default=False): Bool,
},
"db": {
str: {
"url": str,
"username": str,
"password": str,
},
},
}
+22
View File
@@ -0,0 +1,22 @@
from typing import Any, ContextManager, Optional, Union
from . import dbt_query, sqla
from .dbt_models import get_model
from .serializer import export
Adapter = Union[sqla.SQLAlchemyAdapter, dbt_query.DbtAdapter]
def get_adapter(
config,
project_dir: Optional[str] = None,
profile: Optional[str] = None,
target: Optional[str] = None,
**kwargs: Any,
) -> "ContextManager[Adapter]":
if config:
return sqla.adapter(config, **kwargs)
return dbt_query.adapter(project_dir=project_dir, profile=profile, target=target)
__all__ = ["export", "get_adapter", "get_model", "Adapter"]
+40
View File
@@ -0,0 +1,40 @@
from typing import List, Optional
from dvc.log import logger
from .dbt_runner import dbt_show
from .dbt_utils import check_dbt
from .serializer import AgateSerializer
logger = logger.getChild(__name__)
def ref(
name: str,
package: Optional[str] = None,
version: Optional[int] = None,
) -> str:
parts: List[str] = []
if package:
parts.append(repr(package))
parts.append(repr(name))
if version:
parts.append(f"{version=}")
inner = ",".join(parts)
return "{{ ref(" + inner + ") }}"
@check_dbt("model")
def get_model(
name: str,
package: Optional[str] = None,
version: Optional[int] = None,
profile: Optional[str] = None,
target: Optional[str] = None,
) -> AgateSerializer:
model = ref(name, package, version=version)
q = f"select * from {model}" # noqa: S608
table = dbt_show(inline=q, profile=profile, target=target)
return AgateSerializer(table)
+88
View File
@@ -0,0 +1,88 @@
import os
from contextlib import contextmanager
from typing import TYPE_CHECKING, Any, Callable, Dict, Iterator, Optional, Union
from attrs import define, field
from dvc.exceptions import DvcException
from dvc.log import logger
from .dbt_utils import check_dbt
from .serializer import AgateSerializer, PandasSQLSerializer
if TYPE_CHECKING:
from dbt.adapters.base.impl import BaseAdapter
logger = logger.getChild(__name__)
@define
class DbtAdapter:
adapter: "BaseAdapter" = field(repr=lambda o: type(o).__qualname__)
creds: Dict[str, Any] = field(repr=False)
@contextmanager
def query(self, sql: str) -> Iterator[Union[AgateSerializer, PandasSQLSerializer]]:
from dbt.adapters.sql import SQLAdapter
with self.adapter.connection_named("execute"):
if isinstance(self.adapter, SQLAdapter):
# try to use connection to stream results
# otherwise fallback to fetch all at once
try:
connection = self.adapter.connections.get_thread_connection().handle
except Exception: # noqa: BLE001
logger.debug("", exc_info=True)
else:
# pandas raises warning that it does not support
# dbapi2-based raw connection, but it does seem to work.
yield PandasSQLSerializer(sql, connection)
return
_, table = self.adapter.execute(sql, fetch=True)
yield AgateSerializer(table)
def test_connection(self, onerror: Optional[Callable[[], Any]] = None) -> None:
with self.adapter.connection_named("debug"):
try:
self.adapter.debug_query()
except Exception as exc:
if callable(onerror):
onerror()
logger.exception(
"dvc was unable to connect to the specified database. "
"Please check your database credentials and try again.",
exc_info=False,
)
raise DvcException("The database returned the following error") from exc
@contextmanager
@check_dbt("query")
def adapter(
project_dir: Optional[str] = None,
profiles_dir: Optional[str] = None,
profile: Optional[str] = None,
target: Optional[str] = None,
) -> Iterator["DbtAdapter"]:
from dbt.adapters import factory as adapters_factory
from dbt.adapters.base.impl import BaseAdapter
from .dbt_utils import get_or_build_profile, get_profiles_dir, init_dbt
profiles_dir = profiles_dir or get_profiles_dir(project_dir)
flags = init_dbt(profiles_dir, os.getcwd(), target=target)
with flags, adapters_factory.adapter_management():
# likely invalid connection profile or no adapter
profile_obj = get_or_build_profile(project_dir, profile, target)
adapters_factory.register_adapter(profile_obj) # type: ignore[arg-type]
adapter = adapters_factory.get_adapter(profile_obj) # type: ignore[arg-type]
assert isinstance(adapter, BaseAdapter)
try:
creds = dict(profile_obj.credentials.connection_info())
except: # noqa: E722
creds = {}
yield DbtAdapter(adapter, creds)
+61
View File
@@ -0,0 +1,61 @@
from typing import TYPE_CHECKING, List, Optional, Sequence, Union
from dvc.exceptions import DvcException
from dvc.log import logger
if TYPE_CHECKING:
from agate import Table
from dbt.contracts.results import RunResult
logger = logger.getChild(__name__)
class DbtInternalError(DvcException):
pass
def _kw_to_cmd_args(**kwargs: Union[None, bool, str, int]) -> List[str]:
args: List[str] = []
for key, value in kwargs.items():
key = key.replace("_", "-")
if value is None:
continue # skip creating a flag in this case
if value is True:
args.append(f"--{key}")
elif value is False:
args.append(f"--no-{key}")
else:
args.extend([f"--{key}", str(value)])
return args
def _dbt_invoke(*posargs: str, quiet: bool = True, **kw: Union[None, bool, str, int]):
from dbt.cli.main import dbtRunner
args = _kw_to_cmd_args(quiet=quiet or None) # global options
args.extend([*posargs, *_kw_to_cmd_args(**kw)])
runner = dbtRunner()
result = runner.invoke(args)
if result.success:
return result.result
raise DbtInternalError(f"failed to run dbt {posargs[0]}") from result.exception
def dbt_show(
inline: Optional[str] = None,
limit: int = -1,
profile: Optional[str] = None,
target: Optional[str] = None,
) -> "Table":
from dbt.contracts.results import RunExecutionResult
result = _dbt_invoke(
"show", inline=inline, limit=limit, profile=profile, target=target
)
assert isinstance(result, RunExecutionResult)
run_results: Sequence["RunResult"] = result.results
run_result, *_ = run_results
assert run_result.agate_table is not None
return run_result.agate_table
+100
View File
@@ -0,0 +1,100 @@
import os
from contextlib import contextmanager
from importlib.util import find_spec
from typing import TYPE_CHECKING, Optional
from funcy import cut_prefix
from dvc.exceptions import DvcException
from dvc.log import logger
from dvc.utils import packaging
if TYPE_CHECKING:
from dbt.config.profile import Profile
logger = logger.getChild(__name__)
DBT_PROJECT_FILE = "dbt_project.yml"
@contextmanager
def check_dbt(action: Optional[str] = None):
if not (find_spec("dbt") and find_spec("dbt.cli")):
action = f" {action}" if action else ""
raise DvcException(f"Could not run{action}. dbt-core is not installed")
yield packaging.check_required_version(pkg="dbt-core")
@contextmanager
def init_dbt(
profiles_dir: str,
project_dir: str,
target: Optional[str] = None,
):
from argparse import Namespace
from dbt import flags
prev = flags.get_flags()
try:
args = Namespace(
use_colors=True,
project_dir=project_dir,
profiles_dir=profiles_dir,
target=target,
)
flags.set_from_args(args, None)
yield flags.get_flags()
finally:
flags.set_flags(prev)
def get_profiles_dir(project_dir: Optional[str] = None) -> str:
from dbt.cli.resolvers import default_profiles_dir
if profiles_dir := os.getenv("DBT_PROFILES_DIR"):
return profiles_dir
if project_dir and os.path.isfile(os.path.join(project_dir, "profiles.yml")):
return project_dir
return os.fspath(default_profiles_dir())
@contextmanager
def _handle_profile_parsing_error():
from dbt.exceptions import DbtRuntimeError
try:
yield
except DbtRuntimeError as e:
cause = e.__cause__ is not None and e.__cause__.__context__
if isinstance(cause, ModuleNotFoundError) and (
adapter := cut_prefix(cause.name, "dbt.adapters.")
):
# DbtRuntimeError is very noisy, so send it to debug
logger.debug("", exc_info=True)
raise DvcException(f"dbt-{adapter} dependency is missing") from cause
raise DvcException("failed to read connection profiles") from e
def is_dbt_project(project_dir: str):
return os.path.isfile(os.path.join(project_dir, DBT_PROJECT_FILE))
@_handle_profile_parsing_error()
def get_or_build_profile(
project_dir: Optional[str], profile: Optional[str], target: Optional[str]
) -> "Profile":
from dbt.config.profile import Profile
from dbt.config.renderer import ProfileRenderer
from dbt.config.runtime import load_profile
if project_dir and is_dbt_project(project_dir):
return load_profile(
project_dir, {}, profile_name_override=profile, target_override=target
)
if not profile:
raise DvcException("No profile specified to query from.")
renderer = ProfileRenderer({})
return Profile.render(renderer, profile, target_override=target)
+54
View File
@@ -0,0 +1,54 @@
from dataclasses import dataclass
from typing import TYPE_CHECKING, Union
if TYPE_CHECKING:
import sqlalchemy as sa
from agate import Table
def noop(_):
pass
@dataclass
class PandasSQLSerializer:
sql: "Union[sa.TextClause, str]"
con: "sa.Connection"
chunksize: int = 10_000
def to_csv(self, file: str, progress=noop) -> None:
import pandas as pd
with open(file, mode="wb") as f:
idfs = pd.read_sql_query(self.sql, self.con, chunksize=self.chunksize)
for i, df in enumerate(idfs):
df.to_csv(f, header=i == 0, index=False)
progress(len(df))
def to_json(self, file: str, progress=noop) -> None: # noqa: ARG002
import pandas as pd
df = pd.read_sql_query(self.sql, self.con)
df.to_json(file, orient="records")
@dataclass
class AgateSerializer:
table: "Table"
def to_csv(self, file: str, progress=noop) -> None: # noqa: ARG002
return self.table.to_csv(file)
def to_json(self, file: str, progress=noop) -> None: # noqa: ARG002
return self.table.to_json(file)
def export(
serializer: Union[PandasSQLSerializer, AgateSerializer],
file: str,
format: str = "csv", # noqa: A002
progress=noop,
) -> None:
if format == "csv":
return serializer.to_csv(file, progress=progress)
return serializer.to_json(file, progress=progress)
+73
View File
@@ -0,0 +1,73 @@
from contextlib import contextmanager
from dataclasses import dataclass
from typing import Any, Callable, Dict, Iterator, Optional, Union
from sqlalchemy import create_engine, text
from sqlalchemy.engine import URL, Engine
from sqlalchemy.engine import make_url as _make_url
from sqlalchemy.exc import NoSuchModuleError
from dvc.exceptions import DvcException
from dvc.log import logger
from .serializer import PandasSQLSerializer
logger = logger.getChild(__name__)
def make_url(url: Union[URL, str], **kwargs: Any) -> URL:
return _make_url(url).set(**kwargs)
def url_from_config(config: Union[str, URL, Dict[str, str]]) -> URL:
if isinstance(config, (str, URL)):
return make_url(config)
return make_url(**config)
@dataclass
class SQLAlchemyAdapter:
engine: Engine
@contextmanager
def query(self, sql: str) -> Iterator[PandasSQLSerializer]:
with self.engine.connect().execution_options(stream_results=True) as conn:
yield PandasSQLSerializer(text(sql), conn)
def test_connection(self, onerror: Optional[Callable[[], Any]] = None) -> None:
try:
with self.engine.connect() as conn:
conn.execute(text("select 1"))
except Exception as exc:
if callable(onerror):
onerror()
logger.exception(
"dvc was unable to connect to the specified database. "
"Please check your database credentials and try again.",
exc_info=False,
)
raise DvcException("The database returned the following error") from exc
@contextmanager
def handle_error(url: URL):
try:
yield
except (ModuleNotFoundError, NoSuchModuleError) as e:
# TODO: write installation instructions
raise DvcException(
f"Could not load database driver for {url.drivername!r}"
) from e
@contextmanager
def adapter(
url_or_config: Union[str, URL, Dict[str, str]], **engine_kwargs: Any
) -> Iterator[SQLAlchemyAdapter]:
url = url_from_config(url_or_config)
with handle_error(url):
engine = create_engine(url, **engine_kwargs)
try:
yield SQLAlchemyAdapter(engine)
finally:
engine.dispose()
+17 -6
View File
@@ -4,6 +4,7 @@ from typing import Any, Dict, List, Mapping, Set
from dvc.output import ARTIFACT_SCHEMA, DIR_FILES_SCHEMA, Output
from .base import Dependency
from .db import DB_SCHEMA, PARAM_DB, DbDependency, DbtDependency
from .param import ParamsDependency
from .repo import RepoDependency
@@ -14,20 +15,28 @@ from .repo import RepoDependency
SCHEMA: Mapping[str, Any] = {
**ARTIFACT_SCHEMA,
**RepoDependency.REPO_SCHEMA,
**DB_SCHEMA,
Output.PARAM_FILES: [DIR_FILES_SCHEMA],
Output.PARAM_FS_CONFIG: dict,
}
def _get(stage, p, info, **kwargs):
if info and info.get(RepoDependency.PARAM_REPO):
repo = info.pop(RepoDependency.PARAM_REPO)
return RepoDependency(repo, stage, p, info)
d = info or {}
db = d.get(PARAM_DB, {})
params = d.pop(ParamsDependency.PARAM_PARAMS, None)
repo = d.pop(RepoDependency.PARAM_REPO, None)
if info and info.get(ParamsDependency.PARAM_PARAMS):
params = info.pop(ParamsDependency.PARAM_PARAMS)
if params:
return ParamsDependency(stage, p, params)
if DbDependency.PARAM_QUERY in db:
return DbDependency(stage, info)
if db:
return DbtDependency(repo, stage, info)
assert p
if repo:
return RepoDependency(repo, stage, p, info)
return Dependency(stage, p, info, **kwargs)
@@ -44,9 +53,11 @@ def loadd_from(stage, d_list):
return ret
def loads_from(stage, s_list, erepo=None, fs_config=None):
def loads_from(stage, s_list, erepo=None, fs_config=None, db=None):
assert isinstance(s_list, list)
info = {RepoDependency.PARAM_REPO: erepo} if erepo else {}
if db:
info.update({"db": db})
return [
_get(
stage,
+324
View File
@@ -0,0 +1,324 @@
import os
from contextlib import contextmanager, nullcontext
from typing import TYPE_CHECKING, Any, Callable, Dict, Iterator, Optional, Union
from funcy import compact, log_durations
from dvc.exceptions import DvcException
from dvc.log import logger
from dvc.scm import SCM
from .base import Dependency
if TYPE_CHECKING:
from rich.status import Status
from dvc.output import Output
from dvc.stage import Stage
logger = logger.getChild(__name__)
PARAM_DB = "db"
PARAM_PROFILE = "profile"
PARAM_FILE_FORMAT = "file_format"
def _get_dbt_config(config: Dict) -> Dict:
conf = config.get("feature", {})
pref = "dbt_"
return {k.lstrip(pref): v for k, v in conf.items() if k.startswith(pref)}
@contextmanager
def log_status(
msg, status: Optional["Status"] = None, log=logger.debug
) -> Iterator["Status"]:
from funcy import log_durations
from dvc.ui import ui
with log_durations(log, msg), status or ui.status(msg) as st:
st.update(msg)
yield st
@contextmanager
def chdir(path):
wdir = os.getcwd()
os.chdir(path)
try:
yield
finally:
os.chdir(wdir)
@contextmanager
def download_progress(to: "Output") -> Iterator[Callable[[int], Any]]:
from dvc.ui import ui
from dvc.ui._rich_progress import DbDownloadProgress
with log_durations(logger.debug, f"Saving to {to}"), DbDownloadProgress(
console=ui.error_console,
) as progress:
task = progress.add_task("Saving", total=None, output=to)
yield lambda n: progress.advance(task, advance=n)
progress.update(task, description="Saved", total=0)
class AbstractDependency(Dependency):
"""Dependency without workspace/fs/fs_path"""
def __init__(self, stage: "Stage", info: Dict[str, Any], *args, **kwargs):
self.repo = stage.repo
self.stage = stage
self.fs = None
self.fs_path = None
self.def_path = None # type: ignore[assignment]
self.info = info or {}
class DbDependency(AbstractDependency):
PARAM_QUERY = "query"
PARAM_CONNECTION = "connection"
QUERY_SCHEMA = {PARAM_QUERY: str, PARAM_CONNECTION: str}
def __init__(self, stage: "Stage", info, *args, **kwargs):
super().__init__(stage, info, *args, **kwargs)
self.target = None
def __repr__(self):
return "{}:{}".format(
self.__class__.__name__, "".join(f"{k}=={v}" for k, v in self.info.items())
)
def __str__(self):
from dvc.utils.humanize import truncate_text
db_info = self.info.get(PARAM_DB, {})
query = db_info.get(self.PARAM_QUERY, "[query]")
return truncate_text(query, 50)
def workspace_status(self):
return False # no workspace to check
def status(self):
return self.workspace_status()
def save(self):
"""nothing to save."""
def dumpd(self, **kwargs):
db_info = compact(self.info.get(PARAM_DB, {}))
return {PARAM_DB: db_info} if db_info else {}
def update(self, rev=None):
"""nothing to update."""
def download(
self,
to: "Output",
jobs: Optional[int] = None, # noqa: ARG002
file_format: Optional[str] = None,
**kwargs: Any,
) -> None:
from dvc.database import export, get_adapter
db_info = self.info.get(PARAM_DB, {})
query = db_info.get(self.PARAM_QUERY)
if not query:
raise DvcException("Cannot download: no query specified")
dbt_config = _get_dbt_config(self.repo.config)
profile = db_info.get(PARAM_PROFILE) or dbt_config.get(PARAM_PROFILE)
target = self.target or dbt_config.get("target")
connection = db_info.get(self.PARAM_CONNECTION)
db_config = self.repo.config.get("db", {})
config = db_config.get(connection)
if connection and not config:
raise DvcException(f"connection {connection} not found in config")
project_dir = self.repo.root_dir
with get_adapter(
config, project_dir=project_dir, profile=profile, target=target
) as db:
logger.debug("using adapter: %s", db)
with log_status("Testing connection") as status:
db.test_connection(onerror=status.stop)
file_format = file_format or db_info.get(PARAM_FILE_FORMAT, "csv")
assert file_format
with log_status("Executing query") as status, db.query(query) as serializer:
status.stop()
logger.debug("using serializer: %s", serializer)
with download_progress(to) as progress:
return export(
serializer, to.fs_path, format=file_format, progress=progress
)
class DbtDependency(AbstractDependency):
PARAM_MODEL = "model"
PARAM_VERSION = "version"
PARAM_PROJECT_DIR = "project_dir"
DBT_SCHEMA = {
PARAM_MODEL: str,
PARAM_VERSION: str,
PARAM_PROJECT_DIR: str,
}
def __init__(self, def_repo: Dict[str, Any], stage: "Stage", info, *args, **kwargs):
self.def_repo = def_repo or {}
self.target = None
super().__init__(stage, info, *args, **kwargs)
def __repr__(self):
return "{}:{}".format(
self.__class__.__name__,
"".join(f"{k}=={v}" for k, v in {**self.def_repo, **self.info}.items()),
)
def __str__(self):
from .repo import RepoDependency
repo = self.def_repo.get(RepoDependency.PARAM_URL)
rev = self.def_repo.get(RepoDependency.PARAM_REV)
db_info = self.info.get(PARAM_DB, {})
db = db_info.get(self.PARAM_MODEL, "")
project_dir = db_info.get(self.PARAM_PROJECT_DIR, "")
repo_info = ""
if repo:
repo_info += repo
if rev:
repo_info += f"@{rev}"
if project_dir:
repo_info += f":/{project_dir}"
return db + (f"({repo_info})" if repo_info else "")
@property
def locked_rev(self):
from .repo import RepoDependency
return self.def_repo.get(RepoDependency.PARAM_REV_LOCK)
@property
def rev(self):
from .repo import RepoDependency
return self.def_repo.get(RepoDependency.PARAM_REV)
def workspace_status(self):
if not self.def_repo:
return
current = self._get_clone(self.locked_rev or self.rev).get_rev()
updated = self._get_clone(self.rev).get_rev()
if current != updated:
return {str(self): "update available"}
return {}
def status(self):
return self.workspace_status()
def save(self):
from .repo import RepoDependency
if not self.def_repo:
return
rev = self._get_clone(self.locked_rev or self.rev).get_rev()
if self.def_repo.get(RepoDependency.PARAM_REV_LOCK) is None:
self.def_repo[RepoDependency.PARAM_REV_LOCK] = rev
def dumpd(self, **kwargs) -> Dict[str, Union[str, Dict[str, str]]]:
from .repo import RepoDependency
def_repo = {}
if self.def_repo:
def_repo = RepoDependency._dump_def_repo(self.def_repo)
db_info = compact(self.info.get(PARAM_DB, {}))
return compact({RepoDependency.PARAM_REPO: def_repo, PARAM_DB: db_info})
def _get_clone(self, rev):
from dvc.repo.open_repo import _cached_clone
from .repo import RepoDependency
url = self.def_repo.get(RepoDependency.PARAM_URL)
repo_root = self.repo.root_dir if self.repo else os.getcwd()
return SCM(_cached_clone(url, rev) if url else repo_root)
def update(self, rev=None):
from .repo import RepoDependency
if not self.def_repo:
return
if rev:
self.def_repo[RepoDependency.PARAM_REV] = rev
else:
rev = self.rev
self.def_repo[RepoDependency.PARAM_REV_LOCK] = self._get_clone(rev).get_rev()
def download(
self,
to: "Output",
jobs: Optional[int] = None, # noqa: ARG002
file_format: Optional[str] = None,
) -> None:
from .repo import RepoDependency
project_dir = self.info.get(PARAM_DB, {}).get(self.PARAM_PROJECT_DIR, "")
if self.def_repo:
ctx = repo = self._get_clone(self.locked_rev or self.rev)
self.def_repo[RepoDependency.PARAM_REV_LOCK] = repo.get_rev()
root = wdir = repo.root_dir
else:
ctx = nullcontext()
root = self.repo.root_dir
wdir = self.stage.wdir
project_path = os.path.join(wdir, project_dir) if project_dir else root
with ctx, chdir(project_path):
self._download_db(to, file_format=file_format)
def _download_db(
self,
to: "Output",
version: Optional[int] = None,
file_format: Optional[str] = None,
) -> None:
from dvc.database import export, get_model
db_info = self.info.get(PARAM_DB, {})
model = db_info.get(self.PARAM_MODEL)
version = version or db_info.get(self.PARAM_VERSION)
file_format = file_format or db_info.get(PARAM_FILE_FORMAT) or "csv"
assert file_format
if not model:
raise DvcException("Cannot download, no model specified")
dbt_config = _get_dbt_config(self.repo.config)
profile = db_info.get(PARAM_PROFILE) or dbt_config.get(PARAM_PROFILE)
target = self.target or db_info.get("target") or dbt_config.get("target")
with log_status("Downloading model"):
serializer = get_model(
model, version=version, profile=profile, target=target
)
# NOTE: we keep everything in memory, and then export it out later.
with download_progress(to) as progress:
export(serializer, to.fs_path, format=file_format, progress=progress)
DB_SCHEMA = {
PARAM_DB: {
PARAM_PROFILE: str,
PARAM_FILE_FORMAT: str,
**DbDependency.QUERY_SCHEMA,
**DbtDependency.DBT_SCHEMA,
},
}
+14 -11
View File
@@ -64,28 +64,31 @@ class RepoDependency(Dependency):
if self.def_repo.get(self.PARAM_REV_LOCK) is None:
self.def_repo[self.PARAM_REV_LOCK] = rev
def dumpd(self, **kwargs) -> Dict[str, Union[str, Dict[str, str]]]:
repo = {self.PARAM_URL: self.def_repo[self.PARAM_URL]}
@classmethod
def _dump_def_repo(cls, def_repo) -> Dict[str, str]:
repo = {cls.PARAM_URL: def_repo[cls.PARAM_URL]}
rev = self.def_repo.get(self.PARAM_REV)
rev = def_repo.get(cls.PARAM_REV)
if rev:
repo[self.PARAM_REV] = self.def_repo[self.PARAM_REV]
repo[cls.PARAM_REV] = def_repo[cls.PARAM_REV]
rev_lock = self.def_repo.get(self.PARAM_REV_LOCK)
rev_lock = def_repo.get(cls.PARAM_REV_LOCK)
if rev_lock:
repo[self.PARAM_REV_LOCK] = rev_lock
repo[cls.PARAM_REV_LOCK] = rev_lock
config = self.def_repo.get(self.PARAM_CONFIG)
config = def_repo.get(cls.PARAM_CONFIG)
if config:
repo[self.PARAM_CONFIG] = config
repo[cls.PARAM_CONFIG] = config
remote = self.def_repo.get(self.PARAM_REMOTE)
remote = def_repo.get(cls.PARAM_REMOTE)
if remote:
repo[self.PARAM_REMOTE] = remote
repo[cls.PARAM_REMOTE] = remote
return repo
def dumpd(self, **kwargs) -> Dict[str, Union[str, Dict[str, str]]]:
return {
self.PARAM_PATH: self.def_path,
self.PARAM_REPO: repo,
self.PARAM_REPO: self._dump_def_repo(self.def_repo),
}
def update(self, rev: Optional[str] = None):
+1 -1
View File
@@ -15,7 +15,7 @@ def system_config_dir():
def global_config_dir():
return os.getenv(env.DVC_SYSTEM_CONFIG_DIR) or platformdirs.user_config_dir(
return os.getenv(env.DVC_GLOBAL_CONFIG_DIR) or platformdirs.user_config_dir(
APPNAME, APPAUTHOR
)
+7 -1
View File
@@ -5,6 +5,8 @@ from dvc_http import HTTPFileSystem, HTTPSFileSystem # noqa: F401
from dvc.config import ConfigError as RepoConfigError
from dvc.config_schema import SCHEMA, Invalid
# pylint: disable=unused-import
from dvc_objects.fs import ( # noqa: F401
LocalFileSystem,
MemoryFileSystem,
@@ -27,7 +29,7 @@ from dvc_objects.fs.path import Path # noqa: F401
from .callbacks import Callback
from .data import DataFileSystem # noqa: F401
from .dvc import DVCFileSystem # noqa: F401
from .dvc import DVCFileSystem
from .git import GitFileSystem # noqa: F401
known_implementations.update(
@@ -47,6 +49,8 @@ known_implementations.update(
def download(
fs: "FileSystem", fs_path: str, to: str, jobs: Optional[int] = None
) -> int:
from dvc.scm import lfs_prefetch
with Callback.as_tqdm_callback(
desc=f"Downloading {fs.path.name(fs_path)}",
unit="files",
@@ -70,6 +74,8 @@ def download(
from_infos = [fs_path]
to_infos = [to]
if isinstance(fs, DVCFileSystem):
lfs_prefetch(fs, from_infos)
cb.set_size(len(from_infos))
jobs = jobs or fs.jobs
generic.copy(
+1 -1
View File
@@ -1523,7 +1523,7 @@ CLOUD_SCHEMA = vol.All({str: {**META_SCHEMA, **CHECKSUMS_SCHEMA}}, vol.Length(ma
ARTIFACT_SCHEMA: Dict[Any, Any] = {
**CHECKSUMS_SCHEMA,
**META_SCHEMA,
vol.Required(Output.PARAM_PATH): str,
Output.PARAM_PATH: str,
Output.PARAM_PERSIST: bool,
Output.PARAM_CLOUD: CLOUD_SCHEMA,
Output.PARAM_HASH: str,
+1
View File
@@ -76,6 +76,7 @@ class Repo:
from dvc.repo.get import get as _get # type: ignore[misc]
from dvc.repo.get_url import get_url as _get_url # type: ignore[misc]
from dvc.repo.imp import imp # type: ignore[misc]
from dvc.repo.imp_db import imp_db # type: ignore[misc]
from dvc.repo.imp_url import imp_url # type: ignore[misc]
from dvc.repo.install import install # type: ignore[misc]
from dvc.repo.ls import ls as _ls # type: ignore[misc]
+4
View File
@@ -135,6 +135,8 @@ def build_graph(stages, outs_trie=None):
for stage in stages:
if stage.is_repo_import:
continue
if stage.is_db_import:
continue
for dep in stage.deps:
dep_key = dep.fs.path.parts(dep.fs_path)
@@ -160,6 +162,8 @@ def build_outs_graph(graph, outs_trie):
for stage in graph.nodes():
if stage.is_repo_import:
continue
if stage.is_db_import:
continue
for dep in stage.deps:
dep_key = dep.fs.path.parts(dep.fs_path)
overlapping = [n.value for n in outs_trie.prefixes(dep_key)]
+81
View File
@@ -0,0 +1,81 @@
from typing import TYPE_CHECKING, Any, Dict, Optional
from dvc.exceptions import OutputDuplicationError
from dvc.repo.scm_context import scm_context
from dvc.ui import ui
from dvc.utils import resolve_output, resolve_paths
if TYPE_CHECKING:
from . import Repo
from . import locked
@locked
@scm_context
def imp_db( # noqa: PLR0913
self: "Repo",
url: Optional[str] = None,
rev: Optional[str] = None,
project_dir: Optional[str] = None,
sql: Optional[str] = None,
model: Optional[str] = None,
version: Optional[int] = None,
frozen: bool = True,
profile: Optional[str] = None,
target: Optional[str] = None,
output_format: str = "csv",
out: Optional[str] = None,
force: bool = False,
connection: Optional[str] = None,
):
ui.warn("WARNING: import-db is an experimental feature.")
ui.warn(
"The functionality may change or break without notice, "
"which could lead to unexpected behavior."
)
erepo = None
if model and url:
erepo = {"url": url}
if rev:
erepo["rev"] = rev
assert output_format in ("csv", "json")
db: Dict[str, Any] = {"file_format": output_format}
if profile:
db["profile"] = profile
if model:
out = out or f"{model}.{output_format}"
db.update({"model": model, "version": version, "project_dir": project_dir})
else:
out = out or f"results.{output_format}"
db.update({"query": sql, "connection": connection})
out = resolve_output(url or ".", out, force=force)
path, wdir, out = resolve_paths(self, out, always_local=True)
stage = self.stage.create(
single_stage=True,
validate=False,
fname=path,
wdir=wdir,
deps=[url],
outs=[out],
erepo=erepo,
fs_config=None,
db=db,
)
stage.deps[0].target = target
try:
self.check_graph(stages={stage})
except OutputDuplicationError as exc:
raise OutputDuplicationError( # noqa: B904
exc.output, set(exc.stages) - {stage}
)
stage.run()
stage.frozen = frozen
stage.dump()
return stage
+8 -1
View File
@@ -135,7 +135,11 @@ def _load_data_from_outs(index, prefix, outs):
hash_info=out.hash_info,
)
if out.stage.is_import and not out.stage.is_repo_import:
if (
out.stage.is_import
and not out.stage.is_repo_import
and not out.stage.is_db_import
):
dep = out.stage.deps[0]
entry.meta = dep.meta
if out.hash_info:
@@ -183,6 +187,9 @@ def _load_storage_from_out(storage_map, key, out):
except NoRemoteError:
pass
if out.stage.is_db_import:
return
if out.stage.is_import:
dep = out.stage.deps[0]
if not out.hash_info:
+6 -2
View File
@@ -101,7 +101,7 @@ def _get_remote(
return repo.cloud.get_remote(name, command)
def _merge_push_meta(
def _merge_push_meta( # noqa: C901
out: "Output",
index: Union["DataIndex", "DataIndexView"],
remote: Optional[str] = None,
@@ -116,7 +116,11 @@ def _merge_push_meta(
from dvc_data.index.save import build_tree
_, key = out.index_key
entry = index[key]
entry = index.get(key)
if entry is None:
return
repo = out.stage.repo
if out.isdir():
old_tree = out.get_obj()
+29
View File
@@ -24,6 +24,8 @@ from dvc.progress import Tqdm
if TYPE_CHECKING:
from scmrepo.progress import GitProgressEvent
from dvc.fs import FileSystem
class SCMError(DvcException):
"""Base class for source control management errors."""
@@ -262,3 +264,30 @@ def iter_revs(
rev_resolver = partial(resolve_rev, scm)
return group_by(rev_resolver, results)
def lfs_prefetch(fs: "FileSystem", paths: List[str]):
from scmrepo.git.lfs import fetch as _lfs_fetch
from dvc.fs.dvc import DVCFileSystem
from dvc.fs.git import GitFileSystem
if isinstance(fs, DVCFileSystem) and isinstance(fs.repo.fs, GitFileSystem):
git_fs = fs.repo.fs
scm = fs.repo.scm
assert isinstance(scm, Git)
else:
return
try:
if "filter=lfs" not in git_fs.open(".gitattributes").read():
return
except OSError:
return
with TqdmGit(desc="Checking for Git-LFS objects") as pbar:
_lfs_fetch(
scm,
[git_fs.rev],
include=[(path if path.startswith("/") else f"/{path}") for path in paths],
progress=pbar.update_git,
)
+21 -2
View File
@@ -105,7 +105,7 @@ def create_stage(cls: Type[_T], repo, path, **kwargs) -> _T:
fill_stage_outputs(stage, **kwargs)
check_no_externals(stage)
fill_stage_dependencies(
stage, **project(kwargs, ["deps", "erepo", "params", "fs_config"])
stage, **project(kwargs, ["deps", "erepo", "params", "fs_config", "db"])
)
check_circular_dependency(stage)
check_duplicated_arguments(stage)
@@ -281,9 +281,24 @@ class Stage(params.StageParams):
return isinstance(self.deps[0], RepoDependency)
@property
def is_db_import(self) -> bool:
if not self.is_import:
return False
from dvc.dependency import DbDependency, DbtDependency
return isinstance(self.deps[0], (DbDependency, DbtDependency))
@property
def is_versioned_import(self) -> bool:
return self.is_import and self.deps[0].fs.version_aware
from dvc.dependency import DbDependency, DbtDependency
return (
self.is_import
and not isinstance(self.deps[0], (DbDependency, DbtDependency))
and self.deps[0].fs.version_aware
)
def short_description(self) -> Optional["str"]:
desc: Optional["str"] = None
@@ -446,6 +461,9 @@ class Stage(params.StageParams):
) -> None:
if not (self.is_repo_import or self.is_import):
raise StageUpdateError(self.relpath)
# always force update DbDep/DbtDep since we don't know if it's changed
force = self.is_db_import
update_import(
self,
rev=rev,
@@ -453,6 +471,7 @@ class Stage(params.StageParams):
remote=remote,
no_download=no_download,
jobs=jobs,
force=force,
)
def reload(self) -> "Stage":
+2 -1
View File
@@ -7,6 +7,7 @@ from funcy import decorator
def rwlocked(call, read=None, write=None):
import sys
from dvc.dependency.db import AbstractDependency
from dvc.dependency.repo import RepoDependency
from dvc.rwlock import rwlock
@@ -27,7 +28,7 @@ def rwlocked(call, read=None, write=None):
for item in getattr(stage, attr)
# There is no need to lock RepoDependency deps, as there is no
# corresponding OutputREPO, so we can't even write it.
if not isinstance(item, RepoDependency)
if not isinstance(item, (RepoDependency, AbstractDependency))
]
cmd = " ".join(sys.argv)
+9 -3
View File
@@ -18,7 +18,13 @@ def _update_import_on_remote(stage, remote, jobs):
def update_import(
stage, rev=None, to_remote=False, remote=None, no_download=None, jobs=None
stage,
rev=None,
to_remote=False,
remote=None,
no_download=None,
jobs=None,
force=False,
):
stage.deps[0].update(rev=rev)
@@ -30,7 +36,7 @@ def update_import(
if to_remote:
_update_import_on_remote(stage, remote, jobs)
else:
stage.reproduce(no_download=no_download, jobs=jobs)
stage.reproduce(no_download=no_download, jobs=jobs, force=force)
finally:
if no_download and changed:
# Avoid retaining stale information
@@ -55,7 +61,7 @@ def sync_import(
else:
stage.save_deps()
if no_download:
if stage.is_repo_import:
if stage.is_repo_import or stage.is_db_import:
stage.deps[0].update()
else:
stage.deps[0].download(
+4 -2
View File
@@ -77,12 +77,14 @@ def fill_stage_outputs(stage, **kwargs):
)
def fill_stage_dependencies(stage, deps=None, erepo=None, params=None, fs_config=None):
def fill_stage_dependencies(
stage, deps=None, erepo=None, params=None, fs_config=None, db=None
):
from dvc.dependency import loads_from, loads_params
assert not stage.deps
stage.deps = []
stage.deps += loads_from(stage, deps or [], erepo=erepo, fs_config=fs_config)
stage.deps += loads_from(stage, deps or [], erepo=erepo, fs_config=fs_config, db=db)
stage.deps += loads_params(stage, params or [])
@@ -0,0 +1,3 @@
def test_fetch(bench_dvc, tmp_dir, dvc, make_dataset, remote):
make_dataset(cache=False, dvcfile=True, files=False, remote=True)
bench_dvc("fetch")
@@ -1,3 +0,0 @@
def test_pull(bench_dvc, tmp_dir, dvc, make_dataset, remote):
make_dataset(cache=False, dvcfile=True, files=False, remote=True)
bench_dvc("pull")
@@ -11,7 +11,8 @@ def test_sharing(bench_dvc, tmp_dir, dvc, dataset, remote):
shutil.rmtree(dataset)
shutil.rmtree(tmp_dir / ".dvc" / "cache")
bench_dvc("pull")
bench_dvc("pull", name="noop")
bench_dvc("fetch")
bench_dvc("fetch", name="noop")
bench_dvc("checkout")
bench_dvc("checkout", name="noop")
+30 -8
View File
@@ -2,26 +2,48 @@ import os
import shutil
from pathlib import Path
from subprocess import check_output
from typing import Dict, Optional
import pytest
from dulwich.porcelain import clone
from funcy import first
from packaging import version
from dvc.types import StrPath
@pytest.fixture(scope="session")
def bench_config(request):
return request.config.bench_config
class VirtualEnv:
def __init__(self, path: StrPath) -> None:
self.path = Path(path)
self.bin = self.path / ("Scripts" if os.name == "nt" else "bin")
def create(self) -> None:
import virtualenv
virtualenv.cli_run([os.fspath(self.path)])
def run(self, cmd: str, *args: str, env: Optional[Dict[str, str]] = None) -> None:
exe = self.which(cmd)
check_output([exe, *args], env=env) # noqa: S603
def which(self, cmd: str) -> str:
assert self.bin.exists()
return shutil.which(cmd, path=self.bin) or cmd
@pytest.fixture(scope="session")
def make_dvc_venv(tmp_path_factory):
def _make_dvc_venv(name):
from pytest_virtualenv import VirtualEnv
name = _sanitize_venv_name(name)
venv_dir = tmp_path_factory.mktemp(f"dvc-venv-{name}")
return VirtualEnv(workspace=venv_dir)
venv = VirtualEnv(venv_dir)
venv.create()
return venv
return _make_dvc_venv
@@ -74,16 +96,16 @@ def make_dvc_bin(
venv = dvc_venvs.get(dvc_rev)
if not venv:
venv = make_dvc_venv(dvc_rev)
venv.run("pip install -U pip")
venv.run("pip", "install", "-U", "pip")
if bench_config.dvc_install_deps:
egg = f"dvc[{bench_config.dvc_install_deps}]"
else:
egg = "dvc"
venv.run(f"pip install git+file://{dvc_git_repo}@{dvc_rev}#egg={egg}")
venv.run("pip", "install", f"git+file://{dvc_git_repo}@{dvc_rev}#egg={egg}")
if dvc_rev in ["2.18.1", "2.11.0", "2.6.3"]:
venv.run("pip install fsspec==2022.11.0")
venv.run("pip", "install", "fsspec==2022.11.0")
dvc_venvs[dvc_rev] = venv
dvc_bin = venv.virtualenv / "bin" / "dvc"
dvc_bin = venv.which("dvc")
else:
dvc_bin = bench_config.dvc_bin
@@ -171,7 +193,7 @@ def make_dataset(request, bench_config, tmp_dir, dvc_bench_git_repo):
path = tmp_dir / "dataset"
root = dvc_bench_git_repo
src = root / "data" / bench_config.size / "dataset"
src = root / "data" / bench_config.dataset / "dataset"
src_dvc = src.with_suffix(".dvc")
dvc = Repo(root)
+10 -5
View File
@@ -4,6 +4,11 @@ DEFAULT_DVC_BENCH_GIT_REPO = "https://github.com/iterative/dvc-bench"
DEFAULT_PROJECT_GIT_REPO = "https://github.com/iterative/example-get-started"
def pytest_report_header(config):
bconf = config.bench_config
return "dvc-bench: (" f"dataset: '{bconf.dataset}'," f"revs: '{bconf.dvc_revs}'" ")"
def pytest_generate_tests(metafunc):
str_revs = metafunc.config.getoption("--dvc-revs")
revs = str_revs.split(",") if str_revs else [None]
@@ -13,7 +18,7 @@ def pytest_generate_tests(metafunc):
class DVCBenchConfig:
def __init__(self):
self.size = "small"
self.dataset = "small"
self.dvc_bin = DEFAULT_DVC_BIN
self.dvc_revs = None
self.dvc_git_repo = DEFAULT_DVC_GIT_REPO
@@ -29,7 +34,7 @@ def pytest_configure(config):
)
config.bench_config = DVCBenchConfig()
config.bench_config.size = config.getoption("--size")
config.bench_config.dataset = config.getoption("--dataset")
config.bench_config.dvc_bin = config.getoption("--dvc-bin")
config.bench_config.dvc_revs = config.getoption("--dvc-revs")
config.bench_config.dvc_git_repo = config.getoption("--dvc-git-repo")
@@ -41,10 +46,10 @@ def pytest_configure(config):
def pytest_addoption(parser):
parser.addoption(
"--size",
choices=["tiny", "small", "large", "mnist"],
"--dataset",
type=str,
default="small",
help="Size of the dataset/datafile to use in tests",
help="Dataset name to use in tests (e.g. tiny/small/large/mnist/etc)",
)
parser.addoption(
+14 -10
View File
@@ -70,16 +70,20 @@ class TmpDir(pathlib.Path):
def __new__(cls, *args, **kwargs):
if cls is TmpDir:
cls = WindowsTmpDir if os.name == "nt" else PosixTmpDir
# init parameter and `_init` method has been removed in Python 3.10.
kw = {"init": False} if sys.version_info < (3, 10) else {}
self = cls._from_parts(args, **kw) # type: ignore[attr-defined]
if not self._flavour.is_supported:
raise NotImplementedError(
f"cannot instantiate {cls.__name__!r} on your system"
)
if sys.version_info < (3, 10):
self._init()
return self
if sys.version_info >= (3, 12):
return object.__new__(cls)
else: # noqa: RET505
# init parameter and `_init` method has been removed in Python 3.10.
kw = {"init": False} if sys.version_info < (3, 10) else {}
self = cls._from_parts(args, **kw) # type: ignore[attr-defined]
if not self._flavour.is_supported:
raise NotImplementedError(
f"cannot instantiate {cls.__name__!r} on your system"
)
if sys.version_info < (3, 10):
self._init()
return self
def init(self, *, scm=False, dvc=False, subdir=False):
from dvc.repo import Repo
+22
View File
@@ -4,6 +4,7 @@ from rich.progress import (
DownloadColumn,
MofNCompleteColumn,
Progress,
SpinnerColumn,
TextColumn,
TimeElapsedColumn,
TimeRemainingColumn,
@@ -52,3 +53,24 @@ class RichTransferProgress(RichProgress):
yield self.make_tasks_table(summary_tasks)
self.columns = self.TRANSFER_COLS
yield self.make_tasks_table(other_tasks)
class DbDownloadProgress(RichProgress):
PROGRESS_COLS = (
SpinnerColumn(),
TextColumn("[progress.description]{task.description}"),
TextColumn("[progress.download]{task.completed:,} rows"),
TextColumn("to [repr.filename]{task.fields[output]}"),
)
STATUS_COLS = (
SpinnerColumn(),
TextColumn("[progress.description]{task.description}"),
TextColumn("to [repr.filename]{task.fields[output]}"),
)
def get_renderables(self):
if self.tasks:
(task, *_) = self.tasks
cols = self.PROGRESS_COLS if task.completed else self.STATUS_COLS
self.columns = cols[1:] if task.finished else cols
yield self.make_tasks_table(self.tasks)
+32
View File
@@ -0,0 +1,32 @@
import logging
from funcy import once_per_args
from dvc.log import logger
logger = logger.getChild(__name__)
@once_per_args
def check_required_version(pkg: str, dist: str = "dvc", log_level=logging.WARNING):
from importlib import metadata
from packaging.requirements import InvalidRequirement, Requirement
try:
reqs = {
r.name: r.specifier for r in map(Requirement, metadata.requires(dist) or [])
}
version = metadata.version(pkg)
except (metadata.PackageNotFoundError, InvalidRequirement):
return
specifier = reqs.get(pkg)
if specifier and version and version not in specifier:
logger.log(
log_level,
"%s%s is required, but you have %r installed which is incompatible.",
pkg,
specifier,
version,
)
+11 -12
View File
@@ -34,7 +34,7 @@ dependencies = [
"configobj>=5.0.6",
"distro>=1.3",
"dpath<3,>=2.1.0",
"dvc-data>=2.21.2,<2.22.0",
"dvc-data>=2.22.1,<2.23.0",
"dvc-http>=2.29.0",
"dvc-render>=0.3.1,<1",
"dvc-studio-client>=0.13.0,<1",
@@ -58,7 +58,7 @@ dependencies = [
"requests>=2.22",
"rich>=12",
"ruamel.yaml>=0.17.11",
"scmrepo>=1.4.1,<2",
"scmrepo>=1.5.0,<2",
"shortuuid>=0.5",
"shtab<2,>=1.3.4",
"tabulate>=0.8.7",
@@ -77,6 +77,7 @@ gs = ["dvc-gs==2.22.1"]
hdfs = ["dvc-hdfs==2.19"]
lint = [
"mypy==1.7.0",
"pandas-stubs",
"types-colorama",
"types-psutil",
"types-pyinstaller",
@@ -90,9 +91,9 @@ s3 = ["dvc-s3==2.23.0"]
ssh = ["dvc-ssh>=2.22.1,<3"]
ssh_gssapi = ["dvc-ssh[gssapi]>=2.22.1,<3"]
testing = [
"pytest-test-utils",
"pytest-benchmark[histogram]",
"pytest-virtualenv",
"pytest-test-utils",
"virtualenv",
]
tests = [
"dvc[testing]",
@@ -110,6 +111,9 @@ tests = [
"pytest-xdist>=3.2",
'pywin32>=225; sys_platform == "win32"', # optional test dependency
'tzdata; sys_platform == "win32"', # for testing with celery
"dbt-sqlite", # optional dependency for testing `import-db`
"sqlalchemy>=1,<3", # optional dependency for `import-db`
"pandas>=1",
]
webdav = ["dvc-webdav==2.19.1"]
webhdfs = ["dvc-webhdfs==2.19"]
@@ -126,9 +130,6 @@ dvc = "dvc.cli:main"
[project.entry-points."fsspec.specs"]
dvc = "dvc.api:DVCFileSystem"
[project.entry-points."pytest11"]
dvc-testing = "dvc.testing.plugin"
[project.entry-points."pyinstaller40"]
hook-dirs = "dvc.__pyinstaller:get_hook_dirs"
tests = "dvc.__pyinstaller:get_PyInstaller_tests"
@@ -144,7 +145,7 @@ namespaces = false
write_to = "dvc/_dvc_version.py"
[tool.pytest.ini_options]
addopts = "-ra --cov-config pyproject.toml --dist worksteal"
addopts = "-ra --cov-config pyproject.toml --dist worksteal --benchmark-skip"
filterwarnings = [
"error::ResourceWarning",
"error::pytest.PytestUnraisableExceptionWarning",
@@ -155,8 +156,6 @@ filterwarnings = [
# google.logging: https://github.com/googleapis/python-logging/issues/730
# Also happens with `zc.lockfile`.
"ignore:Deprecated call to `pkg_resources.declare_namespace:DeprecationWarning",
# tpi imports pkg_resources
"ignore:pkg_resources is deprecated as an API:DeprecationWarning",
# see https://github.com/networkx/networkx/issues/5723.
"ignore:nx.nx_pydot.* depends on the pydot package, which has.*known issues and is not actively maintained:DeprecationWarning",
]
@@ -207,6 +206,7 @@ warn_unused_configs = true
[[tool.mypy.overrides]]
ignore_missing_imports = true
module = [
"agate.*",
"celery.*",
"configobj.*",
"dpath.*",
@@ -228,12 +228,11 @@ module = [
"pyparsing",
"pytest_benchmark.*",
"pytest_docker.plugin",
"pytest_virtualenv.*",
"ruamel.*",
"ruamel.yaml.*",
"shortuuid",
"shtab",
"tpi.*",
"virtualenv",
"viztracer",
"voluptuous",
"yappi",
+1 -1
View File
@@ -96,7 +96,7 @@ def test_config_unset(dvc):
cmd = args.func(args)
assert isinstance(cmd, CmdConfig)
assert args.unset
assert args.name == (False, "section", "option")
assert args.name == (None, "section", "option")
assert args.value == value
+128
View File
@@ -0,0 +1,128 @@
"""import_db tests without involving any databases."""
import pytest
from agate import Table
from dvc.database.serializer import AgateSerializer
data1 = Table([(i, i) for i in range(1, 10)], ["id", "value"])
data2 = Table([(i, i) for i in range(10, 20)], ["id", "value"])
serializers = AgateSerializer(data1), AgateSerializer(data2)
@pytest.fixture
def adapter(mocker):
m = mocker.patch("dvc.database.get_adapter")
adapter = mocker.MagicMock()
adapter.query.return_value.__enter__.side_effect = serializers
m.return_value.__enter__.return_value = adapter
return m
def test_sql(adapter, tmp_dir, dvc):
stage = dvc.imp_db(
sql="select * from model", profile="profile", output_format="json"
)
db = {"file_format": "json", "profile": "profile", "query": "select * from model"}
assert (tmp_dir / stage.relpath).parse() == {
"md5": "dae475048115315c8c26a10538e4b2ec",
"frozen": True,
"deps": [{"db": db}],
"outs": [
{
"hash": "md5",
"md5": "56226d443067b195c90b427db557e1f2",
"path": "results.json",
"size": 243,
}
],
}
dvc.update(stage.addressing)
assert (tmp_dir / stage.relpath).parse() == {
"md5": "79b42f9ddb2a3ed999eb494ccab470c6",
"frozen": True,
"deps": [{"db": db}],
"outs": [
{
"hash": "md5",
"md5": "08d806ee7e1f309c4561750805f02276",
"path": "results.json",
"size": 290,
}
],
}
def test_sql_conn_string(adapter, tmp_dir, dvc):
with dvc.config.edit(level="local") as conf:
conf["db"] = {"conn": {"url": "conn"}}
stage = dvc.imp_db(
sql="select * from model", connection="conn", output_format="json"
)
db = {"file_format": "json", "connection": "conn", "query": "select * from model"}
assert (tmp_dir / stage.relpath).parse() == {
"md5": "f0dcca8e8411907adb25aa547d7c432c",
"frozen": True,
"deps": [{"db": db}],
"outs": [
{
"hash": "md5",
"md5": "56226d443067b195c90b427db557e1f2",
"path": "results.json",
"size": 243,
}
],
}
dvc.update(stage.addressing)
assert (tmp_dir / stage.relpath).parse() == {
"md5": "8c0441b206d8ee7c7b9e3d54871c3cbb",
"frozen": True,
"deps": [{"db": db}],
"outs": [
{
"hash": "md5",
"md5": "08d806ee7e1f309c4561750805f02276",
"path": "results.json",
"size": 290,
}
],
}
def test_model(mocker, tmp_dir, dvc):
mocker.patch("dvc.database.get_model", side_effect=serializers)
stage = dvc.imp_db(model="model", output_format="json")
assert (tmp_dir / stage.relpath).parse() == {
"md5": "a8157fb5b28457e1910506e9d4d4fca3",
"frozen": True,
"deps": [{"db": {"file_format": "json", "model": "model"}}],
"outs": [
{
"hash": "md5",
"md5": "56226d443067b195c90b427db557e1f2",
"path": "model.json",
"size": 243,
}
],
}
dvc.update(stage.addressing)
assert (tmp_dir / stage.relpath).parse() == {
"md5": "2f84287f109fc2b8755a9e64ad910b5d",
"frozen": True,
"deps": [{"db": {"file_format": "json", "model": "model"}}],
"outs": [
{
"hash": "md5",
"md5": "08d806ee7e1f309c4561750805f02276",
"path": "model.json",
"size": 290,
}
],
}
+142
View File
@@ -0,0 +1,142 @@
"""E2E tests involving dvc/dbt and a ~~real~~ sqlite db.
Any other tests should likely be mocked tests in `test_import_db` rather than here.
"""
import os
import sqlite3
from contextlib import closing
import pytest
from agate import Table
from dvc.types import StrPath
pytest.importorskip("dbt.adapters.sqlite", reason="dbt-sqlite not installed")
@pytest.fixture(autouse=True)
def disable_tracking(monkeypatch):
monkeypatch.setenv("DO_NOT_TRACK", "1")
@pytest.fixture(autouse=True)
def mock_sqlite_adapter(mocker):
# https://github.com/codeforkjeff/dbt-sqlite/issues/47
mocker.patch(
"dbt.adapters.sqlite.connections.SQLiteCredentials.unique_field", "sqlite_host"
)
@pytest.fixture
def db_path(tmp_dir):
d = tmp_dir / "db"
d.mkdir()
return d / "main.db"
@pytest.fixture
def seed_db(db_path):
conn = sqlite3.connect(db_path)
conn.execute("CREATE TABLE model (id INTEGER PRIMARY KEY, value INTEGER)")
def inner(values):
conn.executemany("INSERT INTO model(value) VALUES(?)", [(i,) for i in values])
conn.commit()
with closing(conn):
yield inner
@pytest.fixture
def db_config(dvc, db_path):
# only needed for `sql_conn` tests
with dvc.config.edit(level="local") as conf:
conf["db"] = {"conn": {"url": f"sqlite:///{db_path.fs_path}"}}
return "conn"
@pytest.fixture
def dbt_profile(tmp_dir, scm, db_path):
(tmp_dir / "profiles.yml").dump(
{
"sqlite_profile": {
"target": "dev",
"outputs": {
"dev": {
"type": "sqlite",
"threads": 1,
"database": "database",
"schema": "main",
"schemas_and_paths": {"main": os.fspath(db_path)},
"schema_directory": os.fspath(db_path.parent),
}
},
}
}
)
scm.add_commit(["profiles.yml"], message="add profiles.yml")
return "sqlite_profile"
@pytest.fixture
def dbt_project(tmp_dir, scm, dbt_profile):
(tmp_dir / "dbt_project.yml").dump({"name": "project", "profile": dbt_profile})
scm.add_commit(["dbt_project.yml"], message="add dbt_project")
return tmp_dir
@pytest.fixture
def dbt_model(dbt_project):
dbt_project.scm_gen(
{"models": {"model.sql": "select * from models"}}, commit="add models"
)
return "model"
@pytest.fixture(params=("sql", "model", "external_model", "sql_conn"))
def import_db_parameters(request: pytest.FixtureRequest):
if request.param == "sql":
profile = request.getfixturevalue("dbt_profile")
return {"sql": "select * from model", "profile": profile}
if request.param == "sql_conn":
conn = request.getfixturevalue("db_config")
return {"sql": "select * from model", "connection": conn}
dbt_project = request.getfixturevalue("dbt_project")
return {
"model": request.getfixturevalue("dbt_model"),
"url": None if request.param == "model" else os.fspath(dbt_project),
}
@pytest.fixture
def file_name(import_db_parameters):
if model := import_db_parameters.get("model"):
return model
return "results"
def load_table(file: StrPath, typ: str) -> "Table":
return getattr(Table, f"from_{typ}")(file)
@pytest.mark.filterwarnings("ignore::ResourceWarning") # dbt leaks fileobj from logger
@pytest.mark.parametrize("output_format", ("csv", "json"))
def test_e2e(
tmp_dir, scm, dvc, seed_db, import_db_parameters, file_name, output_format
):
seed_db(values=range(5))
stage = dvc.imp_db(**import_db_parameters, output_format=output_format)
output_file = tmp_dir / f"{file_name}.{output_format}"
output = load_table(output_file, output_format)
assert output.rows == [(i + 1, i) for i in range(5)]
seed_db(values=range(5, 10))
dvc.update(stage.addressing)
output = load_table(output_file, output_format)
assert output.rows == [(i + 1, i) for i in range(10)]
+18 -1
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@@ -3,7 +3,7 @@ import os
import pytest
from git import Repo
from dvc.scm import SCM, Git, NoSCM, SCMError
from dvc.scm import SCM, Git, NoSCM, SCMError, lfs_prefetch
def test_init_none(tmp_dir):
@@ -27,3 +27,20 @@ def test_init_sub_dir(tmp_dir):
scm = SCM(os.fspath(subdir))
assert scm.root_dir == os.fspath(tmp_dir)
def test_lfs_prefetch(tmp_dir, dvc, scm, mocker):
mock_fetch = mocker.patch("scmrepo.git.lfs.fetch")
rev = scm.get_rev()
with dvc.switch(rev):
lfs_prefetch(dvc.dvcfs, ["foo"])
mock_fetch.assert_not_called()
tmp_dir.scm_gen(
".gitattributes", ".lfs filter=lfs diff=lfs merge=lfs -text", commit="init lfs"
)
rev = scm.get_rev()
with dvc.switch(rev):
lfs_prefetch(dvc.dvcfs, ["foo"])
mock_fetch.assert_called_once()
+1 -1
View File
@@ -69,7 +69,7 @@ def test_stage_update(dvc, mocker):
is_repo_import.return_value = True
with dvc.lock:
stage.update()
reproduce.assert_called_once_with(no_download=None, jobs=None)
reproduce.assert_called_once_with(no_download=None, jobs=None, force=False)
is_repo_import.return_value = False
with pytest.raises(StageUpdateError):
+8
View File
@@ -0,0 +1,8 @@
from dvc.dirs import global_config_dir
from dvc.env import DVC_GLOBAL_CONFIG_DIR
def test_global_config_dir_respects_env_var(monkeypatch):
path = "/some/random/path"
monkeypatch.setenv(DVC_GLOBAL_CONFIG_DIR, path)
assert global_config_dir() == path