From ad73ea9306bfb6f96eb7d330630865aa92ac4bd9 Mon Sep 17 00:00:00 2001
From: Martin Weise <martin.weise@tuwien.ac.at>
Date: Sun, 23 Feb 2025 12:10:09 +0100
Subject: [PATCH] Update migration script
Signed-off-by: Martin Weise <martin.weise@tuwien.ac.at>
---
.gitlab-ci.yml | 2 +-
.../target/create-event-listener.jar | Bin 10145 -> 10141 bytes
.../migration/16/gen_data_sql.py | 152 ++++++++++++++++++
.../migration/16/requirements.txt | 1 +
.../tuwien/endpoints/IdentifierEndpoint.java | 2 +-
helm/dbrepo/files/create-event-listener.jar | Bin 10145 -> 10141 bytes
lib/python/dbrepo/RestClient.py | 33 +++-
lib/python/dbrepo/api/dto.py | 19 ++-
lib/python/pyproject.toml | 2 +-
lib/python/setup.py | 2 +-
lib/python/tests/test_unit_image.py | 31 ++++
lib/python/tests/test_unit_messages.py | 31 ++++
12 files changed, 263 insertions(+), 12 deletions(-)
create mode 100644 dbrepo-metadata-db/migration/16/gen_data_sql.py
create mode 100644 dbrepo-metadata-db/migration/16/requirements.txt
create mode 100644 lib/python/tests/test_unit_image.py
create mode 100644 lib/python/tests/test_unit_messages.py
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 5a47aa19e5..0cfcd600cd 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -403,7 +403,7 @@ test-lib:
script:
- "pip install pipenv"
- "pipenv install gunicorn && pipenv install --dev --system --deploy"
- - cd ./lib/python/ && coverage run -m pytest tests/test_unit_analyse.py tests/test_unit_container.py tests/test_unit_database.py tests/test_unit_identifier.py tests/test_unit_license.py tests/test_unit_query.py tests/test_unit_rest_client.py tests/test_unit_table.py tests/test_unit_user.py tests/test_unit_view.py --junitxml=report.xml && coverage html --omit="test/*" && coverage report --omit="test/*" > ./coverage.txt
+ - cd ./lib/python/ && coverage run -m pytest tests/test_unit_analyse.py tests/test_unit_container.py tests/test_unit_database.py tests/test_unit_identifier.py tests/test_unit_image.py tests/test_unit_messages.py tests/test_unit_license.py tests/test_unit_query.py tests/test_unit_rest_client.py tests/test_unit_table.py tests/test_unit_user.py tests/test_unit_view.py --junitxml=report.xml && coverage html --omit="test/*" && coverage report --omit="test/*" > ./coverage.txt
- "cat ./coverage.txt | grep -o 'TOTAL[^%]*%'"
artifacts:
when: always
diff --git a/dbrepo-auth-service/listeners/target/create-event-listener.jar b/dbrepo-auth-service/listeners/target/create-event-listener.jar
index f370c8825750a431296ef68c3d482a2e4eee9389..a33db1e9045a92823996c61a9223aafb0d25404e 100644
GIT binary patch
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diff --git a/dbrepo-metadata-db/migration/16/gen_data_sql.py b/dbrepo-metadata-db/migration/16/gen_data_sql.py
new file mode 100644
index 0000000000..eeade6f3ab
--- /dev/null
+++ b/dbrepo-metadata-db/migration/16/gen_data_sql.py
@@ -0,0 +1,152 @@
+#!/usr/bin/env python3
+import os
+import uuid
+
+from dbrepo.RestClient import RestClient
+
+endpoint = os.getenv('METADATA_SERVICE_ENDPOINT', 'http://localhost')
+username = os.getenv('SYSTEM_USERNAME', 'admin')
+password = os.getenv('SYSTEM_PASSWORD', 'admin')
+client = RestClient(endpoint=endpoint, username=username, password=password)
+
+plan: [str] = []
+
+
+def update_concepts() -> None:
+ plan.append("-- concepts")
+ plan.append("BEGIN;")
+ for concept in client.get_concepts():
+ old_id: int = concept.id
+ new_id: uuid = uuid.uuid4()
+ plan.append(f"UPDATE mdb_columns_concepts SET id = '{new_id}' WHERE id = {old_id};")
+ plan.append(f"UPDATE mdb_concepts SET id = '{new_id}' WHERE id = {old_id};")
+ plan.append("COMMIT;")
+
+
+def update_ontologies() -> None:
+ plan.append("-- ontologies")
+ plan.append("BEGIN;")
+ plan.append(f"UPDATE mdb_ontology SET id = UUID()")
+ plan.append("COMMIT;")
+
+
+def update_units() -> None:
+ plan.append("-- units")
+ plan.append("BEGIN;")
+ for unit in client.get_units():
+ old_id: int = unit.id
+ new_id: uuid = uuid.uuid4()
+ plan.append(f"UPDATE mdb_columns_units SET id = '{new_id}' WHERE id = {old_id};")
+ plan.append(f"UPDATE mdb_units SET id = '{new_id}' WHERE id = {old_id};")
+ plan.append("COMMIT;")
+
+
+def update_images() -> None:
+ plan.append("-- images")
+ plan.append("BEGIN;")
+ for image in client.get_images():
+ old_id: int = image.id
+ new_id: uuid = uuid.uuid4()
+ plan.append(f"UPDATE mdb_images SET id = '{new_id}' WHERE id = {old_id};")
+ plan.append(f"UPDATE mdb_image_operators SET id = UUID(), image_id = '{new_id}' WHERE image_id = {old_id};")
+ plan.append(f"UPDATE mdb_image_types SET id = UUID(), image_id = '{new_id}' WHERE image_id = {old_id};")
+ plan.append(f"UPDATE mdb_containers SET id = UUID(), image_id = '{new_id}' WHERE image_id = {old_id};")
+ plan.append("COMMIT;")
+
+
+def update_containers() -> None:
+ plan.append("-- containers")
+ plan.append("BEGIN;")
+ for containers in client.get_containers():
+ old_id: int = containers.id
+ new_id: uuid = uuid.uuid4()
+ plan.append(f"UPDATE mdb_containers SET id = '{new_id}' WHERE id = {old_id};")
+ plan.append(f"UPDATE mdb_databases SET cid = '{new_id}' WHERE cid = {old_id};")
+ plan.append("COMMIT;")
+
+
+def update_databases() -> None:
+ plan.append("-- databases")
+ plan.append("BEGIN;")
+ for _database in client.get_databases():
+ database = client.get_database(database_id=_database.id)
+ old_id: int = database.id
+ new_id: uuid = uuid.uuid4()
+ plan.append(f"UPDATE mdb_tables SET tDBID = '{new_id}' WHERE tDBID = {old_id};")
+ plan.append(f"UPDATE mdb_have_access SET database_id = '{new_id}' WHERE database_id = {old_id};")
+ plan.append(f"UPDATE mdb_views SET vdbid = '{new_id}' WHERE vdbid = {old_id};")
+ plan.append(f"UPDATE mdb_identifiers SET dbid = '{new_id}' WHERE dbid = {old_id};")
+ plan.append(f"UPDATE mdb_access SET aDBID = '{new_id}' WHERE aDBID = {old_id};")
+ for view in database.views:
+ v_old_id: int = view.id
+ v_new_id: uuid = uuid.uuid4()
+ plan.append(f"UPDATE mdb_identifiers SET vid = '{v_new_id}' WHERE vid = {v_old_id};")
+ plan.append(f"UPDATE mdb_view_columns SET id = UUID(), view_id = '{v_new_id}' WHERE tid = {v_old_id};")
+ for table in database.tables:
+ tbl_old_id: int = table.id
+ tbl_new_id: uuid = uuid.uuid4()
+ plan.append(f"UPDATE mdb_identifiers SET tid = '{tbl_new_id}' WHERE tid = {tbl_old_id};")
+ plan.append(f"UPDATE mdb_constraints_checks SET id = UUID(), tid = '{tbl_new_id}' WHERE tid = {tbl_old_id};")
+ for fk in table.constraints.foreign_keys:
+ fk_old_id: int = fk.id
+ fk_new_id: uuid = uuid.uuid4()
+ plan.append(f"UPDATE mdb_constraints_foreign_key SET id = '{fk_new_id}', tid = '{tbl_new_id}' WHERE id = {fk_old_id};")
+ for fkref in fk.references:
+ plan.append(f"UPDATE mdb_constraints_foreign_key_reference SET id = UUID(), fkid = '{fk_new_id}' WHERE fkid = {fkref};")
+ for pk in table.constraints.primary_key:
+ pk_old_id: int = pk.id
+ plan.append(f"UPDATE mdb_constraints_primary_key SET pkid = UUID(), tID = '{tbl_new_id}' WHERE tID = {pk_old_id};")
+ for uk in table.constraints.uniques:
+ uk_old_id: int = uk.id
+ uk_new_id: uuid = uuid.uuid4()
+ plan.append(f"UPDATE mdb_constraints_unique SET uid = '{uk_new_id}', tid = '{tbl_new_id}' WHERE uid = {uk_old_id}")
+ plan.append(f"UPDATE mdb_constraints_unique_columns SET id = UUID(), uid = '{uk_new_id}' WHERE uid = {uk_old_id}")
+ for column in table.columns:
+ col_old_id: int = column.id
+ col_new_id: uuid = uuid.uuid4()
+ plan.append(f"UPDATE mdb_columns SET ID = '{col_new_id}' WHERE ID = {col_old_id};")
+ plan.append(f"UPDATE mdb_constraints_unique_columns SET cid = '{col_new_id}' WHERE cid = {col_old_id};")
+ plan.append(f"UPDATE mdb_constraints_primary_key SET cid = '{col_new_id}' WHERE cid = {col_old_id};")
+ plan.append(f"UPDATE mdb_constraints_foreign_key_reference SET cid = '{col_new_id}' WHERE cid = {col_old_id};")
+ plan.append(f"UPDATE mdb_constraints_foreign_key_reference SET rcid = '{col_new_id}' WHERE rcid = {col_old_id};")
+ plan.append(f"UPDATE mdb_columns_concepts SET cID = '{col_new_id}' WHERE cID = {col_old_id};")
+ plan.append(f"UPDATE mdb_columns_units SET cID = '{col_new_id}' WHERE cID = {col_old_id};")
+ plan.append(f"UPDATE mdb_columns_sets SET column_id = '{col_new_id}' WHERE column_id = {col_old_id};")
+ plan.append(f"UPDATE mdb_columns_enums SET column_id = '{col_new_id}' WHERE column_id = {col_old_id};")
+ plan.append(f"UPDATE mdb_tables SET ID = '{tbl_new_id}' WHERE ID = {tbl_old_id};")
+ plan.append(f"UPDATE mdb_databases SET id = '{new_id}' WHERE id = {old_id};")
+ plan.append("COMMIT;")
+
+def update_messages() -> None:
+ plan.append("-- messages")
+ plan.append("BEGIN;")
+ plan.append(f"UPDATE mdb_banner_messages SET ID = UUID();")
+ plan.append("COMMIT;")
+
+def update_identifiers() -> None:
+ plan.append("-- identifiers")
+ plan.append("BEGIN;")
+ for identified in client.get_identifiers():
+ i_old_id: int = identified.id
+ i_new_id: uuid = uuid.uuid4()
+ plan.append(f"UPDATE mdb_identifiers SET ID = '{i_new_id}' WHERE id = {i_old_id};")
+ plan.append(f"UPDATE mdb_identifier_creators SET id = UUID(), pid = '{i_new_id}' WHERE pid = {i_old_id};")
+ plan.append(f"UPDATE mdb_identifier_descriptions SET id = UUID(), pid = '{i_new_id}' WHERE pid = {i_old_id};")
+ plan.append(f"UPDATE mdb_identifier_titles SET id = UUID(), pid = '{i_new_id}' WHERE pid = {i_old_id};")
+ plan.append(f"UPDATE mdb_identifier_funders SET id = UUID(), pid = '{i_new_id}' WHERE pid = {i_old_id};")
+ plan.append(f"UPDATE mdb_identifier_licenses SET id = UUID(), pid = '{i_new_id}' WHERE pid = {i_old_id};")
+ plan.append("COMMIT;")
+
+
+if __name__ == '__main__':
+ plan.append("SET FOREIGN_KEY_CHECKS=0;")
+ update_concepts()
+ update_units()
+ update_messages()
+ update_ontologies()
+ update_images()
+ update_containers()
+ update_databases()
+ update_identifiers()
+ plan.append("SET FOREIGN_KEY_CHECKS=1;")
+ print("\n".join(plan))
diff --git a/dbrepo-metadata-db/migration/16/requirements.txt b/dbrepo-metadata-db/migration/16/requirements.txt
new file mode 100644
index 0000000000..3f6fcb0a57
--- /dev/null
+++ b/dbrepo-metadata-db/migration/16/requirements.txt
@@ -0,0 +1 @@
+dbrepo==1.6.5rc6
\ No newline at end of file
diff --git a/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/endpoints/IdentifierEndpoint.java b/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/endpoints/IdentifierEndpoint.java
index b3d699086e..13fe028bcf 100644
--- a/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/endpoints/IdentifierEndpoint.java
+++ b/dbrepo-metadata-service/rest-service/src/main/java/at/tuwien/endpoints/IdentifierEndpoint.java
@@ -106,7 +106,7 @@ public class IdentifierEndpoint extends AbstractEndpoint {
.filter(i -> !Objects.nonNull(qid) || qid.equals(i.getQueryId()))
.filter(i -> !Objects.nonNull(vid) || vid.equals(i.getViewId()))
.filter(i -> !Objects.nonNull(tid) || tid.equals(i.getTableId()))
- .filter(i -> principal != null && i.getStatus().equals(IdentifierStatusType.DRAFT) ? i.getOwnedBy().equals(getId(principal)) : i.getStatus().equals(IdentifierStatusType.PUBLISHED))
+ .filter(i -> principal != null && i.getStatus().equals(IdentifierStatusType.DRAFT) ? (i.getOwnedBy().equals(getId(principal)) || isSystem(principal)) : i.getStatus().equals(IdentifierStatusType.PUBLISHED))
.toList();
if (identifiers.isEmpty()) {
return ResponseEntity.ok(List.of());
diff --git a/helm/dbrepo/files/create-event-listener.jar b/helm/dbrepo/files/create-event-listener.jar
index f370c8825750a431296ef68c3d482a2e4eee9389..a33db1e9045a92823996c61a9223aafb0d25404e 100644
GIT binary patch
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diff --git a/lib/python/dbrepo/RestClient.py b/lib/python/dbrepo/RestClient.py
index a0b4bf60c4..f29f606fd6 100644
--- a/lib/python/dbrepo/RestClient.py
+++ b/lib/python/dbrepo/RestClient.py
@@ -1,9 +1,8 @@
import logging
import os
+import requests
import sys
import time
-
-import requests
from pandas import DataFrame
from pydantic import TypeAdapter
@@ -1966,7 +1965,7 @@ class RestClient:
:raises FormatNotAvailable: If the service could not represent the output.
:raises ResponseCodeError: If something went wrong with the retrieval of the identifiers.
"""
- url = f'/api/identifiers'
+ url = f'/api/identifier'
if database_id is not None:
url += f'?dbid={database_id}'
if subset_id is not None:
@@ -1993,6 +1992,34 @@ class RestClient:
raise ResponseCodeError(f'Failed to get identifiers: response code: {response.status_code} is not '
f'200 (OK): {response.text}')
+ def get_images(self) -> List[ImageBrief] | str:
+ """
+ Get list of container images.
+
+ :returns: List of images, if successful.
+ """
+ url = f'/api/image'
+ response = self._wrapper(method="get", url=url, headers={'Accept': 'application/json'})
+ if response.status_code == 200:
+ body = response.json()
+ return TypeAdapter(List[ImageBrief]).validate_python(body)
+ raise ResponseCodeError(f'Failed to get images: response code: {response.status_code} is not '
+ f'200 (OK): {response.text}')
+
+ def get_messages(self) -> List[BannerMessage] | str:
+ """
+ Get list of messages.
+
+ :returns: List of messages, if successful.
+ """
+ url = f'/api/message'
+ response = self._wrapper(method="get", url=url, headers={'Accept': 'application/json'})
+ if response.status_code == 200:
+ body = response.json()
+ return TypeAdapter(List[BannerMessage]).validate_python(body)
+ raise ResponseCodeError(f'Failed to get messages: response code: {response.status_code} is not '
+ f'200 (OK): {response.text}')
+
def update_table_column(self, database_id: int, table_id: int, column_id: int, concept_uri: str = None,
unit_uri: str = None) -> Column:
"""
diff --git a/lib/python/dbrepo/api/dto.py b/lib/python/dbrepo/api/dto.py
index bd0d13dc18..656c06a9ff 100644
--- a/lib/python/dbrepo/api/dto.py
+++ b/lib/python/dbrepo/api/dto.py
@@ -3,9 +3,8 @@ from __future__ import annotations
import datetime
from dataclasses import field
from enum import Enum
-from typing import List, Optional, Annotated
-
from pydantic import BaseModel, PlainSerializer
+from typing import List, Optional, Annotated
Timestamp = Annotated[
datetime.datetime, PlainSerializer(lambda v: v.strftime('%Y-%m-%dT%H:%M:%S.%f')[:-3] + 'Z', return_type=str)
@@ -41,6 +40,16 @@ class ImageBrief(BaseModel):
name: str
version: str
jdbc_method: str
+ default: bool
+
+
+class BannerMessage(BaseModel):
+ id: int
+ type: str
+ link: Optional[str] = None
+ link_text: Optional[str] = None
+ display_start: Optional[Timestamp] = None
+ display_end: Optional[Timestamp] = None
class CreateDatabase(BaseModel):
@@ -629,13 +638,13 @@ class Identifier(BaseModel):
id: int
database_id: int
type: IdentifierType
- owner: UserBrief
status: IdentifierStatusType
publication_year: int
publisher: str
creators: List[Creator]
titles: List[IdentifierTitle]
descriptions: List[IdentifierDescription]
+ owned_by: str
funders: Optional[List[IdentifierFunder]] = field(default_factory=list)
doi: Optional[str] = None
language: Optional[str] = None
@@ -699,7 +708,7 @@ class ViewBrief(BaseModel):
initial_view: bool
query: str
query_hash: str
- owned_by: str
+ owner: UserBrief
class ConceptBrief(BaseModel):
@@ -1024,7 +1033,7 @@ class Database(BaseModel):
preview_image: Optional[str] = None
description: Optional[str] = None
tables: Optional[List[Table]] = field(default_factory=list)
- views: Optional[List[View]] = field(default_factory=list)
+ views: Optional[List[ViewBrief]] = field(default_factory=list)
accesses: Optional[List[DatabaseAccess]] = field(default_factory=list)
exchange_name: Optional[str] = None
diff --git a/lib/python/pyproject.toml b/lib/python/pyproject.toml
index b956d6afd0..75113e70b0 100644
--- a/lib/python/pyproject.toml
+++ b/lib/python/pyproject.toml
@@ -1,6 +1,6 @@
[project]
name = "dbrepo"
-version = "1.6.4"
+version = "1.6.5rc6"
description = "DBRepo Python Library"
keywords = [
"DBRepo",
diff --git a/lib/python/setup.py b/lib/python/setup.py
index 53f4832404..df4528ab82 100644
--- a/lib/python/setup.py
+++ b/lib/python/setup.py
@@ -2,7 +2,7 @@
from distutils.core import setup
setup(name="dbrepo",
- version="1.6.4",
+ version="1.6.5rc6",
description="A library for communicating with DBRepo",
url="https://www.ifs.tuwien.ac.at/infrastructures/dbrepo/1.6/",
author="Martin Weise",
diff --git a/lib/python/tests/test_unit_image.py b/lib/python/tests/test_unit_image.py
new file mode 100644
index 0000000000..2802efc690
--- /dev/null
+++ b/lib/python/tests/test_unit_image.py
@@ -0,0 +1,31 @@
+import unittest
+
+import requests_mock
+
+from dbrepo.RestClient import RestClient
+
+from dbrepo.api.dto import ImageBrief
+
+
+class ImageUnitTest(unittest.TestCase):
+
+ def test_get_images_empty_succeeds(self):
+ with requests_mock.Mocker() as mock:
+ # mock
+ mock.get('/api/image', json=[])
+ # test
+ response = RestClient().get_images()
+ self.assertEqual([], response)
+
+ def test_get_images_succeeds(self):
+ with requests_mock.Mocker() as mock:
+ exp = [ImageBrief(id=1, name="mariadb", version="11.1.3", jdbc_method="mariadb", default=False)]
+ # mock
+ mock.get('/api/image', json=[exp[0].model_dump()])
+ # test
+ response = RestClient().get_images()
+ self.assertEqual(exp, response)
+
+
+if __name__ == "__main__":
+ unittest.main()
diff --git a/lib/python/tests/test_unit_messages.py b/lib/python/tests/test_unit_messages.py
new file mode 100644
index 0000000000..0bc16394a0
--- /dev/null
+++ b/lib/python/tests/test_unit_messages.py
@@ -0,0 +1,31 @@
+import unittest
+
+import requests_mock
+
+from dbrepo.RestClient import RestClient
+
+from dbrepo.api.dto import ImageBrief
+
+
+class ImageUnitTest(unittest.TestCase):
+
+ def test_get_message_empty_succeeds(self):
+ with requests_mock.Mocker() as mock:
+ # mock
+ mock.get('/api/message', json=[])
+ # test
+ response = RestClient().get_images()
+ self.assertEqual([], response)
+
+ def test_get_images_succeeds(self):
+ with requests_mock.Mocker() as mock:
+ exp = [BannerMessage(id=1, type="info")]
+ # mock
+ mock.get('/api/message', json=[exp[0].model_dump()])
+ # test
+ response = RestClient().get_images()
+ self.assertEqual(exp, response)
+
+
+if __name__ == "__main__":
+ unittest.main()
--
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