WIP

Signed-off-by: Martin Weise <martin.weise@tuwien.ac.at>

.docs/index.md

@@ -16,9 +16,9 @@ author: Martin Weise
 
 Documentation for version: [v1.9.0](https://gitlab.phaidra.org/fair-data-austria-db-repository/fda-services/-/releases).
 
-DBRepo is a repository for data in databases that cover the entire data life cycle supporting data evolution, -citation 
-and -versioning. It implements the query store of the [RDA WGDC](https://doi.org/10.1162/99608f92.be565013) on precisely
-identifying arbitrary subsets of data.
+DBRepo is an open-source research database repository that cover the data life cycle supporting data evolution, 
+-citation and -versioning. It implements the query store of the [RDA WGDC](https://doi.org/10.1162/99608f92.be565013) on
+precisely identifying arbitrary subsets of data.
 
 ## Why use DBRepo?
 

.env

@@ -11,3 +11,4 @@ POSTGRES_VERSION=17.0.0
 PROMETHEUS_VERSION=2.54.1
 RABBITMQ_VERSION=3.13.1
 SEAWEEDFS_VERSION=3.87.0
+LOG_LEVEL=trace

dbrepo-dashboard-service/app.py

@@ -247,8 +247,18 @@ def update_dashboard(uid: str):
                                  code='error.database.malformed').model_dump_json(), 400, headers)
     try:
         dashboard_client().update(database)
-    except DashboardNotFound as e:
+    except DashboardNotFound:
         return Response(ApiError(status='NOT_FOUND', message=f"Failed to update dashboard: not found",
                                  code="error.dashboard.missing").model_dump_json(), 404, headers)
     dashboard_client().update_anonymous_read_access(uid, database.is_public, database.is_schema_public)
     return Response(), 202, headers
+
+
+@app.route("/api/dashboard/<string:uid>/access/<string:username>", methods=["PUT"], endpoint="update_dashboard_access")
+@metrics.gauge(name='dbrepo_update_dashboard_access', description='Time needed to update dashboard access')
+@swag_from("/app/ds-yml/update_dashboard_access.yml")
+@auth.login_required(role=['system'])
+def update_dashboard(uid: str, username: str):
+    logging.debug(f'endpoint update dashboard access, uid={uid}, username={username}')
+    # not implemented
+    return Response(), 202, headers

dbrepo-dashboard-service/ds-yml/update_dashboard_access.yml

+tags:
+  - dashboard-endpoint
+summary: "Update dashboard access"
+operationId: update_dashboard_access
+description: "Updates a dashboard access in the Dashboard UI. Requires role `system`."
+consumes:
+  - "application/json"
+produces:
+  - "application/json"
+parameters:
+  - name: uid
+    in: path
+    required: true
+    schema:
+      type: string
+      format: uuid
+  - name: username
+    in: path
+    required: true
+    schema:
+      type: string
+responses:
+  202:
+    description: Updated dashboard access successfully
+    content:
+      application/json:
+        schema:
+          type: object
+security:
+  - bearerAuth: [ ]
+  - basicAuth: [ ]

dbrepo-data-service/init/Dockerfile

+FROM --platform=$BUILDPLATFORM python:3.11-alpine3.21
+LABEL org.opencontainers.image.authors="martin.weise@tuwien.ac.at"
+
+RUN apk add --no-cache \
+    curl \
+    bash \
+    jq
+
+COPY Pipfile Pipfile.lock ./
+
+COPY ./lib ./lib
+
+RUN pip install pipenv && \
+    pipenv install gunicorn && \
+    pipenv install --system --deploy
+
+RUN adduser -D dbrepo --uid 1001
+
+WORKDIR /app
+
+RUN mkdir -p /var/log/app/service/data && \
+    chown -R 1001:1001 /var/log/app
+
+USER 1001
+
+COPY --chown=1001 ./init.py ./init.py
+
+ENTRYPOINT [ "python", "./init.py" ]

dbrepo-data-service/init/Pipfile

+[[source]]
+url = "https://pypi.org/simple"
+verify_ssl = true
+name = "pypi"
+
+[packages]
+python-dotenv = "~=1.0"
+#dbrepo = {path = "./lib/dbrepo-1.9.0.tar.gz"}
+[dev-packages]
+coverage = "*"
+pytest = "*"
+requests-mock = "*"
+mariadb = "*"
+
+[requires]
+python_version = "3.11"

dbrepo-data-service/init/Pipfile.lock

+{
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+        },
+        "pipfile-spec": 6,
+        "requires": {
+            "python_version": "3.11"
+        },
+        "sources": [
+            {
+                "name": "pypi",
+                "url": "https://pypi.org/simple",
+                "verify_ssl": true
+            }
+        ]
+    },
+    "default": {
+        "python-dotenv": {
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+            ],
+            "index": "pypi",
+            "version": "==1.1.0"
+        }
+    },
+    "develop": {
+        "certifi": {
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+                "sha256:c0d6290a466a6f3fadf6add2dd4ec11deba4e1a6e3db2dd284edd497aadf802f",
+                "sha256:c5757a7b25fe48040fa120ba6597f5f885b01e323e0d13fe21ff95a70c0f76b7",
+                "sha256:ccad4e29ac1b6f75bfeedb2cac4860fe5bd9e0a2f04c3e3218f661fa389ab101",
+                "sha256:cd21de85aa0e247b79c6c41f8b5541b54285550f2da6a9448d82b53234d3611b",
+                "sha256:ce4553a573edb363d5db12be1c044826878bec039159d6d4eafe826ef773396d",
+                "sha256:d074380f587360d2500f3b065232c67ae248aaf739267807adbcd29b88bdf864",
+                "sha256:d41d4da5f2871b1782c6b74948d2d37aac3a5b39b43a6ba31d736b97a02ae1f1",
+                "sha256:d5102e17b81158de17d4b5bc363fcffd15231a38ef3f50b8e6fa01f0c6911194",
+                "sha256:d52d79dfd3b410b153b6d65b0e3afe834eca2b969377f55ad73c67156d35af0d",
+                "sha256:d591f2ddad432b794f77dc1e94334a80015a3fc7fa07fd6aed8f40362083be5b",
+                "sha256:d616b5a543c7d4deffa25eb8d8ae3d0d95097f08ac8b131600bb7fbf967ea0e2",
+                "sha256:d7af3990490982fbd2437156c69edbe82b7edf99bc60302cceeeaf79afb886b8",
+                "sha256:d8a6c35afd5b912101fabf42975d92d750cfce33c571508a82ff334a133c40d5",
+                "sha256:db181a1896e0bad75b3bf4916c49fd3cf6751f9cc203fe0e0ecbee1fc43590fa",
+                "sha256:dd5c305faa2e69334a53061b3168987847dadc2449bab95735242a9bde92fde8",
+                "sha256:e1f8e96455907496b3e4ea16f63bb578da31e17d2805278b193525e7714f17f2",
+                "sha256:e233a56bbf99e4cb134c4f8e63b16c77714e3987daf2c5aa10c3ba8c4232d730",
+                "sha256:e3f65da9701648d226b6b24ded3e2528b72075e48d7540968cd857c3bd4c5321",
+                "sha256:e4e893c7f7fb12271a667d5c1876710fae06d7580343afdb5f3fc4488b73209e",
+                "sha256:e54b80885b0e61d346accc5709daf8762471a452345521cc9281604a907162c2",
+                "sha256:e93f36a5c9d995f40e9c4cd9bbabd83fd78705792fa250980256c93accd07bb6",
+                "sha256:ebdf212e1ed85af63fa1a76d556c0a3c7b34348ffba6e145a64b15f003ad0a2b",
+                "sha256:f7a95b0dce364535a63fde0ec1b1ca36400037175d3b62ce04d85dbca5e33832",
+                "sha256:f82c1a1c1897d2293cb6c50f20fe8a9ea2add1a228eff479380917a1fe7bbb68",
+                "sha256:fe4877c24711458f7990392181be30166cc3ae72158036ecb48a73c30c99fb6f",
+                "sha256:ff619c58322d9d6df0a859dc76c3532d7bdbc125cb040f7cd642141446b4f654"
+            ],
+            "index": "pypi",
+            "version": "==7.8.1"
+        },
+        "idna": {
+            "hashes": [
+                "sha256:12f65c9b470abda6dc35cf8e63cc574b1c52b11df2c86030af0ac09b01b13ea9",
+                "sha256:946d195a0d259cbba61165e88e65941f16e9b36ea6ddb97f00452bae8b1287d3"
+            ],
+            "markers": "python_version >= '3.6'",
+            "version": "==3.10"
+        },
+        "iniconfig": {
+            "hashes": [
+                "sha256:3abbd2e30b36733fee78f9c7f7308f2d0050e88f0087fd25c2645f63c773e1c7",
+                "sha256:9deba5723312380e77435581c6bf4935c94cbfab9b1ed33ef8d238ea168eb760"
+            ],
+            "markers": "python_version >= '3.8'",
+            "version": "==2.1.0"
+        },
+        "mariadb": {
+            "hashes": [
+                "sha256:194045d2f59b2c9100dad210dbd8ba3008120f8a434e792dae15b711e5449022",
+                "sha256:50b02ff2c78b1b4f4628a054e3c8c7dd92972137727a5cc309a64c9ed20c878c",
+                "sha256:5ae99af48ba92e3e2edad1dcda293f352c1b65e335007943b9def4cdde622fab",
+                "sha256:69b284ed12e6ef8dda6314cb1ca9d20d53b8a32a07bed2924beb25488e7d9502",
+                "sha256:8b49fc1e8c38bf5a779d46f8cea61c99660adb08d5d15cb7dbc7911a6439ffc2",
+                "sha256:8cc4068bdd14f4907746ec3bb37005682e47f84438cf56bdc6d901c2587f792a",
+                "sha256:992064971e0ff4b4154b80b16589ec86237ce4bd33debe1be5212141c056858a",
+                "sha256:b69bc18418e72fcf359d17736cdc3f601a271203aff13ef7c57a415c8fd52ab0",
+                "sha256:ba43c42130d41352f32a5786c339cc931d05472ef7640fa3764d428dc294b88e",
+                "sha256:dd9d0ca112eb670dfa99a2fb7c4398bcc2a8c452dbf5507a8e4b5c4ae991bb2a",
+                "sha256:e3ce7c47be58897822d07f119461b2aa6aa41a53f3505bec517b14fc6c3611a6"
+            ],
+            "index": "pypi",
+            "version": "==1.1.12"
+        },
+        "packaging": {
+            "hashes": [
+                "sha256:29572ef2b1f17581046b3a2227d5c611fb25ec70ca1ba8554b24b0e69331a484",
+                "sha256:d443872c98d677bf60f6a1f2f8c1cb748e8fe762d2bf9d3148b5599295b0fc4f"
+            ],
+            "markers": "python_version >= '3.8'",
+            "version": "==25.0"
+        },
+        "pluggy": {
+            "hashes": [
+                "sha256:7dcc130b76258d33b90f61b658791dede3486c3e6bfb003ee5c9bfb396dd22f3",
+                "sha256:e920276dd6813095e9377c0bc5566d94c932c33b27a3e3945d8389c374dd4746"
+            ],
+            "markers": "python_version >= '3.9'",
+            "version": "==1.6.0"
+        },
+        "pytest": {
+            "hashes": [
+                "sha256:c69214aa47deac29fad6c2a4f590b9c4a9fdb16a403176fe154b79c0b4d4d820",
+                "sha256:f4efe70cc14e511565ac476b57c279e12a855b11f48f212af1080ef2263d3845"
+            ],
+            "index": "pypi",
+            "version": "==8.3.5"
+        },
+        "requests": {
+            "hashes": [
+                "sha256:55365417734eb18255590a9ff9eb97e9e1da868d4ccd6402399eaf68af20a760",
+                "sha256:70761cfe03c773ceb22aa2f671b4757976145175cdfca038c02654d061d6dcc6"
+            ],
+            "markers": "python_version >= '3.8'",
+            "version": "==2.32.3"
+        },
+        "requests-mock": {
+            "hashes": [
+                "sha256:b1e37054004cdd5e56c84454cc7df12b25f90f382159087f4b6915aaeef39563",
+                "sha256:e9e12e333b525156e82a3c852f22016b9158220d2f47454de9cae8a77d371401"
+            ],
+            "index": "pypi",
+            "version": "==1.12.1"
+        },
+        "urllib3": {
+            "hashes": [
+                "sha256:414bc6535b787febd7567804cc015fee39daab8ad86268f1310a9250697de466",
+                "sha256:4e16665048960a0900c702d4a66415956a584919c03361cac9f1df5c5dd7e813"
+            ],
+            "markers": "python_version >= '3.9'",
+            "version": "==2.4.0"
+        }
+    }
+}

dbrepo-data-service/init/database.py

+import mariadb
+from mariadb.connections import Connection
+
+
+class DatabaseClient:
+
+    def __init__(self, username: str, password: str):
+        self.username = username
+        self.password = password
+
+    def connect(self, hostname: str, port: int, database: str | None = None) -> Connection:
+        """
+        :param hostname: The database hostname
+        :param port: The database port
+        :param database: The database name
+
+        :return: Connection The database connection.
+
+        :raises mariadb.Error If the connection cannot be established.
+        """
+        return mariadb.connect(user=self.username, password=self.password, host=hostname, port=port, database=database)
+
+    def get_users(self, hostname: str, port: int, database: str) -> [str]:
+        connection = self.connect(hostname, port, database)
+        cur = connection.cursor()
+        cur.execute(f'SELECT user FROM mysql.user;')
+        users = []
+        for (user,) in cur:
+            users.append(user)
+        connection.close()
+        return users

dbrepo-data-service/init/debug.py

+import logging
+
+from database import DatabaseClient
+from dbrepo.RestClient import RestClient
+from dbrepo.api.exceptions import AccessExistsError
+
+rest_client = RestClient("http://127.0.0.1", "admin", "admin")
+
+database_client = DatabaseClient(username='root', password='dbrepo')
+
+for db in rest_client.get_databases():
+    database = rest_client.get_database(db.id)
+    # create query store if necessary
+    if not rest_client.exists_query_store(db.id):
+        rest_client.create_query_store(db.id)
+        logging.info(f'Created query store in database: {db.internal_name}', extra={'database_id': db.id})
+    # check if user exist
+    for access in database.accesses:
+        print(f'User {access.user.username} has no grant(s) in database: {database.internal_name}')
+        try:
+            rest_client.create_database_access(database.id, access.user.id, access.type)
+            print(f'Created access grant(s) for user {access.user.username} in database: {database.internal_name}')
+        except AccessExistsError:
+            pass
+        print(f'update permission {access.type} for user {access.user.username} in database: {database.internal_name}')
+        rest_client.update_database_access(database.id, access.user.id, access.type)

dbrepo-data-service/init/init.py

+import logging
+import os
+from logging.config import dictConfig
+
+from dbrepo.RestClient import RestClient
+
+from database import DatabaseClient
+
+level = os.getenv("LOG_LEVEL", "DEBUG").upper()
+logging.basicConfig(level=level)
+
+# logging configuration
+dictConfig({
+    'version': 1,
+    'formatters': {
+        'default': {
+            'format': '[%(asctime)s] %(levelname)s in %(module)s: %(message)s',
+        },
+        'simple': {
+            'format': '[%(asctime)s] [%(levelname)s] %(message)s',
+        },
+        "ecs": {
+            "()": "ecs_logging.StdlibFormatter"
+        },
+    },
+    'handlers': {
+        'stream': {
+            'class': 'logging.StreamHandler',
+            'stream': 'ext://sys.stdout',
+            'formatter': 'simple'
+        },
+        'file': {
+            'class': 'logging.handlers.TimedRotatingFileHandler',
+            'formatter': 'ecs',
+            'filename': '/var/log/app/worker/airquality/app.log',
+            'when': 'midnight',
+            'interval': 1,
+            'backupCount': 7,
+            'encoding': 'utf8'
+        },
+    },
+    'root': {
+        'level': 'DEBUG',
+        'handlers': ['stream', 'file']
+    }
+})
+
+rest_client = RestClient(endpoint=os.getenv("METADATA_SERVICE_ENDPOINT", "http://metadata-service:8080"),
+                         username=os.getenv("SYSTEM_USERNAME", "admin"),
+                         password=os.getenv("SYSTEM_PASSWORD", "admin"))
+
+database_client = DatabaseClient(username=os.getenv("SYSTEM_USERNAME", "admin"),
+                                 password=os.getenv("SYSTEM_PASSWORD", "admin"))
+
+if __name__ == "__main__":
+    for db in rest_client.get_databases():
+        database = rest_client.get_database(db.id)
+        # create query store if necessary
+        if not rest_client.exists_query_store(db.id):
+            rest_client.create_query_store(db.id)
+            logging.info(f'Created query store in database: {db.internal_name}', extra={'database_id': db.id})
+        # check if user exist
+        users = database_client.get_users(db.host, db.port, db.internal_name)
+        missing = [access.user.username in [u for u in users] for access in database.accesses]
+        print(f'===> {missing}')
+        # database.accesses
+    # check all users exist in data-db and have correct grants
+    # remove queries from query store older than x days
+    logging.info("Finished. Exiting.")

dbrepo-data-service/rest-service/src/main/java/at/ac/tuwien/ifs/dbrepo/DataServiceApplication.java

 package at.ac.tuwien.ifs.dbrepo;
 
-import at.ac.tuwien.ifs.dbrepo.core.api.database.DatabaseBriefDto;
-import at.ac.tuwien.ifs.dbrepo.core.api.database.DatabaseDto;
-import at.ac.tuwien.ifs.dbrepo.core.api.database.ViewDto;
-import at.ac.tuwien.ifs.dbrepo.core.api.database.table.TableDto;
-import at.ac.tuwien.ifs.dbrepo.core.exception.*;
-import at.ac.tuwien.ifs.dbrepo.gateway.MetadataServiceGateway;
-import at.ac.tuwien.ifs.dbrepo.service.CacheService;
-import at.ac.tuwien.ifs.dbrepo.service.ContainerService;
-import at.ac.tuwien.ifs.dbrepo.service.DatabaseService;
 import lombok.extern.slf4j.Slf4j;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.boot.CommandLineRunner;
 import org.springframework.boot.SpringApplication;
 import org.springframework.boot.autoconfigure.SpringBootApplication;
-import org.springframework.context.ApplicationContext;
-import org.springframework.scheduling.annotation.EnableScheduling;
-
-import java.sql.SQLException;
-import java.util.List;
 
 @Slf4j
-@EnableScheduling
 @SpringBootApplication
-public class DataServiceApplication implements CommandLineRunner {
-
-    private final CacheService cacheService;
-    private final DatabaseService databaseService;
-    private final ContainerService containerService;
-    private final ApplicationContext applicationContext;
-    private final MetadataServiceGateway metadataServiceGateway;
-
-    @Autowired
-    public DataServiceApplication(CacheService cacheService, DatabaseService databaseService,
-                                  ContainerService containerService, ApplicationContext applicationContext,
-                                  MetadataServiceGateway metadataServiceGateway) {
-        this.cacheService = cacheService;
-        this.databaseService = databaseService;
-        this.containerService = containerService;
-        this.applicationContext = applicationContext;
-        this.metadataServiceGateway = metadataServiceGateway;
-    }
+public class DataServiceApplication {
 
     public static void main(String[] args) {
         SpringApplication.run(DataServiceApplication.class, args);
     }
-
-    @Override
-    public void run(String... args) throws MetadataServiceException, RemoteUnavailableException, SQLException,
-            DatabaseNotFoundException, QueryStoreCreateException, TableNotFoundException, DatabaseMalformedException,
-            ViewNotFoundException {
-        if (args.length == 0) {
-            return;
-        }
-        for (DatabaseBriefDto d : metadataServiceGateway.getDatabases()) {
-            final DatabaseDto database = cacheService.getDatabase(d.getId());
-            containerService.createQueryStore(database.getContainer(), database.getInternalName());
-            final List<TableDto> tables = databaseService.exploreTables(database);
-            if (database.getTables().size() != tables.size()) {
-                final List<TableDto> missingTables = tables.stream()
-                        .filter(table -> database.getTables()
-                                .stream()
-                                .noneMatch(t -> table.getInternalName().equals(t.getInternalName())))
-                        .toList();
-                if (!missingTables.isEmpty()) {
-                    log.warn("Failed to obtain metadata on table(s): {}", missingTables);
-                    metadataServiceGateway.updateTableSchemas(d.getId());
-                }
-            }
-            final List<ViewDto> views = databaseService.exploreViews(database);
-            if (database.getViews().size() != views.size()) {
-                final List<ViewDto> missingViews = views.stream()
-                        .filter(view -> database.getTables()
-                                .stream()
-                                .noneMatch(v -> view.getInternalName().equals(v.getInternalName())))
-                        .toList();
-                if (!missingViews.isEmpty()) {
-                    log.warn("Failed to obtain metadata on view(s): {}", missingViews);
-                    metadataServiceGateway.updateViewSchemas(d.getId());
-                }
-            }
-        }
-        log.info("Finished initialization");
-        SpringApplication.exit(applicationContext, () -> 0);
-    }
 }