Merge 8cdb3c5 into a9e9555

.isort.cfg

@@ -4,4 +4,4 @@ include_trailing_comma = true
 force_grid_wrap = 0
 use_parentheses = true
 line_length = 100
-known_third_party =alembic,dateutil,geoalchemy2,geopy,halo,iterfzf,loguru,pg8000,pint,prompt_toolkit,pyfiglet,pygments,pytest,setuptools,shapely,sqlalchemy,tabulate,testing,tqdm
+known_third_party =alembic,dateutil,geoalchemy2,geopy,halo,iterfzf,loguru,pg8000,pint,prompt_toolkit,pyfiglet,pygments,pytest,setuptools,shapely,sqlalchemy,sqlalchemy_utils,tabulate,testing,tqdm

docs/conf.py

@@ -63,11 +63,7 @@
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ["_static"]
 
-html_context = {
-    "css_files": [
-        "_static/theme_overrides.css",
-    ],  # override wide tables in RTD theme
-}
+html_css_files = ["_static/theme_overrides.css"]  # override wide tables in RTD theme
 
 
 # -- Extension configuration -------------------------------------------------

migrations/latest_revisions.json

@@ -1,4 +1,4 @@
 {
     "LATEST_POSTGRES_VERSION": "1be821cb7908",
-    "LATEST_SQLITE_VERSION": "cb9a5f93f0aa"
+    "LATEST_SQLITE_VERSION": "a382a0f4b1be"
 }

migrations/sqlite_versions/2021-02-10_a382a0f4b1be_correct_privacy_id_type_of_hostedby.py

@@ -0,0 +1,37 @@
+"""Correct privacy_id type of HostedBy
+
+Revision ID: a382a0f4b1be
+Revises: cb9a5f93f0aa
+Create Date: 2021-02-10 16:20:41.425779+00:00
+
+"""
+import sqlalchemy as sa
+from alembic import op
+
+import pepys_import
+
+# revision identifiers, used by Alembic.
+revision = "a382a0f4b1be"
+down_revision = "cb9a5f93f0aa"
+branch_labels = None
+depends_on = None
+
+
+def upgrade():
+    with op.batch_alter_table("HostedBy", schema=None) as batch_op:
+        batch_op.alter_column(
+            "privacy_id",
+            existing_type=sa.INTEGER(),
+            type_=pepys_import.utils.sqlalchemy_utils.UUIDType(length=16),
+            existing_nullable=False,
+        )
+
+
+def downgrade():
+    with op.batch_alter_table("HostedBy", schema=None) as batch_op:
+        batch_op.alter_column(
+            "privacy_id",
+            existing_type=pepys_import.utils.sqlalchemy_utils.UUIDType(length=16),
+            type_=sa.INTEGER(),
+            existing_nullable=False,
+        )

pepys_admin/maintenance/gui.py

@@ -44,6 +44,7 @@
 from pepys_admin.maintenance.widgets.dropdown_box import DropdownBox
 from pepys_admin.maintenance.widgets.filter_widget import FilterWidget
 from pepys_admin.maintenance.widgets.filter_widget_utils import filter_widget_output_to_query
+from pepys_import.core.store import constants
 from pepys_import.core.store.data_store import DataStore
 
 logger.remove()
@@ -335,7 +336,7 @@ def do_merge(platform_list, master_platform, set_percentage=None, is_cancelled=N
             # outside of the GUI context too)
             set_percentage(10)
             with self.data_store.session_scope():
-                self.data_store.merge_platforms(platform_list, master_platform)
+                self.data_store.merge_generic(constants.PLATFORM, platform_list, master_platform)
             time.sleep(3)
             set_percentage(90)
             time.sleep(1)

pepys_import/core/store/common_db.py

@@ -226,7 +226,7 @@ def get_sensor(
 class TaskMixin:
     @declared_attr
     def parent(self):
-        return relationship("Task", lazy="joined", join_depth=1, innerjoin=True, uselist=False)
+        return relationship("Task")
 
     @declared_attr
     def parent_name(self):

pepys_import/core/store/data_store.py

@@ -1,15 +1,17 @@
 import os
 import sys
+import uuid
 from contextlib import contextmanager
 from datetime import datetime
 from getpass import getuser
 from importlib import import_module
 
-from sqlalchemy import create_engine, inspect, or_
+from sqlalchemy import create_engine, inspect
 from sqlalchemy.event import listen
 from sqlalchemy.exc import ArgumentError, OperationalError
 from sqlalchemy.orm import sessionmaker, undefer
 from sqlalchemy.sql import func
+from sqlalchemy_utils import merge_references
 
 from paths import PEPYS_IMPORT_DIRECTORY
 from pepys_import import __version__
@@ -31,6 +33,7 @@
 
 from ...utils.error_handling import handle_first_connection_error
 from ...utils.sqlalchemy_utils import get_primary_key_for_table
+from ...utils.table_name_utils import table_name_to_class_name
 from ...utils.text_formatting_utils import custom_print_formatted_text, format_error_message
 from .db_base import BasePostGIS, BaseSpatiaLite
 from .db_status import TableTypes
@@ -1649,7 +1652,7 @@ def get_logs_by_change_id(self, change_id):
             .all()
         )
 
-    def merge_platforms(self, platform_list, master_id) -> bool:
+    def merge_platforms(self, platform_list, master_id, change_id) -> bool:
         """Merges given platforms. Moves sensors from other platforms to the Target platform.
         If sensor with same name is already present on Target platform, moves measurements
         to that sensor. Also moves entities in Comments, Participants, LogsHoldings, Geometry, Media
@@ -1664,33 +1667,10 @@ def merge_platforms(self, platform_list, master_id) -> bool:
         """
         Platform = self.db_classes.Platform
         Sensor = self.db_classes.Sensor
-        State = self.db_classes.State
-        Contact = self.db_classes.Contact
-
-        if isinstance(master_id, Platform):
-            master_id = master_id.platform_id
-
-        master_platform = (
-            self.session.query(Platform).filter(Platform.platform_id == master_id).scalar()
-        )
-        if not master_platform:
-            raise ValueError(f"No platform found with the given master_id: '{master_id}'!")
+        self._check_master_id(Platform, master_id)
         master_sensor_names = self.session.query(Sensor.name).filter(Sensor.host == master_id).all()
         master_sensor_names = set([n for (n,) in master_sensor_names])
-
         sensor_list = list()
-        if isinstance(platform_list[0], Platform):  # Extract platform_ids from platform objects
-            platform_list = [p.platform_id for p in platform_list]
-
-        if master_id in platform_list:
-            platform_list.remove(master_id)  # We don't need to change these values
-
-        reason_platform_list = ",".join([str(p) for p in platform_list])
-        change_id = self.add_to_changes(
-            user=USER,
-            modified=datetime.utcnow(),
-            reason=f"Merging Platforms '{reason_platform_list}' to '{master_id}'.",
-        ).change_id
         for p_id in platform_list:
             self.update_platform_ids(p_id, master_id, change_id)
 
@@ -1717,36 +1697,12 @@ def merge_platforms(self, platform_list, master_id) -> bool:
                     .filter(Sensor.host == master_id, Sensor.name == sensor.name)
                     .scalar()
                 )
-                query = self.session.query(State).filter(State.sensor_id == sensor.sensor_id)
-                [
-                    self.add_to_logs(
-                        table=constants.STATE,
-                        row_id=s.sensor_id,
-                        field="sensor_id",
-                        new_value=str(sensor.sensor_id),
-                        change_id=change_id,
-                    )
-                    for s in query.all()
-                ]
-                query.update({"sensor_id": master_sensor_id})  # Update States
-
-                query = self.session.query(Contact).filter(
-                    or_(Contact.sensor_id == sensor.sensor_id, Contact.subject_id == master_id)
+                self.merge_measurements(
+                    constants.SENSOR, [sensor.sensor_id], master_sensor_id, change_id
                 )
-                [
-                    self.add_to_logs(
-                        table=constants.CONTACT,
-                        row_id=s.sensor_id,
-                        field="sensor_id",
-                        new_value=str(sensor.sensor_id),
-                        change_id=change_id,
-                    )
-                    for s in query.all()
-                ]
-                query.update({"sensor_id": master_sensor_id})  # Update Contacts
 
-        for p_id in platform_list:  # Delete merged platforms
-            self.session.query(Platform).filter(Platform.platform_id == p_id).delete()
+        # Delete merged platforms
+        self._delete_merged_objects(Platform, platform_list)
         self.session.flush()
         return True
 
@@ -1784,3 +1740,119 @@ def update_platform_ids(self, merge_platform_id, master_platform_id, change_id):
                 except Exception:
                     pass
         self.session.flush()
+
+    def _check_master_id(self, table_obj, master_id):
+        master_obj = (
+            self.session.query(table_obj)
+            .filter(getattr(table_obj, get_primary_key_for_table(table_obj)) == master_id)
+            .scalar()
+        )
+        if not master_obj:
+            raise ValueError(f"No object found with the given master_id: '{master_id}'!")
+        return master_obj
+
+    def _delete_merged_objects(self, table_obj, id_list):
+        # Delete merged objects
+        self.session.query(table_obj).filter(
+            getattr(table_obj, get_primary_key_for_table(table_obj)).in_(id_list)
+        ).delete(synchronize_session="fetch")
+        self.session.flush()
+
+    def merge_measurements(self, table_name, id_list, master_id, change_id):
+        if table_name == constants.SENSOR:
+            table_obj = self.db_classes.Sensor
+            field = "sensor_id"
+            self._check_master_id(table_obj, master_id)
+            table_objects = [self.db_classes.State, self.db_classes.Contact]
+        elif table_name == constants.DATAFILE:
+            table_obj = self.db_classes.Datafile
+            field = "source_id"
+            self._check_master_id(table_obj, master_id)
+            table_objects = [
+                self.db_classes.State,
+                self.db_classes.Contact,
+                self.db_classes.Activation,
+                self.db_classes.LogsHolding,
+                self.db_classes.Comment,
+                self.db_classes.Geometry1,
+                self.db_classes.Media,
+            ]
+        else:
+            raise ValueError(
+                f"You should give one of the following tables to merge measurements: "
+                f"{constants.SENSOR}, {constants.DATAFILE}"
+            )
+        values = ",".join(map(str, id_list))
+        for t_obj in table_objects:
+            query = self.session.query(t_obj).filter(getattr(t_obj, field).in_(id_list))
+            [
+                self.add_to_logs(
+                    table=t_obj.__tablename__,
+                    row_id=getattr(s, field),
+                    field=field,
+                    new_value=values,
+                    change_id=change_id,
+                )
+                for s in query.all()
+            ]
+            query.update({field: master_id}, synchronize_session="fetch")
+
+        # Delete merged objects
+        self._delete_merged_objects(table_obj, id_list)
+
+    def merge_objects(self, table_name, id_list, master_id, change_id):
+        # Table names are plural in the database, therefore make it singular
+        table = table_name_to_class_name(table_name)
+        table_obj = getattr(self.db_classes, table)
+        to_obj = self._check_master_id(table_obj, master_id)
+
+        for obj_id in id_list:
+            primary_key_field = get_primary_key_for_table(table_obj)
+            from_obj = (
+                self.session.query(table_obj)
+                .filter(getattr(table_obj, primary_key_field) == obj_id)
+                .scalar()
+            )
+            merge_references(from_obj, to_obj)
+            self.add_to_logs(
+                table=table_obj.__tablename__,
+                row_id=getattr(from_obj, primary_key_field),
+                field=primary_key_field,
+                new_value=str(obj_id),
+                change_id=change_id,
+            )
+            self.session.flush()
+        # Delete merged objects
+        self._delete_merged_objects(table_obj, id_list)
+
+    def merge_generic(self, table_name, id_list, master_id) -> bool:
+        reference_table_objects = self.meta_classes[TableTypes.REFERENCE]
+        reference_table_names = [obj.__tablename__ for obj in reference_table_objects]
+
+        table = table_name_to_class_name(table_name)
+        table_obj = getattr(self.db_classes, table)
+        if id_list and not isinstance(id_list[0], uuid.UUID):
+            id_list = [getattr(i, get_primary_key_for_table(table_obj)) for i in id_list]
+
+        if not isinstance(master_id, uuid.UUID):
+            master_id = getattr(master_id, get_primary_key_for_table(table_obj))
+
+        reason_list = ",".join([str(p) for p in id_list])
+        change_id = self.add_to_changes(
+            user=USER,
+            modified=datetime.utcnow(),
+            reason=f"Merging {table_name} '{reason_list}' to '{master_id}'.",
+        ).change_id
+
+        if master_id in id_list:
+            id_list.remove(master_id)  # We don't need to change these values
+
+        if table_name == constants.PLATFORM:
+            self.merge_platforms(id_list, master_id, change_id)
+        elif table_name in [constants.SENSOR, constants.DATAFILE]:
+            self.merge_measurements(table_name, id_list, master_id, change_id)
+        elif table_name in reference_table_names + [constants.TAG, constants.TASK]:
+            self.merge_objects(table_name, id_list, master_id, change_id)
+        else:
+            return False
+        return True

pepys_import/core/store/sqlite_db.py

@@ -55,7 +55,7 @@ class HostedBy(BaseSpatiaLite, HostedByMixin):
     hosted_from = Column(DATE, nullable=False)
     host_to = Column(DATE, nullable=False)
     privacy_id = Column(
-        Integer, ForeignKey("Privacies.privacy_id", onupdate="cascade"), nullable=False
+        UUIDType, ForeignKey("Privacies.privacy_id", onupdate="cascade"), nullable=False
     )
     created_date = Column(DateTime, default=datetime.utcnow)
 

requirements.txt

@@ -15,4 +15,5 @@ setuptools>=40.8.0
 Pygments>=2.6.1
 geopy>=1.22
 halo>=0.0.31
-loguru
+loguru
+sqlalchemy-utils==0.36.8