#112 - converted most session.query.get calls to session.get (step 2 …

…& 3 partly)

odmf/dataimport/base.py

@@ -391,7 +391,7 @@ def to_config(self) -> RawConfigParser:
         from .. import db
         config = RawConfigParser(allow_no_value=True)
         with db.session_scope() as session:
-            inst = session.query(db.Datasource).get(self.instrument)
+            inst = session.get(db.Datasource, self.instrument)
             if not inst:
                 raise ValueError(
                     'Error in import description: %s is not a valid instrument id')

odmf/dataimport/importlog.py

@@ -87,7 +87,7 @@ def __init__(self, filename, user, sheetname=0):
             df[c] = df[c].astype('Int64')
 
         with db.session_scope() as session:
-            _user: db.Person = session.query(db.Person).get(user)
+            _user: db.Person = session.get(db.Person, user)
             if not _user:
                 raise RuntimeError('%s is not a valid user' % user)
             else:
@@ -150,7 +150,7 @@ def logexists(self, session, site, time, timetolerance=30):
 
     def get_dataset(self, session, row, data) -> db.Timeseries:
         """Loads the dataset from a row and checks if it is manually measured and at the correct site"""
-        ds = session.query(db.Dataset).get(data.dataset)
+        ds = session.get(db.Dataset, data.dataset)
         if not ds:
             raise LogImportRowError(row, f'Dataset {data.dataset} does not exist')
         # check dataset is manual measurement
@@ -193,8 +193,8 @@ def row_to_log(self, session, row, data):
         Creates a new db.Log object from a row without dataset
         """
         time = data.time.to_pydatetime()
-        site = session.query(db.Site).get(data.site)
-        user = session.query(db.Person).get(self.user)
+        site = session.get(db.Site, data.site)
+        user = session.get(db.Person, self.user)
 
         if not site:
             raise LogImportRowError(row, f'Log: Site #{data.site} not found')

odmf/dataimport/pandas_import.py

@@ -41,7 +41,7 @@ def __init__(self, session, idescr: ImportDescription, col: ImportColumn,
 
         if col.append:
             try:
-                self.dataset: db.Timeseries = session.query(db.Dataset).get(int(col.append))
+                self.dataset: db.Timeseries = session.get(db.Dataset, int(col.append))
                 assert self.dataset.type == 'timeseries'
                 self.dataset.start = min(start, self.dataset.start)
                 self.dataset.end = max(end, self.dataset.end)
@@ -101,11 +101,11 @@ def columndatasets_from_description(
     """
     with session.no_autoflush:
         # Get instrument, user and site object from db
-        inst = session.query(db.Datasource).get(idescr.instrument)
-        user = session.query(db.Person).get(user)
-        site = session.query(db.Site).get(siteid)
+        inst = session.get(db.Datasource, idescr.instrument)
+        user = session.get(db.Person, user)
+        site = session.get(db.Site, siteid)
         # Get "raw" as data quality, to use as a default value
-        raw = session.query(db.Quality).get(0)
+        raw = session.get(db.Quality, 0)
         # Get all the relevant valuetypes (vt) from db as a dict for fast look up
         valuetypes = {
             vt.id: vt for vt in
@@ -332,7 +332,7 @@ def get_newid_range(ds: db.Timeseries):
         dsid = int(dsid)
         # int conversion is necessary to prevent
         # (psycopg2.ProgrammingError) can't adapt type 'numpy.int64'
-        ds = session.query(db.Dataset).get(dsid)
+        ds = session.get(db.Dataset, dsid)
         if ds:
             # Filter data for the current ds
             ds_data = data[ds_ids == dsid]

odmf/db/base.py

@@ -8,7 +8,6 @@
 
 import sqlalchemy as sql
 import sqlalchemy.orm as orm
-from sqlalchemy.ext.declarative import declarative_base
 from contextlib import contextmanager
 from functools import total_ordering
 
@@ -112,10 +111,10 @@ def query(cls, session):
 
     @classmethod
     def get(cls, session, id):
-        return session.query(cls).get(id)
+        return session.get(cls, id)
 
 
-Base = declarative_base(cls=Base)
+Base = orm.declarative_base(cls=Base)
 metadata = Base.metadata
 
 
@@ -150,7 +149,7 @@ def q(self) -> orm.Query:
         return self.session.query(self.cls).filter_by(**self.filter)
 
     def __getitem__(self, item):
-        if (res:=self.q.get(item)) is not None:
+        if (res:=self.session.get(self.cls, item)) is not None:
             return res
         else:
             raise KeyError(f'{item} not found in {self.cls}')

odmf/db/dataset.py

@@ -307,7 +307,7 @@ def removedataset(*args):
     """Removes a dataset and its records entirely from the database
     !!Handle with care, there will be no more checking!!"""
     with session_scope() as session:
-        datasets = [session.query(Dataset).get(int(a)) for a in args]
+        datasets = [session.get(Dataset, int(a)) for a in args]
         for ds in datasets:
             dsid = ds.id
             if ds.is_timeseries():

odmf/plot/plot.py

@@ -115,14 +115,14 @@ def load(self, start=None, end=None):
         return series
 
     def valuetype(self, session):
-        return session.query(db.ValueType).get(
+        return session.get(db.ValueType, 
             int(self.valuetypeid)) if self.valuetypeid else None
 
     def site(self, session):
-        return session.query(db.Site).get(int(self.siteid)) if self.siteid else None
+        return session.get(db.Site, int(self.siteid)) if self.siteid else None
 
     def instrument(self, session):
-        return session.query(db.Datasource).get(
+        return session.get(db.Datasource, 
             int(self.instrumentid)) if self.instrumentid else None
 
     def export_csv(self, stream, start=None, end=None):
@@ -194,7 +194,7 @@ def get_ylabel(self):
         elif self.lines:
             with db.session_scope() as session:
                 l = self.lines[0]
-                valuetype = session.query(db.ValueType).get(l.valuetypeid)
+                valuetype = session.get(db.ValueType, l.valuetypeid)
                 return f'{valuetype.name} [{valuetype.unit}]'
         else:
             return 'unknown'

odmf/tools/create_db.py

@@ -30,7 +30,7 @@ def add_admin(password=None):
     from odmf import db
     from odmf.tools import hashpw
     with db.session_scope() as session:
-        if session.query(db.Person).get('odmf.admin'):
+        if session.get(db.Person, 'odmf.admin'):
             logger.info('odmf.admin exists already')
         else:
             user = db.Person(username='odmf.admin', firstname='odmf', surname='admin', access_level=4)
@@ -50,7 +50,7 @@ def add_quality_data(data):
     with db.session_scope() as session:
 
         for q in data:
-            if not session.query(db.Quality).get(q['id']):
+            if not session.get(db.Quality, q['id']):
                 session.add(db.Quality(**q))
                 logger.debug(f'Added quality level {q["id"]}')
                 active=True

odmf/webpage/api/dataset_api.py

@@ -54,7 +54,7 @@ def parse_id(dsid: str) -> int:
     def get_dataset(dsid: str, check_access=True) -> db.Dataset:
         dsid = DatasetAPI.parse_id(dsid)
         with db.session_scope() as session:
-            ds = session.query(db.Dataset).get(dsid)
+            ds = session.get(db.Dataset, dsid)
             if not ds:
                 raise web.APIError(404, f'ds{dsid} does not exist')
             elif check_access and ds.access > ds.get_access_level(users.current):
@@ -158,11 +158,11 @@ def new(self, **kwargs):
         """
         with db.session_scope() as session:
             try:
-                pers = session.query(db.Person).get(kwargs.get('measured_by'))
-                vt = session.query(db.ValueType).get(kwargs.get('valuetype'))
-                q = session.query(db.Quality).get(kwargs.get('quality'))
-                s = session.query(db.Site).get(kwargs.get('site'))
-                src = session.query(db.Datasource).get(kwargs.get('source'))
+                pers = session.get(db.Person, kwargs.get('measured_by'))
+                vt = session.get(db.ValueType, kwargs.get('valuetype'))
+                q = session.get(db.Quality, kwargs.get('quality'))
+                s = session.get(db.Site, kwargs.get('site'))
+                src = session.get(db.Datasource, kwargs.get('source'))
 
                 ds = db.Timeseries()
                 # Get properties from the keyword arguments kwargs
@@ -214,7 +214,7 @@ def new(self, **kwargs):
     @web.method.post_or_delete
     def delete(self, dsid: int):
         with db.session_scope() as session:
-            if not (ds := session.query(db.Dataset).get(dsid)):
+            if not (ds := session.get(db.Dataset, dsid)):
                 raise web.APIError(404, f'Dataset {dsid} not found')
             if isinstance(ds, db.Timeseries) and ds.size():
                 raise web.APIError(500, f'Dataset ds{dsid} has {ds.size()} records. Call api.dataset.delete_records({dsid}) first, to delete all records')
@@ -226,7 +226,7 @@ def delete(self, dsid: int):
     def count_records(self, dsid: int):
         web.mime.plain.set()
         with db.session_scope() as session:
-            if not (ds := session.query(db.Dataset).get(dsid)):
+            if not (ds := session.get(db.Dataset, dsid)):
                 raise web.APIError(404, f'Dataset {dsid} not found')
             return f'{ds.size()}'.encode('utf-8')
 
@@ -239,7 +239,7 @@ def delete_records(self, dsid: int, start=None, end=None):
         """
         web.mime.plain.set()
         with db.session_scope() as session:
-            if not (ds := session.query(db.Timeseries).get(dsid)):
+            if not (ds := session.get(db.Timeseries, dsid)):
                 raise web.APIError(404, f'Dataset {dsid} not found')
             if ds.access > ds.get_access_level(users.current):
                 raise web.APIError(403, 'Not enough privileges')
@@ -276,7 +276,7 @@ def addrecord(self, dsid: int, value: float, time: str,
         with db.session_scope() as session:
             try:
                 dsid = self.parse_id(dsid)
-                ds = session.query(db.Timeseries).get(dsid)
+                ds = session.get(db.Timeseries, dsid)
                 if ds.access > ds.get_access_level(users.current):
                     raise web.APIError(403, 'Not enough privileges')
 
@@ -332,7 +332,7 @@ def addrecords_json(self):
                                     f'(allowed keywords are dsid, dataset and dataset_id)')
                 if not dataset or dataset.id != dsid:
                     # load dataset from db
-                    dataset = session.query(db.Dataset).get(dsid)
+                    dataset = session.get(db.Dataset, dsid)
                 else:
                     ...  # reuse last dataset
                 if not dataset:

odmf/webpage/api/site_api.py

@@ -31,7 +31,7 @@ def index(self, siteid: int=None):
             url, res = get_help(self, self.url)
             return web.json_out(res)
         with db.session_scope() as session:
-            if not (site := session.query(db.Site).get(siteid)):
+            if not (site := session.get(db.Site, siteid)):
                 raise web.APIError(404, f'#{site} does not exist')
             else:
                 return web.json_out(site)