Notebook

In [1]:

import sqlalchemy
from sqlalchemy import create_engine, Column, String, Boolean, Integer, Float, MetaData, Table, type_coerce, ForeignKey, case, update
from sqlalchemy.orm import mapper, create_session, relationship, aliased, Session
from sqlalchemy.ext.declarative import declarative_base
import csv
from sqlalchemy import case
import numpy as np
from sqlalchemy.ext.automap import automap_base
import matplotlib.pyplot as plt
import sqlalchemy.types as types
import numbers
from sqlalchemy.sql import and_, or_, not_, func
from sqlalchemy.sql import select
import os
import glob
import re
from os.path import isfile
import gsw

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basedir='/ocean/shared/SalishSeaCastData/DFO/CTD/'
dbname='DFO_CTD.sqlite'
datelims=()
engine = create_engine('sqlite:///' + basedir + dbname, echo = False)
Base = automap_base()
# reflect the tables in salish.sqlite:
Base.prepare(engine, reflect=True)
# mapped classes have been created
# existing tables:
StationTBL=Base.classes.StationTBL
ObsTBL=Base.classes.ObsTBL
CalcsTBL=Base.classes.CalcsTBL
session = create_session(bind = engine, autocommit = False, autoflush = True)
SA=case([(CalcsTBL.Salinity_T0_C0_SA!=None, CalcsTBL.Salinity_T0_C0_SA)], else_=
         case([(CalcsTBL.Salinity_T1_C1_SA!=None, CalcsTBL.Salinity_T1_C1_SA)], else_=
         case([(CalcsTBL.Salinity_SA!=None, CalcsTBL.Salinity_SA)], else_= None)))
CT=case([(CalcsTBL.Temperature_Primary_CT!=None, CalcsTBL.Temperature_Primary_CT)], else_=
         case([(CalcsTBL.Temperature_Secondary_CT!=None, CalcsTBL.Temperature_Secondary_CT)], else_=CalcsTBL.Temperature_CT))
ZD=case([(ObsTBL.Depth!=None,ObsTBL.Depth)], else_= CalcsTBL.Z)

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qry=session.query(StationTBL.sourceFile,ObsTBL.sourceFile).\
        select_from(StationTBL).join(ObsTBL,ObsTBL.StationTBLID==StationTBL.ID).\
        join(CalcsTBL,CalcsTBL.ObsTBLID==ObsTBL.ID).filter(and_(StationTBL.Lat>47-3/2.5*(StationTBL.Lon+123.5),
                                                            StationTBL.Lat<47-3/2.5*(StationTBL.Lon+121),
                                                            StationTBL.Include==True,ObsTBL.Include==True,CalcsTBL.Include==True,
                                                               StationTBL.StartYear==2015,StationTBL.StartMonth==2,CT>11))

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for row in qry.distinct():
    print(row)

('req20181116/EO UBC November 16, 2018 (2015 data)/2015-29-0002.ctd', 'req20181116/EO UBC November 16, 2018 (2015 data)/2015-29-0002.ctd')

add to processDFO_CTD.py in case zip is re-extracted and file reverts to original: fnameErr='req20181116/EO UBC November 16, 2018 (2015 data)/2015-29-0002.ctd' if session.query(StationTBL).filter(and_(StationTBL.sourceFile==fnameErr,StationTBL.StartMonth==2)).count(): session0.query(StationTBL0).filter(StationTBL0.sourceFile==fnameErr).update({"StartMonth":8,"StartDay":2})

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fnameErr='req20181116/EO UBC November 16, 2018 (2015 data)/2015-29-0002.ctd'
for row in session.query(StationTBL.ID,StationTBL.StartMonth).filter(StationTBL.sourceFile==fnameErr).one():
    print(row)
session.query(StationTBL).filter(StationTBL.sourceFile==fnameErr).update({"StartMonth":8,"StartDay":2})

1897
2.0

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session.commit()

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session.close()
engine.dispose()

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