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Sqlalchemy 2.0 update #25

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35a07a4
feat: begin update to sqlalchemy2, update models and reqs
brucetony Sep 15, 2023
86022d8
feat: finish updating models for sqla2 and blacken code
brucetony Sep 15, 2023
b61e876
fix: add optional to clinvar props
brucetony Sep 15, 2023
f87311a
build: upgrade click version to work with flask deps
brucetony Sep 18, 2023
05a4214
fix: disgenet URLs and merge method
brucetony Sep 18, 2023
84da7eb
fix: disgenet nullable fields, now working
brucetony Sep 18, 2023
02142f9
fix: hgnc sqla2 import
brucetony Sep 18, 2023
fce5280
feat: drugbank sqla2 import
brucetony Sep 18, 2023
dfe6bcd
feat: gwas catalog sqla2 import
brucetony Sep 18, 2023
c0baf71
feat: clinvar sqla2 import
brucetony Sep 18, 2023
f8502ae
feat: mirtarbase sqla2 import
brucetony Sep 18, 2023
9bf2046
feat: intact sqla2 import
brucetony Sep 18, 2023
6b060d3
feat: pc sqla2 import
brucetony Sep 18, 2023
6ab734f
feat: stringdb sqla2 import
brucetony Sep 18, 2023
0dc24ef
feat: protein atlas sqla2 import
brucetony Sep 18, 2023
fb2c89e
feat: get ncbi and pc working
brucetony Sep 20, 2023
608c4b6
fix: ncbi constraint
brucetony Sep 20, 2023
d4f6670
feat: update iuphar to sqla 2
brucetony Sep 21, 2023
c1856ca
style: black and isort
brucetony Sep 21, 2023
201ef8a
feat: update intact and iuphar to select stmts
brucetony Sep 21, 2023
ad2b9a1
fix: chebi inster replace table instead of append
brucetony Sep 21, 2023
3499b8d
chore: remove test code
brucetony Sep 21, 2023
f87ebfc
build: update pandas version in reqs
brucetony Sep 21, 2023
db184b8
Merge branch 'sqlalchemy-update' of github.com:e-bel/ebel into sqlalc…
brucetony Sep 21, 2023
f778baf
fix: pandas version in requirements.txt
brucetony Sep 22, 2023
48418e5
fix: gwas catalog nullable props
brucetony Sep 22, 2023
d645b5d
fix: add Ensembl update to ClinVar
brucetony Sep 22, 2023
191ca91
fix: add hgnc update to stringdb
brucetony Sep 23, 2023
c39de4f
chore: remove test code from stringdb
brucetony Sep 23, 2023
6c03eb2
build: update sqlalchemy-utils version in deps
brucetony Sep 25, 2023
107676f
fix: add check/create database step to abstract graph init
brucetony Sep 25, 2023
3b9e9b6
fix: dafaults dir path
brucetony Sep 25, 2023
0755a47
feat: begin updating biogrid to sql2
brucetony Sep 25, 2023
ded1170
fix: add defaults import to odb_meta to ensure logging init
brucetony Sep 25, 2023
d447e93
fix: convert biogrid update sql text to sqla2 stmt
brucetony Sep 25, 2023
ae93f1a
fix: pathway commons super table join in update
brucetony Sep 25, 2023
ca26a17
fix: remove database init
brucetony Sep 25, 2023
0122f00
fix: pc pmid model upgraded to big integer
brucetony Sep 25, 2023
8ddd492
feat: update biogrid to use sqla2 stmts
brucetony Sep 25, 2023
3b14d3a
feat: update remaining biodbs to sqla2 select stmts
brucetony Sep 26, 2023
770d9a8
fix: remaining problems with sqla2 updates
brucetony Sep 26, 2023
fec21f5
chore: remove run blocks
brucetony Sep 27, 2023
128376f
fix: ncbi nullable props
brucetony Sep 27, 2023
c5b00ae
build: update logging and copyright year
brucetony Sep 27, 2023
d9e213f
fix: optimize unirpto rid call
brucetony Sep 27, 2023
c51943f
perf: disable Uniprot update step in intact
brucetony Sep 27, 2023
cf10492
fix: set query_class method with empty cols to avoid * in cmd
brucetony Sep 27, 2023
d620192
revert: logging setup
brucetony Sep 27, 2023
d00277b
revert: query_class default columns to None
brucetony Sep 27, 2023
77de7c4
chore: remove previous sql text after check
brucetony Sep 28, 2023
889035e
perf: improve intact update
brucetony Sep 28, 2023
b610d93
fix: change intact update to use itertuples
brucetony Sep 28, 2023
83addcc
fix: replace nans with None in intact update
brucetony Sep 28, 2023
697da19
Bump version: 1.0.37 → 1.1.0
brucetony Sep 28, 2023
71fb54b
perf: improve intact update by caching bel string
brucetony Sep 28, 2023
fe8991a
perf: improve intact update by caching uniprot nn
brucetony Sep 28, 2023
a2cdd5c
perf: apply caching techniques to stringdb
brucetony Sep 28, 2023
36337f4
style: black and isort
brucetony Sep 28, 2023
7ef4fa5
fix: specify columns in pc dict method
brucetony Sep 29, 2023
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fix: replace nans with None in intact update
  • Loading branch information
brucetony committed Sep 28, 2023
commit 83addcc8e4d8944e462b1f86e866d170c56247bd
3 changes: 2 additions & 1 deletion ebel/manager/orientdb/biodbs/intact.py
Original file line number Diff line number Diff line change
@@ -4,6 +4,7 @@
import zipfile
from typing import Dict

import numpy as np
import pandas as pd
from pyorientdb import OrientDB
from sqlalchemy import select, or_
@@ -202,7 +203,7 @@ def update_interactions(self) -> int:
it.confidence_value,
)

intact_df = pd.read_sql(sql, self.engine)
intact_df = pd.read_sql(sql, self.engine).replace({np.nan: None})

for uniprot_accession in tqdm(uniprot_accessions, desc="Update IntAct interactions"):
filtered_df = intact_df[