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Sqlalchemy 2.0 update #25

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@brucetony brucetony commented Sep 15, 2023

Update code to use SqlAlchemy 2.0

@brucetony brucetony linked an issue Sep 15, 2023 that may be closed by this pull request
Change to SQLAlchemy >= 2 #24
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brucetony and others added 27 commits September 15, 2023 13:56
@brucetony
fix: add optional to clinvar props
b61e876
@brucetony
build: upgrade click version to work with flask deps
f87311a
@brucetony
fix: disgenet URLs and merge method
05a4214
@brucetony
fix: disgenet nullable fields, now working
84da7eb
@brucetony
fix: hgnc sqla2 import
02142f9
@brucetony
feat: drugbank sqla2 import
fce5280
@brucetony
feat: gwas catalog sqla2 import
dfe6bcd
@brucetony
feat: clinvar sqla2 import
c0baf71
@brucetony
feat: mirtarbase sqla2 import
f8502ae
@brucetony
feat: intact sqla2 import
9bf2046
@brucetony
feat: pc sqla2 import
6b060d3
@brucetony
feat: stringdb sqla2 import
6ab734f
@brucetony
feat: protein atlas sqla2 import
0dc24ef
@brucetony
feat: get ncbi and pc working
fb2c89e
@brucetony
fix: ncbi constraint
608c4b6
@brucetony
feat: update iuphar to sqla 2
d4f6670
@brucetony
style: black and isort
c1856ca
@brucetony
feat: update intact and iuphar to select stmts
201ef8a
@brucetony
fix: chebi inster replace table instead of append
ad2b9a1
@brucetony
chore: remove test code
3499b8d
@brucetony
build: update pandas version in reqs
f87ebfc
@brucetony
Merge branch 'sqlalchemy-update' of github.com:e-bel/ebel into sqlalc…
db184b8 
…hemy-update
@brucetony
fix: pandas version in requirements.txt
f778baf
@brucetony
fix: gwas catalog nullable props
48418e5
@brucetony
fix: add Ensembl update to ClinVar
d645b5d
@brucetony
fix: add hgnc update to stringdb
191ca91
@brucetony
chore: remove test code from stringdb
c39de4f
brucetony and others added 21 commits September 25, 2023 11:10
@brucetony
feat: begin updating biogrid to sql2
0755a47
@brucetony
fix: add defaults import to odb_meta to ensure logging init
ded1170
@brucetony
fix: convert biogrid update sql text to sqla2 stmt
d447e93
@brucetony
fix: pathway commons super table join in update
ae93f1a
@brucetony
fix: remove database init
ca26a17
@brucetony
fix: pc pmid model upgraded to big integer
0122f00
@brucetony
feat: update biogrid to use sqla2 stmts
8ddd492
@brucetony
feat: update remaining biodbs to sqla2 select stmts
3b14d3a
@brucetony
fix: remaining problems with sqla2 updates
770d9a8
@brucetony
chore: remove run blocks
fec21f5
@brucetony
fix: ncbi nullable props
128376f
@brucetony
build: update logging and copyright year
c5b00ae
@brucetony
fix: optimize unirpto rid call
d9e213f
@brucetony
perf: disable Uniprot update step in intact
c51943f
@brucetony
fix: set query_class method with empty cols to avoid * in cmd
cf10492
@brucetony
revert: logging setup
d620192
@brucetony
revert: query_class default columns to None
d00277b
@brucetony
chore: remove previous sql text after check
77de7c4
@brucetony
perf: improve intact update
889035e
@brucetony
fix: change intact update to use itertuples
b610d93
@brucetony
fix: replace nans with None in intact update
83addcc
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brucetony commented Sep 28, 2023

All RDBMS models have been updated and most of the text SQL statements were converted to use the ORM functions of sqlalchemy instead. All update methods were tested using a fresh database and import and the branch is ready for review

@brucetony brucetony requested a review from cebel September 28, 2023 07:31
@brucetony brucetony marked this pull request as ready for review September 28, 2023 07:31
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Change to SQLAlchemy >= 2

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