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fix rxnorm concept build
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Co-authored-by: @Panthevm <[email protected]>
Co-authored-by: @Nikita_Sinc <[email protected]>
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@ApricotLace @Panthevm @NikitaSinc
3 people committed Jan 11, 2024
1 parent 95d5e24 commit 2495fc0
Showing 1 changed file with 30 additions and 18 deletions.
48 changes: 30 additions & 18 deletions src/ftr/extraction/rxnorm.clj
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Original file line number Diff line number Diff line change
Expand Up @@ -210,11 +210,13 @@
:from :rxnsat
:where ^:pg/op[:<> :sab "RXNORM"]})

(create-idx db :rxnconso "code")
(create-idx db :rxnconso "rxcui")
(create-idx db :rxnconso "suppress")
(create-idx db :rxnconso "tty")
(create-idx db :rxnrel "rxcui1")
(create-idx db :rxnrel "rxcui2")
(create-idx db :rxnrel "rela")
(create-idx db :rxnsat "rxcui")
(create-idx db :rxnsat "atv")
(create-idx db :rxnsat "atn")))

Expand Down Expand Up @@ -291,18 +293,17 @@
(defmethod u/*fn ::create-concepts-copy-out-obj [{:as _cfg,
:keys [db]
{:keys [value-set code-system]} ::result}]
(let [connection (jdbc/get-connection db)
query {:ql/type :pg/cte
(let [query {:ql/type :pg/cte
:with {:preparations
{:ql/type :pg/select
:select {:suppress :suppress
:rxcui :rxcui
:displays [:pg/sql "jsonb_agg(str order by CASE WHEN tty='SCD' THEN 110 WHEN tty='SCDG' THEN 120 WHEN tty='SCDF' THEN 130 WHEN tty='SCDC' THEN 140 WHEN tty='SBD' THEN 210 WHEN tty='SBDG' THEN 220 WHEN tty='SBDF' THEN 230 WHEN tty='SBDC' THEN 240 WHEN tty='MIN' THEN 310 WHEN tty='PIN' THEN 320 WHEN tty='IN' THEN 330 WHEN tty='GPCK' THEN 410 WHEN tty='BPCK' THEN 420 WHEN tty='PSN' THEN 510 WHEN tty='SY' THEN 520 WHEN tty='TMSY' THEN 530 WHEN tty='BN' THEN 610 WHEN tty='DF' THEN 710 WHEN tty='ET' THEN 720 WHEN tty='DFG' THEN 730 ELSE NULL END)"]}
;; ^--- RXCONSO might contain multiple entries for a single RXCUI value. These entries
;; represent various additional variations of the same atom. We empirically determine
;; the 'priorities' of such variations to select the primary variant for the 'display'
;; value, while preserving the additional variants in the 'other-display' property.
;; https://www.nlm.nih.gov/research/umls/rxnorm/docs/appendix5.html
;; ^--- RXCONSO might contain multiple entries for a single RXCUI value. These entries
;; represent various additional variations of the same atom. We empirically determine
;; the 'priorities' of such variations to select the primary variant for the 'display'
;; value, while preserving the additional variants in the 'other-display' property.
;; https://www.nlm.nih.gov/research/umls/rxnorm/docs/appendix5.html
:from :rxnconso
:group-by {:rxcui :rxcui :suppress :suppress}}}
:select {:ql/type :pg/select
Expand All @@ -329,36 +330,47 @@
:from :rxnsat
:where [:and
[:= :rxcui :preparations.rxcui]
[:in :atn [:pg/params-list (:multi rxnsat-atn-collections)]]]
[:in :atn [:pg/inplace-params-list (:multi rxnsat-atn-collections)]]]
:group-by :atn
:union-all {:wha {:ql/type :pg/sub-select
:select {:name :atn
:value ^:pg/fn[:to_jsonb :atv]}
:from :rxnsat
:where [:and
[:= :rxcui :preparations.rxcui]
[:in :atn [:pg/params-list (:single rxnsat-atn-collections)]]]}}}}
[:in :atn [:pg/inplace-params-list (:single rxnsat-atn-collections)]]]}}}}
:select {:ql/type :pg/select
:select ^:pg/fn[:jsonb_object_agg :name :value]
:select {:attrs_res [:pg/coalesce ^:pg/fn[:jsonb_object_agg :name :value] ^:pg/obj {}]}
:from :attrs}}

{:ql/type :pg/cte
:with {:rels
{:ql/type :pg/select
:select {:relation :rela
:object ^:pg/fn[:jsonb_agg :rxcui1]}
:object
^:pg/fn [:jsonb_agg
^:pg/fn [:jsonb_build_object
"code" :rxcui1
"display" {:ql/type :pg/sub-select
:select :conso.str
:from {:conso :rxnconso}
:where [:and
[:not-in :conso.tty [:pg/inplace-params-list ["SY" "TMSY" "PSN"]]]
[:= :conso.rxcui :rxcui1]]}]]}
:from :rxnrel
:where [:= :rxcui2 :preparations.rxcui]
:group-by :relation}}
:select {:ql/type :pg/select
:select ^:pg/fn[:jsonb_object_agg :relation :object]
:from :rels}

}]]}}
:select {:rels_res [:pg/coalesce ^:pg/fn[:jsonb_object_agg :relation :object] ^:pg/obj {}]}
:from :rels}}]]}}
:from :preparations
:order-by :rxcui}}
pstmnt ^PreparedStatement (jdbc/prepare connection (dsql/format query) {:fetch-size 1000})]
{::result {:concepts pstmnt}}))
_ (jdbc/execute! (jdbc/get-connection db) ["VACUUM FULL ANALYZE"])
prepared-statement (jdbc/prepare
(jdbc/get-connection db)
(dsql/format query)
{:fetch-size 1000})]
{::result {:concepts prepared-statement}}))


(defn import-from-cfg [cfg]
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