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Add tty prop to rxnorm concept, impl zen project stuff generation for…
… rxnorm Co-authored-by: ApricotLace <[email protected]> Co-authored-by: Panthevm <[email protected]>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,332 @@ | ||
| (ns gen | ||
| (:require | ||
| [next.jdbc :as jdbc] | ||
| [ftr.extraction.rxnorm] | ||
| [dsql.pg :as dsql] | ||
| [clojure.string :as str])) | ||
|
|
||
| (comment ;Samples | ||
| '{Concept | ||
| {:zen/tags #{zen/schema zen.fhir/base-schema} | ||
| :confirms #{zen.fhir/Resource} | ||
| :zen.fhir/type "Concept" | ||
| :zen.fhir/version "0.5.11" | ||
| :type zen/map | ||
| :require #{:system :code}, | ||
| :validation-type :open | ||
| :keys {:resourceType {:const {:value "Concept"}} | ||
| :deprecated {:type zen/boolean | ||
| :zen.fhir/type "boolean"} | ||
| :system {:type zen/string | ||
| :zen.fhir/type "string"} | ||
| :code {:type zen/string | ||
| :zen.fhir/type "string"} | ||
| :display {:type zen/string | ||
| :zen.fhir/type "string"} | ||
| :definition {:type zen/string | ||
| :zen.fhir/type "string"} | ||
| :ancestors {:type zen/map | ||
| :validation-type :open} | ||
| :hierarchy {:type zen/map | ||
| :validation-type :open} | ||
| :valueset {:type zen/vector | ||
| :every {:type zen/string | ||
| :zen.fhir/type "string"}} | ||
| :property {:type zen/map | ||
| :validation-type :open | ||
| :keys | ||
| {:has_ingredient ; relation (for all) | ||
| {:type zen/vector | ||
| :every {:type zen/map | ||
| :keys {:code {:type zen/string | ||
| :zen.fhir/type "string"} | ||
| :display {:type zen/string | ||
| :zen.fhir/type "string"}}}} | ||
| :rxn_human_drug ;attr single | ||
| {:type zen/string | ||
| :zen.fhir/type "string"} | ||
|
|
||
| :rxn_am | ||
| {:type zen/vector | ||
| :every {:type zen/string | ||
| :zen.fhir/type "string"}}}}}} | ||
|
|
||
| has-ingredient-code | ||
| {:zen/tags #{aidbox.search-parameter.v1/search-parameter} | ||
| :name "hasIngredientCode" | ||
| :type :token | ||
| :resource {:resourceType "Entity" :id "Concept"} | ||
| :expression [["property" "has_ingredient" "code"]]} | ||
|
|
||
| has-ingredient-display | ||
| {:zen/tags #{aidbox.search-parameter.v1/search-parameter} | ||
| :name "hasIngredientDisplay" | ||
| :type :string | ||
| :resource {:resourceType "Entity" :id "Concept"} | ||
| :expression [["property" "has_ingredient" "display"]]} | ||
|
|
||
| has-ingredient-code-index | ||
| {:zen/tags #{aidbox.index.v1/auto-index} | ||
| :for has-ingredient-code} | ||
|
|
||
| has-ingredient-display-index | ||
| {:zen/tags #{aidbox.index.v1/auto-index} | ||
| :for has-ingredient-display} | ||
|
|
||
| concept-repository | ||
| {:zen/tags #{aidbox.repository.v1/repository} | ||
| :resourceType "Concept" | ||
| :base-profile Concept | ||
| :indexes #{has-ingredient-code-index has-ingredient-display-index} | ||
| :extra-parameter-sources :all | ||
| :search-parameters #{has-ingredient-code has-ingredient-display}} | ||
| }) | ||
|
|
||
| (def rxnsat-atn-collections | ||
| {:all ["AMBIGUITY_FLAG" | ||
| "NDC" | ||
| "ORIG_CODE" | ||
| "ORIG_SOURCE" | ||
| "RXN_ACTIVATED" | ||
| "RXN_AI" | ||
| "RXN_AM" | ||
| "RXN_AVAILABLE_STRENGTH" | ||
| "RXN_BN_CARDINALITY" | ||
| "RXN_BOSS_FROM" | ||
| "RXN_BOSS_STRENGTH_DENOM_UNIT" | ||
| "RXN_BOSS_STRENGTH_DENOM_VALUE" | ||
| "RXN_BOSS_STRENGTH_NUM_UNIT" | ||
| "RXN_BOSS_STRENGTH_NUM_VALUE" | ||
| "RXN_HUMAN_DRUG" | ||
| "RXN_IN_EXPRESSED_FLAG" | ||
| "RXN_OBSOLETED" | ||
| "RXN_QUALITATIVE_DISTINCTION" | ||
| "RXN_QUANTITY" | ||
| "RXN_STRENGTH" | ||
| "RXN_VET_DRUG" | ||
| "RXTERM_FORM"] | ||
|
|
||
| :multi ["ORIG_SOURCE" | ||
| "RXN_AM" | ||
| "RXN_BOSS_FROM" | ||
| "AMBIGUITY_FLAG" | ||
| "RXN_AVAILABLE_STRENGTH" | ||
| "RXN_OBSOLETED" | ||
| "RXN_ACTIVATED" | ||
| "ORIG_CODE" | ||
| "RXN_AI"] | ||
|
|
||
| :single ["RXN_IN_EXPRESSED_FLAG" | ||
| "RXN_HUMAN_DRUG" | ||
| "RXN_BOSS_STRENGTH_DENOM_VALUE" | ||
| "RXN_BOSS_STRENGTH_NUM_VALUE" | ||
| "RXN_QUANTITY" | ||
| "RXN_BOSS_STRENGTH_NUM_UNIT" | ||
| "RXN_BOSS_STRENGTH_DENOM_UNIT" | ||
| "RXN_BN_CARDINALITY" | ||
| "RXN_STRENGTH" | ||
| "RXN_VET_DRUG" | ||
| "RXTERM_FORM" | ||
| "RXN_QUALITATIVE_DISTINCTION"]}) | ||
|
|
||
| (def helpful-map | ||
| (let [connection (jdbc/get-connection "jdbc:postgresql://localhost:5125/ftr?user=ftr&password=password") | ||
| multi-attrs (:multi rxnsat-atn-collections) | ||
| single-attrs (:single rxnsat-atn-collections) | ||
| rels (->> | ||
| (dsql/format {:ql/type :pg/select | ||
| :select {:rel [:distinct :rela]} | ||
| :from :rxnrel}) | ||
| (jdbc/execute! connection) | ||
| (map #(get % :rxnrel/rel)) | ||
| (filter #(not (nil? %)))) | ||
| rels (->> rels | ||
| (reduce | ||
| (fn [acc value] | ||
| (assoc acc (keyword (str/lower-case value)) :multi-rel)) | ||
| {})) | ||
| multi-attrs (->> multi-attrs | ||
| (reduce | ||
| (fn [acc value] | ||
| (assoc acc (keyword (str/lower-case value)) :multi-attr)) | ||
| {})) | ||
| single-attrs (->> single-attrs | ||
| (reduce | ||
| (fn [acc value] | ||
| (assoc acc (keyword (str/lower-case value)) :single-attr)) | ||
| {})) | ||
| attrs (merge rels multi-attrs single-attrs)] | ||
| attrs)) | ||
|
|
||
| (defn to-zen-name [kw & [postfix]] | ||
| (let [res (-> kw | ||
| (str) | ||
| (str/replace-first #":" "") | ||
| (str/lower-case) | ||
| (str/replace #"_" "-"))] | ||
| (if postfix | ||
| (symbol (str res "-" postfix)) | ||
| (symbol res)))) | ||
|
|
||
| (defn to-camel-name [input-string & [postfix]] | ||
| (let [input-string (str/replace-first (str input-string) #":" "") | ||
| words (str/split input-string #"[\s_-]+") | ||
| res (str/join "" (cons (str/lower-case (first words)) (map str/capitalize (rest words))))] | ||
| (if postfix | ||
| (str res (str/capitalize postfix)) | ||
| res))) | ||
|
|
||
| (defn kw-to-string [kw] | ||
| (-> kw | ||
| (str) | ||
| (str/replace-first #":" "") | ||
| )) | ||
|
|
||
| (defn generate-concept-schema [] | ||
| (let [all-keys (reduce | ||
| (fn [acc [k v]] | ||
| (case v | ||
| :single-attr | ||
| (assoc acc | ||
| (keyword (str/lower-case (kw-to-string k))) | ||
| '{:type zen/map | ||
| :keys {:type zen/string | ||
| :zen.fhir/type "string"}}) | ||
| :multi-attr | ||
| (assoc acc | ||
| (keyword (str/lower-case (kw-to-string k))) | ||
| '{:type zen/vector | ||
| :every {:type zen/string | ||
| :zen.fhir/type "string"}}) | ||
| :multi-rel | ||
| (assoc acc | ||
| (keyword (str/lower-case (kw-to-string k))) | ||
| '{:type zen/vector | ||
| :every {:type zen/map | ||
| :keys {:code {:type zen/string | ||
| :zen.fhir/type "string"} | ||
| :display {:type zen/string | ||
| :zen.fhir/type "string"}}}}))) | ||
| {} | ||
| helpful-map)] | ||
| `{:zen/tags #{zen/schema zen.fhir/base-schema} | ||
| :confirms #{zen.fhir/Resource} | ||
| :zen.fhir/type "Concept" | ||
| :zen.fhir/version "0.5.11" | ||
| :type zen/map | ||
| :require #{:system :code}, | ||
| :validation-type :open | ||
| :keys {:resourceType {:const {:value "Concept"}} | ||
| :deprecated {:type zen/boolean | ||
| :zen.fhir/type "boolean"} | ||
| :system {:type zen/string | ||
| :zen.fhir/type "string"} | ||
| :code {:type zen/string | ||
| :zen.fhir/type "string"} | ||
| :display {:type zen/string | ||
| :zen.fhir/type "string"} | ||
| :definition {:type zen/string | ||
| :zen.fhir/type "string"} | ||
| :ancestors {:type zen/map | ||
| :validation-type :open} | ||
| :hierarchy {:type zen/map | ||
| :validation-type :open} | ||
| :valueset {:type zen/vector | ||
| :every {:type zen/string | ||
| :zen.fhir/type "string"}} | ||
| :property {:type zen/map | ||
| :validation-type :open | ||
| :keys ~all-keys}}} | ||
| )) | ||
|
|
||
|
|
||
| (defn generate-search-schemas [] | ||
| (let [all-keys (reduce | ||
| (fn [acc [k v]] | ||
| (case v | ||
| :single-attr | ||
| (assoc acc | ||
| (to-zen-name k) | ||
| `{:zen/tags #{aidbox.search-parameter.v1/search-parameter} | ||
| :name ~(to-camel-name k) | ||
| :type :string | ||
| :resource {:resourceType "Entity" :id "Concept"} | ||
| :expression [["property" ~(kw-to-string k)]]}) | ||
| :multi-attr | ||
| (assoc acc | ||
| (to-zen-name k) | ||
| `{:zen/tags #{aidbox.search-parameter.v1/search-parameter} | ||
| :name ~(to-camel-name k) | ||
| :type :string | ||
| :resource {:resourceType "Entity" :id "Concept"} | ||
| :expression [["property" ~(kw-to-string k)]]}) | ||
| :multi-rel | ||
| (assoc acc | ||
| (to-zen-name k "code") | ||
| `{:zen/tags #{aidbox.search-parameter.v1/search-parameter} | ||
| :name ~(to-camel-name "code") | ||
| :type :token | ||
| :resource {:resourceType "Entity" :id "Concept"} | ||
| :expression [["property" ~(kw-to-string k) "code"]]} | ||
| (to-zen-name k "display") | ||
| `{:zen/tags #{aidbox.search-parameter.v1/search-parameter} | ||
| :name ~(to-camel-name "display") | ||
| :type :string | ||
| :resource {:resourceType "Entity" :id "Concept"} | ||
| :expression [["property" ~(kw-to-string k) "display"]]}))) | ||
| {} | ||
| helpful-map)] | ||
| all-keys)) | ||
|
|
||
| (defn generate-index-schemas [] | ||
| (let [all-keys (reduce | ||
| (fn [acc [k v]] | ||
| (case v | ||
| :single-attr | ||
| (assoc acc | ||
| (to-zen-name k "index") | ||
| `{:zen/tags #{aidbox.index.v1/auto-index} | ||
| :for ~(to-zen-name k)}) | ||
| :multi-attr | ||
| (assoc acc | ||
| (to-zen-name k "index") | ||
| `{:zen/tags #{aidbox.index.v1/auto-index} | ||
| :for ~(to-zen-name k)}) | ||
| :multi-rel | ||
| (assoc acc | ||
| (to-zen-name k "code-index") | ||
| `{:zen/tags #{aidbox.index.v1/auto-index} | ||
| :for ~(to-zen-name k "code")} | ||
| (to-zen-name k "display-index") | ||
| `{:zen/tags #{aidbox.index.v1/auto-index} | ||
| :for ~(to-zen-name k "display")}))) | ||
| {} | ||
| helpful-map)] | ||
| all-keys)) | ||
|
|
||
| (comment | ||
| (generate-concept-schema) | ||
|
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||
| (generate-search-schemas) | ||
|
|
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| (generate-index-schemas) | ||
|
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||
| (merge | ||
| `{~(symbol nil "Concept") | ||
| ~(generate-concept-schema) | ||
|
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| ~(symbol nil "concept-repository") | ||
| {:zen/tags #{aidbox.repository.v1/repository} | ||
| :resourceType "Concept" | ||
| :base-profile ~(symbol nil "Concept") | ||
| :indexes ~(-> (generate-index-schemas) | ||
| keys | ||
| set) | ||
| :extra-parameter-sources :all | ||
| :search-parameters ~(-> (generate-search-schemas) | ||
| keys | ||
| set)}} | ||
| (generate-index-schemas) | ||
| (generate-search-schemas)) | ||
|
|
||
| ) |