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Add new extractor engine - :serialized-objects-array
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,99 @@ | ||
| (ns ftr.extraction.serialized-objects-array | ||
| (:require [clojure.java.io :as io] | ||
| [ftr.utils.unifn.core :as u] | ||
| [ftr.utils.core] | ||
| [clojure.string :as str] | ||
| [clj-yaml.core])) | ||
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| (defmethod u/*fn ::create-value-set [cfg] | ||
| {::result {:value-set | ||
| (-> (:value-set cfg) | ||
| (assoc :resourceType "ValueSet") | ||
| (->> (merge {:status "unknown" | ||
| :compose {:include [{:system (get-in cfg [:code-system :url])}]}})))}}) | ||
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| (defmethod u/*fn ::create-code-system [cfg] | ||
| {::result {:code-system (-> (:code-system cfg) | ||
| (assoc :resourceType "CodeSystem") | ||
| (->> (merge {:status "unknown" | ||
| :content "not-present" | ||
| :valueSet (get-in cfg [:value-set :url])}) | ||
| (conj #{})))}}) | ||
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| (defn extract-mapped-value [mapping source] | ||
| (update-vals mapping | ||
| (fn [el] | ||
| (let [v (get-in source (:path el))] | ||
| (cond-> el | ||
| (not (str/blank? v)) | ||
| (assoc :value v)))))) | ||
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| (defn extract-mapping [deserialized-object mapping] | ||
| (update-vals mapping #(extract-mapped-value % deserialized-object))) | ||
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| (ftr.utils.core/strip-nils {}) | ||
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| (defn format-concept-resource [extracted-mapping {:keys [system valueset]}] | ||
| (let [code (get-in extracted-mapping [:concept :code :value]) | ||
| display (get-in extracted-mapping [:concept :display :value]) | ||
| status (get-in extracted-mapping [:concept :deprecated? :value]) | ||
| deprecation-mark (get-in extracted-mapping [:concept :deprecated? :true-values]) | ||
| parent-id (get-in extracted-mapping [:concept :parent-id :value]) | ||
| hierarchy-id (get-in extracted-mapping [:concept :hierarchy-id :value]) | ||
| concept (ftr.utils.core/strip-nils | ||
| {:resourceType "Concept" | ||
| :system system | ||
| :valueset [valueset] | ||
| :code code | ||
| :deprecated (if (some #(= status %) deprecation-mark) true nil) | ||
| :display display | ||
| :parent-id parent-id | ||
| :hierarchy-id hierarchy-id | ||
| :property (-> (:property extracted-mapping) | ||
| (update-vals :value) | ||
| ftr.utils.core/strip-nils | ||
| not-empty)})] | ||
| (when (:code concept) | ||
| concept))) | ||
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| (defn process-deserialized-objects [deserialized-objects | ||
| {:as cfg, :keys [mapping]}] | ||
| (->> deserialized-objects | ||
| (map (fn process-deserialized-object [do] | ||
| (-> do | ||
| (extract-mapping mapping) | ||
| (format-concept-resource cfg)))) | ||
| (filter identity))) | ||
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| (defmethod u/*fn ::import [{:as cfg, | ||
| :keys [source-url]}] | ||
| (let [deserialized-objects | ||
| (clj-yaml.core/parse-stream (io/reader source-url)) | ||
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| deserialized-objects-seq | ||
| (process-deserialized-objects | ||
| deserialized-objects | ||
| (merge cfg | ||
| {:system (get-in cfg [:code-system :url]) | ||
| :valueset (get-in cfg [:value-set :url]) | ||
| :mapping (:mapping cfg)}))] | ||
| {::result {:concepts deserialized-objects-seq}})) | ||
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| (defn import-from-cfg [cfg] | ||
| (::result (u/*apply [::create-value-set | ||
| ::create-code-system | ||
| ::import] cfg))) | ||
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| (comment | ||
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| (clj-yaml.core/parse-stream (io/reader "/Users/ghrp/Downloads/external-care-team-relationship.yaml") ) | ||
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| ) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,24 @@ | ||
| - code: "SPS" | ||
| display: "Spouse" | ||
| system: "http://terminology.hl7.org/CodeSystem/v3-RoleCode" | ||
| - code: "CAREGIVER" | ||
| display: "Caregiver" | ||
| system: "http://terminology.hl7.org/CodeSystem/v3-RoleCode" | ||
| - code: "CHILD" | ||
| display: "Children" | ||
| system: "http://terminology.hl7.org/CodeSystem/v3-RoleCode" | ||
| - code: "NMTH" | ||
| display: "Parents" | ||
| system: "http://terminology.hl7.org/CodeSystem/v3-RoleCode" | ||
| - code: "SIGOTHR" | ||
| display: "Significant Other" | ||
| system: "http://terminology.hl7.org/CodeSystem/v3-RoleCode" | ||
| - code: "HOMPART" | ||
| display: "Partner(s)" | ||
| system: "http://terminology.hl7.org/CodeSystem/v3-RoleCode" | ||
| - Healthcare Proxy | ||
| - Relative | ||
| - code: "STPPRN" | ||
| display: "Step-Parent(s)" | ||
| system: "http://terminology.hl7.org/CodeSystem/v3-RoleCode" | ||
| - Other |
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