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bb.edn
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{:deps {}
:tasks {:requires ([clojure.string :as str]
[clojure.java.io :as io]
[clojure.java.shell]
[babashka.fs :as fs]
[cheshire.core :as json]
[clojure.pprint])
:init (do
(def green "\u001B[32m")
(def purple "\u001B[35m")
(def clear-color "\u001B[0m")
(def bold "\033[0;1m")
(def bold-end "\033[22m")
(def green-underline "\033[32;4m")
(defn colored-printer [map & [ks]]
(doseq [[k v] (if ks (select-keys map ks) map)]
(println (str bold (str/capitalize (name k)) ": " bold-end (str v)))))
(defn sh
"clojure.java.shell/sh wrapper-simplifier
command - shell command represented as a single string"
[command & {:keys [dir]}]
(let [args (str/split command (re-pattern "\\s"))
args-w-dir (concat args (when dir [:dir dir]))
cmd-str (str "$ " command (when dir (str " :dir " dir)))]
(println cmd-str)
(:out (apply clojure.java.shell/sh args-w-dir))))
(defn pull-deps
"deps-maps - [{:url url, :dirname dirname} ...]
:url - FHIR NPM package url
:dirname - destination folder"
[deps-maps]
(doseq [{:keys [url dirname]} deps-maps]
(let [arch-name (format "%s_arch.tgz" (gensym))]
(shell (format "mkdir -p %s" dirname))
(shell (format "curl -o %s %s" (str dirname \/ arch-name) url))
(shell {:dir dirname} (format "tar -xzf %s" arch-name))
(shell {:dir dirname} (format "rm -rf %s" arch-name))
(shell {:dir dirname} (format "cp -a package/. ." arch-name))
(shell {:dir dirname} "rm -rf package")))))
:enter (do
(println (str purple "Executing: " clear-color bold (:name (current-task)) bold-end))
(def task-start-ts (System/currentTimeMillis)))
:leave (do
(println
(str green "Task: " bold (:name (current-task)) bold-end
" " green-underline "finished in "
(- (System/currentTimeMillis) task-start-ts) " ms" clear-color \newline)))
set-zen-fhir-version {:doc "Setup zen.fhir/version regex"
:task (let [current-git-repo-tag (or (first *command-line-args*) (-> "git describe --tag --abbrev=0" sh str/trim-newline))
semantic-version-pattern (re-pattern "(\\d+)\\.(\\d+)\\.(\\d+)(-.+)?")
[match major minor _patch _pre-release] (re-find semantic-version-pattern current-git-repo-tag)]
(println (str "Version: " bold match bold-end))
(spit "resources/zen-fhir-version" match))}
set-zen-fhir-lib-version {:doc "Setup zen.fhir lib version"
:task (let [current-git-repo-tag (or (first *command-line-args*)
(str/trim-newline (sh "git describe --tag --abbrev=0"
:dir "zen.fhir")))]
(println (str "Version: " bold current-git-repo-tag bold-end))
(spit "resources/zen-fhir-lib-version" current-git-repo-tag))}
clean-up-npm {:doc "Deletes node_module directory to prevent npm fail because of custom-populated node_modules directory."
:task (shell "rm -rf node_modules")}
install-npm
{:depends [clean-up-npm]
:task (let [s1 (rand-int 100000)
s2 (rand-int 100000)]
(println "- SLEEP #1" s1)
(Thread/sleep s1)
(println "- SLEEP #1 done")
(shell "npm --registry=https://packages.simplifier.net install")
(println "- SLEEP #2")
(Thread/sleep s2)
(println "- SLEEP #2 done")
(shell "npm --registry=https://packages.simplifier.net install"))}
pull-nz-igs
{:task (do
(shell "mkdir -p node_modules")
(clojure "-X zen.fhir.igs-etl.nz/etl! :package-dir-dest '\"node_modules\"'"))}
pull-r4b
{:task (pull-deps [{:url "http://packages2.fhir.org/packages/hl7.fhir.r4b.core/4.3.0"
:dirname "r4b/hl7.fhir.r4b.core"}
{:url "http://packages2.fhir.org/packages/hl7.terminology.r4/5.0.0"
:dirname "r4b/hl7.terminology.r4"}
{:url "http://packages2.fhir.org/packages/hl7.fhir.uv.subscriptions-backport.r4b/1.1.0"
:dirname "r4b/hl7.fhir.uv.subscriptions-backport.r4b"}])}
pull-r5
{:task (pull-deps [{:url "http://packages2.fhir.org/packages/hl7.fhir.r5.core/5.0.0"
:dirname "r5/hl7.fhir.r5.core"}
{:url "http://packages2.fhir.org/packages/hl7.terminology.r5/4.0.0"
:dirname "r5/hl7.terminology.r5"}
{:url "http://packages2.fhir.org/packages/hl7.fhir.uv.extensions.r5/1.0.0"
:dirname "r5/hl7.fhir.uv.extensions.r5"}
#_{:url "http://packages2.fhir.org/packages/hl7.fhir.r5.search/5.0.0"
:dirname "r5/hl7.fhir.r5.search"}])}
pull-au-igs
{:task (pull-deps [{:url "http://hl7.org.au/fhir/4.1.0/package.tgz"
:dirname "node_modules/hl7.fhir.au.base"}
{:url "http://hl7.org.au/fhir/core/0.1.0-draft/package.tgz"
:dirname "node_modules/hl7.fhir.au.core"}
{:url "https://build.fhir.org/ig/hl7au/draft-diagnostic-orders/package.tgz"
:dirname "node_modules/hl7.fhir.au.draft.diagnostic-orders"}])}
pull-chile-igs
{:task (pull-deps [{:url "https://hl7chile.cl/fhir/ig/CoreCL/package.tgz"
:dirname "node_modules/hl7.fhir.cl.corecl"}
{:url "http://hl7.org/fhir/uv/ips/STU1/package.tgz"
:dirname "node_modules/hl7.fhir.uv.ips"}])}
my-debug {:task (sh "cat node_modules/hl7.org.nz.fhir.ig.nhi/ValueSet-nhi-address-type.json || echo \"FAIL. but it's ok\"")}
kbv-basis-patch
{:task (shell "cp resources/KBV_PR_Base_Patient.json node_modules/kbv.basis/KBV_PR_Base_Patient.json")}
init {:depends [set-zen-fhir-version set-zen-fhir-lib-version install-npm kbv-basis-patch #_pull-nz-igs pull-r4b pull-r5 #_pull-au-igs #_pull-chile-igs build-us-core-601]}
repl {:depends [set-zen-fhir-version set-zen-fhir-lib-version]
:task (clojure "-M:test:nrepl -m nrepl.cmdline --middleware [cider.nrepl/cider-middleware]")}
test {:depends [set-zen-fhir-version set-zen-fhir-lib-version pull-au-igs]
:task (clojure "-M:test:kaocha")}
ci-test {:depends [set-zen-fhir-version set-zen-fhir-lib-version init test]}
init-r3 {:depends [set-zen-fhir-version set-zen-fhir-lib-version]
:task (do
(Thread/sleep (rand-int 100000))
(shell {:dir "r3"} "npm --registry=https://packages.simplifier.net install")
(Thread/sleep (rand-int 100000))
(shell {:dir "r3"} "npm --registry=https://packages.simplifier.net install"))}
init-r3-nictiz-hack {:depends [set-zen-fhir-version set-zen-fhir-lib-version]
:task (do
(Thread/sleep (rand-int 100000))
(shell {:dir "r3-tmp-nictiz-hack"} "npm --registry=https://packages.simplifier.net install")
(Thread/sleep (rand-int 100000))
(shell {:dir "r3-tmp-nictiz-hack"} "npm --registry=https://packages.simplifier.net install"))}
build-r3-nictiz-hack (binding [*command-line-args* (list "r3-tmp-nictiz-hack/"
"zrc/standalone_projects/"
nil
nil
true)]
(run 'build-stanadlone-projects))
build-us-core-601 {:task (do
(Thread/sleep (rand-int 100000))
(shell {:dir "us-core-610"} "npm --registry=https://packages.simplifier.net install")
(Thread/sleep (rand-int 100000))
(shell {:dir "us-core-610"} "npm --registry=https://packages.simplifier.net install")
(let [root-manifest-file (io/file "us-core-610/package.json")
root-manifest-deps (:dependencies (json/parse-string (slurp root-manifest-file) keyword))
us-core-manifest-file (io/file "us-core-610/node_modules/hl7.fhir.us.core/package.json")
updated-manifest (assoc (json/parse-string (slurp us-core-manifest-file) keyword)
:name "hl7.fhir.us.core610"
:dependencies (dissoc root-manifest-deps :hl7.fhir.us.core))
_ (spit us-core-manifest-file (json/generate-string updated-manifest))
_ (.renameTo
^File (io/file "us-core-610/node_modules/hl7.fhir.us.core")
(io/file "us-core-610/node_modules/hl7.fhir.us.core610"))]))}
build (clojure "-X:build all")
zen-profiles (let [[node-modules zrc ver package] *command-line-args*]
(clojure (str "-M -m zen.fhir.tooling " node-modules " " zrc " " ver " " package)))
zen-profiles-packages (clojure (str "-J-Xmx16g -M -m zen.fhir.tooling-packages " (str/join " " *command-line-args*)))
build-stanadlone-projects (let [[node-modules zrc preserve-package alt-package-name rename-package] *command-line-args*
opts (cond-> {}
preserve-package
(assoc "preserve-package" preserve-package)
alt-package-name
(assoc "alt-package-name" alt-package-name)
rename-package
(assoc "rename-package" rename-package))]
(clojure (str "-M -m zen.fhir.tooling.aidbox-standalone-v2 " node-modules " " zrc " " (str/join " " (flatten (seq opts))))))
build-standalone-zen-profiles-all-versions
(let [get-dependency-meta (fn [dependency] (-> (sh (str "npm --registry https://packages.simplifier.net --json view " dependency))
(json/parse-string keyword)))
{:as top-level-deps, :keys [dependencies]} (read-string (slurp "resources/package.edn"))]
(doseq [dependency dependencies
:let [{:as npm-view-obj, versions :versions dependency-name :name {latest-dep-version :latest} :dist-tags}
(get-dependency-meta dependency)]]
(doseq [v versions
:let [dependency-meta (get-dependency-meta (str dependency "@" v))
dep-folder (str dependency "-" v "/")]
:when (= "R4" (:fhirVersion dependency-meta))]
(try
(println "\nProcessing dependency...")
(colored-printer dependency-meta [:fhirVersion :name :version])
(sh (str "npm --prefix " dep-folder " --registry https://packages.simplifier.net install " (:url dependency-meta)))
(let [package-json-path (str/join "/" [dep-folder "node_modules" dependency-name "package.json"])
package-json (slurp package-json-path)
package-info (json/parse-string package-json keyword)
fhir-dep (get-in package-info [:dependencies :hl7.fhir.r4.core])
fhir-4.0.1-core-iself? (and (= (:name package-info) "hl7.fhir.r4.core")
(= (:version package-info) "4.0.1"))]
(cond
(and (nil? fhir-dep) (not fhir-4.0.1-core-iself?))
(println (str purple "WARNING:" clear-color " package doesn't contain FHIR core dependency"))
#_(str/starts-with? (str fhir-dep) "4")
(or fhir-4.0.1-core-iself? (= "4.0.1" fhir-dep)) #_"NOTE: simplifier hosts onle 4.0.1 currently"
(binding [*command-line-args* (list (str dep-folder "node_modules/")
"zrc/standalone_projects/"
dependency-name
(if (= v latest-dep-version)
dependency
(str dependency "-" v)))]
(run 'build-stanadlone-projects)
#_"NOTE: this is latest IG version zip name hotfix"
(when (= v latest-dep-version)
(let [zip-location "zrc/standalone_projects/"
zip-name (str dependency ".zip")
zip-fixed-name (str (str/replace dependency \. \-) ".zip")
zip-version-name (str dependency "-" v ".zip")]
(sh (str "cp " zip-name " " zip-fixed-name) :dir zip-location)
(sh (str "cp " zip-name " " zip-version-name) :dir zip-location))))
:else
(println (str purple "WARNING:" clear-color " package FHIR core version is not r4"))))
(catch Exception e
(println (str purple "ERROR:" clear-color " " (.getMessage e))))
(finally
(try (sh (str "rm -rf " dep-folder))
(catch Exception _)))))))
build-terminology-bundles (clojure "-M:terminology-build -m zen.fhir.tooling.terminology")
outdated {:doc "Check outdated libraries"
:task (clojure " -Sdeps '{:deps {com.github.liquidz/antq {:mvn/version \"RELEASE\"}}} '-M -m antq.core ")}
lint {:doc "Lint source code"
:task (clojure "-Sdeps '{:deps {clj-kondo/clj-kondo {:mvn/version \"RELEASE\"}}} '-m clj-kondo.main --lint src:test --parallel --fail-level error")}}}