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Misc Improvements #2274

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Dec 18, 2024
Merged

Misc Improvements #2274

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5cc8a3e
Add Missing FHIR Type Tags
alexanderkiel Dec 13, 2024
71bd188
Ensure Uniform Jackson Dependencies
alexanderkiel Dec 14, 2024
1a2eeca
Ensure Stream is Closed
alexanderkiel Dec 14, 2024
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6 changes: 3 additions & 3 deletions modules/admin-api/src/blaze/admin_api.clj
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Expand Up @@ -454,9 +454,9 @@
(defn- load-profile [context name]
(log/debug "Load profile" name)
(let [parser (.newJsonParser ^FhirContext context)
classloader (.getContextClassLoader (Thread/currentThread))
source (.getResourceAsStream classloader name)]
(.parseResource parser source)))
classloader (.getContextClassLoader (Thread/currentThread))]
(with-open [source (.getResourceAsStream classloader name)]
(.parseResource parser source))))

(defn- profile-validation-support [context]
(let [s (PrePopulatedValidationSupport. context)]
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4 changes: 2 additions & 2 deletions modules/admin-api/test/blaze/admin_api_test.clj
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Expand Up @@ -675,7 +675,7 @@
[#fhir/Coding
{:system #fhir/uri"https://samply.github.io/blaze/fhir/CodeSystem/JobType"
:code #fhir/code"re-index"
:display "(Re)Index a Search Parameter"}]}
:display #fhir/string"(Re)Index a Search Parameter"}]}
:authoredOn #fhir/dateTime"2024-04-13T10:05:20.927Z"
:input
[{:fhir/type :fhir.Task/input
Expand All @@ -696,7 +696,7 @@
[#fhir/Coding
{:system #fhir/uri"https://samply.github.io/blaze/fhir/CodeSystem/JobType"
:code #fhir/code"compact"
:display "Compact a Database Column Family"}]}
:display #fhir/string"Compact a Database Column Family"}]}
:authoredOn #fhir/dateTime"2024-04-13T10:05:20.927Z"
:input
[{:fhir/type :fhir.Task/input
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22 changes: 11 additions & 11 deletions modules/cql/test/blaze/elm/compiler/reusing_logic_test.clj
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Expand Up @@ -386,9 +386,9 @@
(are [x res] (= res (core/-eval expr {:parameters {"x" x}} nil nil))
nil
nil
#fhir/Coding{:system "system-140820"
:version "version-140924"
:code "code-140828"}
#fhir/Coding{:system #fhir/uri"system-140820"
:version #fhir/string"version-140924"
:code #fhir/code"code-140828"}
(code/code "system-140820" "version-140924" "code-140828")))

(testing "expression is dynamic"
Expand Down Expand Up @@ -471,9 +471,9 @@
nil
#fhir/CodeableConcept
{:coding
[#fhir/Coding{:system "system-172740"
:version "version-172819"
:code "code-172745"}]}
[#fhir/Coding{:system #fhir/uri"system-172740"
:version #fhir/string"version-172819"
:code #fhir/code"code-172745"}]}
(concept
[(code/code "system-172740" "version-172819" "code-172745")])))

Expand All @@ -487,14 +487,14 @@
(testing "resolve parameters"
(has-form (core/-resolve-params expr {"x" #fhir/CodeableConcept
{:coding
[#fhir/Coding{:system "system-172740"
:version "version-172819"
:code "code-172745"}]}})
[#fhir/Coding{:system #fhir/uri"system-172740"
:version #fhir/string"version-172819"
:code #fhir/code"code-172745"}]}})
'(call "ToConcept" #fhir/CodeableConcept
{:coding
[#fhir/Coding{:system "system-172740"
[#fhir/Coding{:system #fhir/uri"system-172740"
:version "version-172819"
:code "code-172745"}]}))
:code #fhir/code"code-172745"}]}))

(testing-function-ref-optimize "ToConcept")

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16 changes: 8 additions & 8 deletions modules/db/test/blaze/db/api_test.clj
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Expand Up @@ -4387,14 +4387,14 @@
[#fhir/Coding
{:system #fhir/uri"http://loinc.org"
:code #fhir/code"94564-2"
:display "SARS-CoV-2 (COVID-19) IgM Ab [Presence]"}]}
:display #fhir/string"SARS-CoV-2 (COVID-19) IgM Ab [Presence]"}]}
:value
#fhir/CodeableConcept
{:coding
[#fhir/Coding
{:system #fhir/uri"http://snomed.info/sct"
:code #fhir/code"260373001"
:display "Detected (qualifier value)"}]}}]
:display #fhir/string"Detected (qualifier value)"}]}}]
[:put {:fhir/type :fhir/Observation :id "id-1"
:status #fhir/code"final"
:code
Expand All @@ -4403,14 +4403,14 @@
[#fhir/Coding
{:system #fhir/uri"http://loinc.org"
:code #fhir/code"94564-2"
:display "SARS-CoV-2 (COVID-19) IgM Ab [Presence]"}]}
:display #fhir/string"SARS-CoV-2 (COVID-19) IgM Ab [Presence]"}]}
:value
#fhir/CodeableConcept
{:coding
[#fhir/Coding
{:system #fhir/uri"http://snomed.info/sct"
:code #fhir/code"260415000"
:display "Not detected (qualifier value)"}]}}]
:display #fhir/string"Not detected (qualifier value)"}]}}]
[:put {:fhir/type :fhir/Observation :id "id-2"
:status #fhir/code"final"
:code
Expand All @@ -4419,14 +4419,14 @@
[#fhir/Coding
{:system #fhir/uri"http://loinc.org"
:code #fhir/code"94564-2"
:display "SARS-CoV-2 (COVID-19) IgM Ab [Presence]"}]}
:display #fhir/string"SARS-CoV-2 (COVID-19) IgM Ab [Presence]"}]}
:value
#fhir/CodeableConcept
{:coding
[#fhir/Coding
{:system #fhir/uri"http://snomed.info/sct"
:code #fhir/code"260373001"
:display "Detected (qualifier value)"}]}}]]]
:display #fhir/string"Detected (qualifier value)"}]}}]]]

(testing "missing second value part"
(given (d/type-query (d/db node) "Observation" [["code-value-concept" "http://loinc.org|94564-2"]])
Expand Down Expand Up @@ -4540,7 +4540,7 @@
[#fhir/Coding
{:system #fhir/uri"http://loinc.org"
:code #fhir/code"94564-2"
:display "SARS-CoV-2 (COVID-19) IgM Ab [Presence]"}]}
:display #fhir/string"SARS-CoV-2 (COVID-19) IgM Ab [Presence]"}]}
:subject #fhir/Reference{:reference "Patient/0"}}]
[:put {:fhir/type :fhir/Observation :id "1"
:code
Expand All @@ -4549,7 +4549,7 @@
[#fhir/Coding
{:system #fhir/uri"http://loinc.org"
:code #fhir/code"94564-2"
:display "SARS-CoV-2 (COVID-19) IgM Ab [Presence]"}]}
:display #fhir/string"SARS-CoV-2 (COVID-19) IgM Ab [Presence]"}]}
:subject #fhir/Reference{:reference "Patient/1"}}]]]

(doseq [code ["http://loinc.org|94564-2" "94564-2"]]
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4 changes: 2 additions & 2 deletions modules/fhir-structure/test-perf/blaze/fhir/hash_test_perf.clj
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Expand Up @@ -18,11 +18,11 @@
[#fhir/Coding
{:system #fhir/uri"http://terminology.hl7.org/CodeSystem/observation-category"
:code #fhir/code"vital-signs"
:display "vital-signs"}]}]
:display #fhir/string"vital-signs"}]}]
:code #fhir/CodeableConcept
{:coding [#fhir/Coding{:system #fhir/uri"http://loinc.org"
:code #fhir/code"39156-5"
:display "Body Mass Index"}]
:display #fhir/string"Body Mass Index"}]
:text "Body Mass Index"}
:subject #fhir/Reference{:reference "Patient/DACG22233TWT7CKL"}
:effective #fhir/dateTime"2013-01-04T23:45:50Z"
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8 changes: 4 additions & 4 deletions modules/fhir-structure/test-perf/blaze/fhir/spec_test_perf.clj
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Expand Up @@ -35,11 +35,11 @@
[#fhir/Coding
{:system #fhir/uri"http://terminology.hl7.org/CodeSystem/observation-category"
:code #fhir/code"vital-signs"
:display "vital-signs"}]}]
:display #fhir/string"vital-signs"}]}]
:code #fhir/CodeableConcept
{:coding [#fhir/Coding{:system #fhir/uri"http://loinc.org"
:code #fhir/code"39156-5"
:display "Body Mass Index"}]
:display #fhir/string"Body Mass Index"}]
:text "Body Mass Index"}
:subject #fhir/Reference{:reference "Patient/DACG22233TWT7CKL"}
:effective #fhir/dateTime"2013-01-04T23:45:50Z"
Expand Down Expand Up @@ -68,11 +68,11 @@
[#fhir/Coding
{:system #fhir/uri"http://terminology.hl7.org/CodeSystem/observation-category"
:code #fhir/code"vital-signs"
:display "vital-signs"}]}]
:display #fhir/string"vital-signs"}]}]
:code #fhir/CodeableConcept
{:coding [#fhir/Coding{:system #fhir/uri"http://loinc.org"
:code #fhir/code"39156-5"
:display "Body Mass Index"}]
:display #fhir/string"Body Mass Index"}]
:text "Body Mass Index"}
:subject #fhir/Reference{:reference "Patient/DACG22233TWT7CKL"}
:effective #fhir/dateTime"2013-01-04T23:45:50Z"
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4 changes: 2 additions & 2 deletions modules/fhir-structure/test/blaze/fhir/spec/type_test.clj
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Expand Up @@ -1508,7 +1508,7 @@
#fhir/Coding
{:system #fhir/uri"http://fhir.de/CodeSystem/gender-amtlich-de"
:code #fhir/code"D"
:display "divers"}})
:display #fhir/string"divers"}})

(def extended-gender-code
(type/code {:extension [gender-extension] :value "other"}))
Expand Down Expand Up @@ -2205,7 +2205,7 @@
#fhir/Coding{:code #fhir/code"code-202828"}
"74e3328d"

#fhir/Coding{:display "display-154256"}
#fhir/Coding{:display #fhir/string"display-154256"}
"baac923d"))

(testing "references"
Expand Down
6 changes: 3 additions & 3 deletions modules/fhir-structure/test/blaze/fhir/spec_test.clj
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Expand Up @@ -561,7 +561,7 @@
#fhir/Coding
{:system #fhir/uri"http://fhir.de/CodeSystem/gender-amtlich-de"
:code #fhir/code"D"
:display "divers"}}]
:display #fhir/string"divers"}}]
:value "other"}}))))

(testing "Patient with Narrative"
Expand Down Expand Up @@ -3370,13 +3370,13 @@
#fhir/Coding{:system #fhir/uri"system-185812"}
{:system "system-185812"}

#fhir/Coding{:version "version-185951"}
#fhir/Coding{:version #fhir/string"version-185951"}
{:version "version-185951"}

#fhir/Coding{:code #fhir/code"code-190226"}
{:code "code-190226"}

#fhir/Coding{:display "display-190327"}
#fhir/Coding{:display #fhir/string"display-190327"}
{:display "display-190327"}))

(testing "XML"
Expand Down
2 changes: 1 addition & 1 deletion modules/job-async-interaction/src/blaze/job/async_interaction.clj
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Expand Up @@ -34,7 +34,7 @@
[#fhir/Coding
{:system #fhir/uri"https://samply.github.io/blaze/fhir/CodeSystem/JobType"
:code #fhir/code"async-interaction"
:display "Asynchronous Interaction Request"}]}
:display #fhir/string"Asynchronous Interaction Request"}]}
:authoredOn authored-on
:input
[(u/request-bundle-input (str "Bundle/" bundle-id))
Expand Down
2 changes: 1 addition & 1 deletion modules/job-async-interaction/test/blaze/job/async_interaction_test.clj
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Expand Up @@ -311,7 +311,7 @@
[#fhir/Coding
{:system #fhir/uri"https://samply.github.io/blaze/fhir/CodeSystem/JobType"
:code #fhir/code"async-interaction"
:display "Asynchronous Interaction Request"}]}})
:display #fhir/string"Asynchronous Interaction Request"}]}})

(testing "the job is failed"
(given @(jtu/pull-job system :failed)
Expand Down
2 changes: 1 addition & 1 deletion modules/job-compact/src/blaze/job/compact.clj
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Expand Up @@ -44,7 +44,7 @@
[#fhir/Coding
{:system #fhir/uri"https://samply.github.io/blaze/fhir/CodeSystem/JobType"
:code #fhir/code"compact"
:display "Compact a Database Column Family"}]}
:display #fhir/string"Compact a Database Column Family"}]}
:authoredOn authored-on
:input
[{:fhir/type :fhir.Task/input
Expand Down
2 changes: 1 addition & 1 deletion modules/job-compact/test/blaze/job/compact_test.clj
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Expand Up @@ -166,7 +166,7 @@
[#fhir/Coding
{:system #fhir/uri"https://samply.github.io/blaze/fhir/CodeSystem/JobType"
:code #fhir/code"compact"
:display "Compact a Database Column Family"}]}})
:display #fhir/string"Compact a Database Column Family"}]}})

(def job-missing-column-family
(assoc
Expand Down
2 changes: 1 addition & 1 deletion modules/job-re-index/test/blaze/job/re_index_test.clj
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Expand Up @@ -215,7 +215,7 @@
[#fhir/Coding
{:system #fhir/uri"https://samply.github.io/blaze/fhir/CodeSystem/JobType"
:code #fhir/code"re-index"
:display "(Re)Index a Search Parameter"}]}})
:display #fhir/string"(Re)Index a Search Parameter"}]}})

(def job-clinical-code
(assoc
Expand Down
10 changes: 9 additions & 1 deletion modules/openid-auth/deps.edn
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Expand Up @@ -17,7 +17,15 @@

;; newer version for buddy-core dependency
cheshire/cheshire
{:mvn/version "5.13.0"}}
{:mvn/version "5.13.0"}

;; newer version for cheshire dependency
com.fasterxml.jackson.dataformat/jackson-dataformat-cbor
{:mvn/version "2.18.2"}

;; newer version for cheshire dependency
com.fasterxml.jackson.dataformat/jackson-dataformat-smile
{:mvn/version "2.18.2"}}

:aliases
{:test
Expand Down
7 changes: 4 additions & 3 deletions modules/rest-util/deps.edn
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Expand Up @@ -8,15 +8,16 @@
blaze/fhir-structure
{:local/root "../fhir-structure"}

blaze/job-scheduler
{:local/root "../job-scheduler"}

blaze/page-id-cipher
{:local/root "../page-id-cipher"}

buddy/buddy-core
{:mvn/version "1.12.0-430"}

;; newer version for cheshire dependency
com.fasterxml.jackson.dataformat/jackson-dataformat-smile
{:mvn/version "2.18.2"}

org.apache.httpcomponents.core5/httpcore5
{:mvn/version "5.3.1"}

Expand Down
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