From 8e1cad063756e29d2721f04022aa40aa6ae0ec3d Mon Sep 17 00:00:00 2001 From: Mary McGrath Date: Thu, 12 Dec 2024 10:46:06 -0500 Subject: [PATCH 1/8] fix: wip - spec source --- data/Templates/eCR/Entry/Result/_entry.liquid | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/data/Templates/eCR/Entry/Result/_entry.liquid b/data/Templates/eCR/Entry/Result/_entry.liquid index d1ddf4b1..febf6d83 100644 --- a/data/Templates/eCR/Entry/Result/_entry.liquid +++ b/data/Templates/eCR/Entry/Result/_entry.liquid @@ -51,12 +51,15 @@ {% elsif playingEntity.code.displayName -%} {% assign specValue = playingEntity.code.displayName -%} {% else -%} - {% assign specValue = "None" -%} + {% comment %} {% assign specValue = "None" -%} {% endcomment %} {% endif -%} {% else -%} - {% assign specValue = "None" -%} + {% comment %} {% assign specValue = "None" -%} {% endcomment %} {% endif -%} {% endif -%} + {% if specValue == null and receiveTime != null %} + {{ comp.procedure | print_object }} + {% endif %} {% endfor-%} {% for component in comps %} {% include 'Entry/Result/entry_organizer_component' with component, text: text %} From 3e7f44ccf4610db849368ec3eb5f913213ac6f20 Mon Sep 17 00:00:00 2001 From: Mary McGrath Date: Thu, 12 Dec 2024 10:54:26 -0500 Subject: [PATCH 2/8] fix: none => null cleanup --- data/Templates/eCR/Entry/Result/_entry.liquid | 9 --------- data/Templates/eCR/Resource/_Observation.liquid | 8 ++++---- 2 files changed, 4 insertions(+), 13 deletions(-) diff --git a/data/Templates/eCR/Entry/Result/_entry.liquid b/data/Templates/eCR/Entry/Result/_entry.liquid index febf6d83..6d344b38 100644 --- a/data/Templates/eCR/Entry/Result/_entry.liquid +++ b/data/Templates/eCR/Entry/Result/_entry.liquid @@ -22,8 +22,6 @@ {% assign collectTime = entry.organizer.effectiveTime.high.value -%} {% elsif entry.organizer.effectiveTime and entry.organizer.effectiveTime.value and entry.organizer.effectiveTime.value != "UNK"-%} {% assign collectTime = entry.organizer.effectiveTime.value -%} - {% else -%} - {% assign collectTime = "None" -%} {% endif -%} {% assign comps = entry.organizer.component | to_array -%} @@ -50,16 +48,9 @@ {% assign specValue = playingEntity.code.originalText._ -%} {% elsif playingEntity.code.displayName -%} {% assign specValue = playingEntity.code.displayName -%} - {% else -%} - {% comment %} {% assign specValue = "None" -%} {% endcomment %} {% endif -%} - {% else -%} - {% comment %} {% assign specValue = "None" -%} {% endcomment %} {% endif -%} {% endif -%} - {% if specValue == null and receiveTime != null %} - {{ comp.procedure | print_object }} - {% endif %} {% endfor-%} {% for component in comps %} {% include 'Entry/Result/entry_organizer_component' with component, text: text %} diff --git a/data/Templates/eCR/Resource/_Observation.liquid b/data/Templates/eCR/Resource/_Observation.liquid index 5864390f..f21b483f 100644 --- a/data/Templates/eCR/Resource/_Observation.liquid +++ b/data/Templates/eCR/Resource/_Observation.liquid @@ -140,23 +140,23 @@ {% assign observationValueReferenceValue = observationEntry.value.reference.value -%} "extension": [ { - {% if specimenValue and specimenValue != "None" or collectTime and collectTime != "None" or observationTextReferenceValue != "None" or observationValueReferenceValue != "None" -%} + {% if specimenValue != null or collectTime != null or receiveTime != null or observationTextReferenceValue != null or observationValueReferenceValue != null -%} "url" : "http://hl7.org/fhir/R4/specimen.html", "extension": [ - {% if specimenValue and specimenValue != "None" -%} + {% if specimenValue != null -%} { "url" : "specimen source", "valueString" : "{{ specimenValue }}", }, {% endif -%} - {% if collectTime and collectTime != "None" -%} + {% if collectTime != null -%} { "url" : "specimen collection time", "valueDateTime" : "{{ collectTime | format_as_date_time }}", }, {% endif -%} - {% if receiveTime and receiveTime != "None" -%} + {% if receiveTime != null -%} { "url" : "specimen receive time", "valueDateTime" : "{{ receiveTime | format_as_date_time }}", From 464a3f6c99b773efd1f809aa3396a70b0c7c1a8c Mon Sep 17 00:00:00 2001 From: Mary McGrath Date: Thu, 12 Dec 2024 11:05:06 -0500 Subject: [PATCH 3/8] style: make data passing more explicit --- data/Templates/eCR/Entry/Result/_entry.liquid | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/data/Templates/eCR/Entry/Result/_entry.liquid b/data/Templates/eCR/Entry/Result/_entry.liquid index 6d344b38..74a394c0 100644 --- a/data/Templates/eCR/Entry/Result/_entry.liquid +++ b/data/Templates/eCR/Entry/Result/_entry.liquid @@ -16,6 +16,7 @@ {% include 'Reference/DiagnosticReport/Performer' ID: diagnosticId, REF: fullPerformerId -%} {% endif -%} {% endif -%} + {% assign collectTime = null %} {% if entry.organizer.effectiveTime.low and entry.organizer.effectiveTime.low.value -%} {% assign collectTime = entry.organizer.effectiveTime.low.value -%} {% elsif entry.organizer.effectiveTime.high and entry.organizer.effectiveTime.high.value -%} @@ -24,6 +25,8 @@ {% assign collectTime = entry.organizer.effectiveTime.value -%} {% endif -%} + {% assign specValue = null %} + {% assign recieveTime = null %} {% assign comps = entry.organizer.component | to_array -%} {% for comp in comps -%} {% if comp.procedure -%} @@ -53,6 +56,6 @@ {% endif -%} {% endfor-%} {% for component in comps %} - {% include 'Entry/Result/entry_organizer_component' with component, text: text %} + {% include 'Entry/Result/entry_organizer_component' with component, text: text, specValue: specValue, collectTime: collectTime, receiveTime: receiveTime, diagnosticId: diagnosticId %} {% endfor %} {% endif -%} From 4cf966f7af5843e57a33edb3da0dad58dcf64598 Mon Sep 17 00:00:00 2001 From: Mary McGrath Date: Thu, 12 Dec 2024 13:59:19 -0500 Subject: [PATCH 4/8] fix: prevent leaks --- data/Templates/eCR/Entry/Result/_entry.liquid | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/data/Templates/eCR/Entry/Result/_entry.liquid b/data/Templates/eCR/Entry/Result/_entry.liquid index 74a394c0..56b41f9b 100644 --- a/data/Templates/eCR/Entry/Result/_entry.liquid +++ b/data/Templates/eCR/Entry/Result/_entry.liquid @@ -26,7 +26,7 @@ {% endif -%} {% assign specValue = null %} - {% assign recieveTime = null %} + {% assign receiveTime = null %} {% assign comps = entry.organizer.component | to_array -%} {% for comp in comps -%} {% if comp.procedure -%} @@ -59,3 +59,7 @@ {% include 'Entry/Result/entry_organizer_component' with component, text: text, specValue: specValue, collectTime: collectTime, receiveTime: receiveTime, diagnosticId: diagnosticId %} {% endfor %} {% endif -%} +{% comment %} Prevent weird variable leakage {% endcomment %} +{% assign specValue = null %} +{% assign receiveTime = null %} +{% assign collectTime = null %} From 4d43a93e6d1433e65d25b0d1c855e941a673d2cf Mon Sep 17 00:00:00 2001 From: Mary McGrath Date: Fri, 13 Dec 2024 08:50:52 -0500 Subject: [PATCH 5/8] fix: tighter if condition --- data/Templates/eCR/Resource/_Observation.liquid | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data/Templates/eCR/Resource/_Observation.liquid b/data/Templates/eCR/Resource/_Observation.liquid index f21b483f..2fb35edc 100644 --- a/data/Templates/eCR/Resource/_Observation.liquid +++ b/data/Templates/eCR/Resource/_Observation.liquid @@ -140,7 +140,7 @@ {% assign observationValueReferenceValue = observationEntry.value.reference.value -%} "extension": [ { - {% if specimenValue != null or collectTime != null or receiveTime != null or observationTextReferenceValue != null or observationValueReferenceValue != null -%} + {% if specimenValue != null or collectTime != null or receiveTime != null -%} "url" : "http://hl7.org/fhir/R4/specimen.html", "extension": [ From cd0077829fd32ca0454ef1f2b57da044b5f3dfa6 Mon Sep 17 00:00:00 2001 From: Mary McGrath Date: Fri, 13 Dec 2024 10:04:31 -0500 Subject: [PATCH 6/8] test: add functional snapshot test for eCR --- data/SampleData/eCR/eCR_full.xml | 5790 ++++++++++++++++ data/Templates/eCR/Entry/Result/_entry.liquid | 2 +- .../BaseConvertDataFunctionalTests.cs | 28 +- ...emplateDirectoryProviderFunctionalTests.cs | 10 + .../DiffHelper.cs | 63 + .../Expected/eCR/EICR/eCR_full-expected.json | 6024 +++++++++++++++++ 6 files changed, 11914 insertions(+), 3 deletions(-) create mode 100644 data/SampleData/eCR/eCR_full.xml create mode 100644 src/Microsoft.Health.Fhir.Liquid.Converter.FunctionalTests/DiffHelper.cs create mode 100644 src/Microsoft.Health.Fhir.Liquid.Converter.FunctionalTests/TestData/Expected/eCR/EICR/eCR_full-expected.json diff --git a/data/SampleData/eCR/eCR_full.xml b/data/SampleData/eCR/eCR_full.xml new file mode 100644 index 00000000..8f246a56 --- /dev/null +++ b/data/SampleData/eCR/eCR_full.xml @@ -0,0 +1,5790 @@ + + + + + + + + + + Initial Public Health Case Report + + + + + + + + + + 9 Post Lane + NEWPORT BEACH + CA + 92663 + USA + + + + + + + + + + Adam + Test + + + + + + + + + + + + + + + + + + + Providence California + + + 4733 TORRANCE BLVD #4400 + LOS ANGELES + TORRANCE + CA + 90503 + USA + + + + + + + + + + + + + Providence California + + + 4733 TORRANCE BLVD #4400 + LOS ANGELES + TORRANCE + CA + 90503 + USA + + + + + + + + + + + + + + + + + + Lab Requisition + + + + + + + + + + + + + + + + + + + + + + + + Providence California + + 4733 TORRANCE BLVD #4400 + LOS ANGELES + TORRANCE + CA + 90503 + USA + + + + + + + + + + + Lab + + + PROVIDENCE ST JOSEPH MED CTR LABORATORY + + 501 S Buena Vista St + LOS ANGELES + Burbank + CA + 91505-4809 + USA + + + + + Providence St Joseph Medical Center + + + 501 S Buena Vista St + LOS ANGELES + Burbank + CA + 91505-4809 + USA + + + + Providence California + + + + + + + + + + + +
+ + + Miscellaneous Notes + + Not on file + documented in this + encounter + +
+ + +
+ + + + + + + Immunizations + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
NameAdministration DatesNext Due
DTAP-HIB-IPV (PENTACEL) + 04/16/2010 + +
HEP A (ADULT) 2 DOSE + 11/11/2011 + +
HEP B (PED,ADOLESCENT) 3 DOSE + 03/21/1974 + +
MENINGOCOCCAL CONJUGATE,MENACTRA + (PED/ADOL/ADULT) + 11/16/2020 + +
TDAP, (ADOL/ADULT) + 11/10/2020 + +
+ documented as of this + encounter + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 369258741 + + + Sanofi Pasteur + + + + + + + + + + + + + + + + Provma + Two + Ambtest + CMA + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 1 + + + Sanofi Pasteur + + + + + + + + + + + + + + + + Provma + Two + Ambtest + CMA + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ + + + + Administered Medications + + Not on file + documented in this + encounter + +
+ + +
+ + + + Plan of Treatment + + Not on file + documented as of this + encounter + +
+ + +
+ + + + + + Problems + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Active ProblemsNoted Date
Bipolar I disorder11/19/20
Reactive depression11/19/20
Rheumatoid arthritis with negative + rheumatoid factor11/16/20
Arthralgia of both ankles11/16/20
Anxiety11/10/20
Asthma11/10/20
Knee pain4/29/19
Sprain of calcaneofibular ligament of + right ankle4/16/19
+ A note: + Last Assessment & + Plan: + Formatting of this note + might be different from the original.
This + is my note about this problem. +
+
+ documented as of this + encounter (statuses as of 09/28/2022) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ + + Reason for Visit + + Not on file + +
+ + +
+ + + + + + + Results + + + + Stool + Pathogens, NAAT, 12 to 25 Targets (09/28/2022 1:51 PM PDT) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ComponentValueRef RangeTest MethodAnalysis TimePerformed AtPathologist Signature
Campylobacter, + NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
Plesiomonas + shigelloides, NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
Salmonella, + NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
Vibrio, + NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
Vibrio + cholerae, NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
Yersinia + enterocolitica, NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
E. + Coli (EAEC), NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
E. + Coli (EPEC), NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
E. + Coli (ETEC), NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
Shiga-Like + Toxin E. Coli (STEC), NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
Shigella/EIEC, + NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
Cryptosporidium, + NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
Cyclospora + cayetanensis, NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
E. + histolytica, NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
Giardia + lamblia, NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
Adenovirus + F 40/41, NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
Astrovirus, + NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
Norovirus, + NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
Rotavirus + A, NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
Sapovirus, + NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
+ + + + + + + + + + + + + + + + + + + + + +
Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
+ StoolSTOOL SPECIMEN / Unknown + 09/28/2022 1:51 PM PDT09/28/2022 1:51 PM PDT
+ + + + + + + + + + + + + + + + + +
Authorizing ProviderResult Type
Ambhp1 Test MDMICROBIOLOGY - GENERAL ORDERABLES
+ + + + + + + + + + + + + + + + + + + + + +
Performing OrganizationAddressCity/State/ZIP CodePhone Number
+ PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + 501 S. Buena Vista Street + + Burbank, CA 91505 + + 818-847-6000 +
+ + + (ABNORMAL) Stool Pathogens, NAAT, 12 to 25 + Targets (09/28/2022 1:51 PM PDT) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
ComponentValueRef RangeTest MethodAnalysis TimePerformed AtPathologist Signature
Campylobacter, + NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
Plesiomonas + shigelloides, NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
Salmonella, + NAAT + DETECTED + (AA) + Not Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
Vibrio, + NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
Vibrio + cholerae, NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
Yersinia + enterocolitica, NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
E. + Coli O157, NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
E. + Coli (EAEC), NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
E. + Coli (EPEC), NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
E. + Coli (ETEC), NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
Shiga-Like + Toxin E. Coli (STEC), NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
Shigella/EIEC, + NAAT + DETECTED + (AA) + Not Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
Cryptosporidium, + NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
Cyclospora + cayetanensis, NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
E. + histolytica, NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
Giardia + lamblia, NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
Adenovirus + F 40/41, NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
Astrovirus, + NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
Norovirus, + NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
Rotavirus + A, NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
Sapovirus, + NAATNot DetectedNot Detected + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
GI + Pathogens PanelAcceptable + + LAB + DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM + 09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY + (CLIA 05D0672675) +
+ + + + + + + + + + + + + + + + + + + + + +
Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
+ StoolSTOOL SPECIMEN / Unknown + 09/28/2022 1:51 PM PDT09/28/2022 1:51 PM PDT
+ + + + + + + + + + + + + + + + + +
Authorizing ProviderResult Type
Ambhp1 Test MDMICROBIOLOGY - GENERAL ORDERABLES
+ + + + + + + + + + + + + + + + + + + + + +
Performing OrganizationAddressCity/State/ZIP CodePhone Number
+ PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + 501 S. Buena Vista Street + + Burbank, CA 91505 + + 818-847-6000 +
+ + + documented in this + encounter + + + + + + + + Stool Pathogens, NAAT, 12 to 25 Targets + + + + + + + + + + + + + + + + + + + Providence Health and Services Oregon and California + (TST) + + + + + + + + Endocrinology + + + + + 2001 LIND AVE + RENTON + WA + 98059 + + + + + Ambhp1 + Test + MD + + + + + + + + + + + + + + + + + + + + + + Stool + + + + + + + + + + + + + + + + + + + + + Campylobacter, NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + Plesiomonas shigelloides, NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + Salmonella, NAAT + + + + + + + + DETECTED + + + Abnormal Alert + + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + Vibrio, NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + Vibrio cholerae, NAAT + + + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + Yersinia enterocolitica, NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + E. Coli O157, NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + E. Coli (EAEC), NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + E. Coli (EPEC), NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + E. Coli (ETEC), NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + + Shiga-Like Toxin E. Coli (STEC), NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + Shigella/EIEC, NAAT + + + + + + + + DETECTED + + + Abnormal Alert + + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + Cryptosporidium, NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + Cyclospora cayetanensis, NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + E. histolytica, NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + Giardia lamblia, NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + Adenovirus F 40/41, NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + Astrovirus, NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + Norovirus, NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + Rotavirus A, NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + Sapovirus, NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + GI Pathogens Panel + + + + + + + + Acceptable + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + + + + + + + + Lab Interpretation + + + + Abnormal + + + + + + + + + + + + + + + + + + + + + Stool Pathogens, NAAT, 12 to 25 Targets + + + + + + + + + + + + + + + + + + + Providence Health and Services Oregon and California + (TST) + + + + + + + + Endocrinology + + + + + 2001 LIND AVE + RENTON + WA + 98059 + + + + + Ambhp1 + Test + MD + + + + + + + + + + + + + + + + + + + + + + Stool + + + + + + + + + + + + + + + + + + + + + Campylobacter, NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + Plesiomonas shigelloides, NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + Salmonella, NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + Vibrio, NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + Vibrio cholerae, NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + Yersinia enterocolitica, NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + E. Coli (EAEC), NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + E. Coli (EPEC), NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + E. Coli (ETEC), NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + Shiga-Like Toxin E. Coli (STEC), NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + Shigella/EIEC, NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + Cryptosporidium, NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + Cyclospora cayetanensis, NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + E. histolytica, NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + Giardia lamblia, NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + Adenovirus F 40/41, NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + Astrovirus, NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + Norovirus, NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + Rotavirus A, NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + Sapovirus, NAAT + + + + + + + Not Detected + + + + + PROVIDENCE ST. JOSEPH MEDICAL CENTER + LABORATORY (CLIA 05D0672675) + + + 501 S. Buena Vista Street + Burbank + CA + 91505 + + + + + + + + + Kiran + B + Qidwai + + + + + + + Not Detected + Not Detected + + + + + + + + + + + + + Lab Interpretation + + + + Normal + + + + + + + + + + + + + + +
+ + +
+ + + + Social History + + + + + + + + + + + + + + + + + + + + + + + + + +
Tobacco UseTypesPacks/DayYears UsedDate
Smoking Tobacco: Never + + + +
Smokeless Tobacco: Never + + + +
+ + + + + + + + + + + + + + + + + + +
Alcohol UseStandard Drinks/WeekComments
Yes0 (1 standard drink = 0.6 oz pure alcohol) +
+ + + + + + + + + + + + + + + + +
Sex Assigned at BirthDate Recorded
Not on file +
+ documented as of this + encounter + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ + + + + + Encounter Details + + + + + + + + + + + + + + + + + + + + + + + + +
DateTypeDepartmentCare TeamDescription
9/28/22Lab Requisition + PROVIDENCE ST JOSEPH MED CTR LABORATORY + 501 S Buena Vista St + Burbank, CA 91505-4809 + 818-847-6060 + + Test, Ambhp1, MD + 2001 LIND AVE + RENTON, WA 98059 + +
+ + + + + + + + + + + + + + + + + + + + + + + + + Endocrinology + + + + + 2001 LIND AVE + RENTON + WA + 98059 + + + + + Ambhp1 + Test + MD + + + + + + + + + + Lab + + + 501 S Buena Vista St + LOS ANGELES + Burbank + CA + 91505-4809 + USA + + + PROVIDENCE ST JOSEPH MED CTR LABORATORY + Lab + + + + + +
+ + + + diff --git a/data/Templates/eCR/Entry/Result/_entry.liquid b/data/Templates/eCR/Entry/Result/_entry.liquid index 56b41f9b..4ddfc0df 100644 --- a/data/Templates/eCR/Entry/Result/_entry.liquid +++ b/data/Templates/eCR/Entry/Result/_entry.liquid @@ -54,7 +54,7 @@ {% endif -%} {% endif -%} {% endif -%} - {% endfor-%} + {% endfor -%} {% for component in comps %} {% include 'Entry/Result/entry_organizer_component' with component, text: text, specValue: specValue, collectTime: collectTime, receiveTime: receiveTime, diagnosticId: diagnosticId %} {% endfor %} diff --git a/src/Microsoft.Health.Fhir.Liquid.Converter.FunctionalTests/BaseConvertDataFunctionalTests.cs b/src/Microsoft.Health.Fhir.Liquid.Converter.FunctionalTests/BaseConvertDataFunctionalTests.cs index 0d902ea2..40d91727 100644 --- a/src/Microsoft.Health.Fhir.Liquid.Converter.FunctionalTests/BaseConvertDataFunctionalTests.cs +++ b/src/Microsoft.Health.Fhir.Liquid.Converter.FunctionalTests/BaseConvertDataFunctionalTests.cs @@ -3,6 +3,7 @@ // Licensed under the MIT License (MIT). See LICENSE in the repo root for license information. // ------------------------------------------------------------------------------------------------- +using System; using System.Collections.Generic; using System.IO; using System.Linq; @@ -213,6 +214,20 @@ public static IEnumerable GetDataForCcda() }); } + public static IEnumerable GetDataForEcr() + { + var data = new List + { + new[] { @"EICR", @"eCR_full.xml", @"eCR_full-expected.json" }, + }; + return data.Select(item => new[] + { + item[0], + Path.Join(Constants.SampleDataDirectory, "eCR", item[1]), + Path.Join(Constants.ExpectedDataFolder, "eCR", item[0], item[2]), + }); + } + public static IEnumerable GetDataForJson() { var data = new List @@ -332,8 +347,17 @@ protected void ConvertCCDAMessageAndValidateExpectedResponse(ITemplateProvider t var actualObject = JObject.Parse(actualContent); // Remove DocumentReference, where date is different every time conversion is run and gzip result is OS dependent - expectedObject["entry"]?.Last()?.Remove(); - actualObject["entry"]?.Last()?.Remove(); + if (expectedObject["entry"]?.Last()["resource"]["resourceType"].ToString() == "DocumentReference") + { + expectedObject["entry"]?.Last()?.Remove(); + actualObject["entry"]?.Last()?.Remove(); + } + + var diff = DiffHelper.FindDiff(actualObject, expectedObject); + if (diff.HasValues) + { + Console.WriteLine(diff); + } Assert.True(JToken.DeepEquals(expectedObject, actualObject)); } diff --git a/src/Microsoft.Health.Fhir.Liquid.Converter.FunctionalTests/ConvertDataTemplateDirectoryProviderFunctionalTests.cs b/src/Microsoft.Health.Fhir.Liquid.Converter.FunctionalTests/ConvertDataTemplateDirectoryProviderFunctionalTests.cs index 59d5e318..e103ddb2 100644 --- a/src/Microsoft.Health.Fhir.Liquid.Converter.FunctionalTests/ConvertDataTemplateDirectoryProviderFunctionalTests.cs +++ b/src/Microsoft.Health.Fhir.Liquid.Converter.FunctionalTests/ConvertDataTemplateDirectoryProviderFunctionalTests.cs @@ -88,6 +88,16 @@ public void GivenCcdaDocument_WhenConverting_ExpectedFhirResourceShouldBeReturne ConvertCCDAMessageAndValidateExpectedResponse(templateProvider, rootTemplate, inputFile, expectedFile); } + [Theory] + [MemberData(nameof(GetDataForEcr))] + public void GivenEcrDocument_WhenConverting_ExpectedFhirResourceShouldBeReturned(string rootTemplate, string inputFile, string expectedFile) + { + var templateDirectory = Path.Join(AppDomain.CurrentDomain.BaseDirectory, Constants.TemplateDirectory, "eCR"); + var templateProvider = new TemplateProvider(templateDirectory, DataType.Ccda); + + ConvertCCDAMessageAndValidateExpectedResponse(templateProvider, rootTemplate, inputFile, expectedFile); + } + [Theory] [MemberData(nameof(GetDataForStu3ToR4))] public void GivenStu3FhirData_WhenConverting_ExpectedR4FhirResourceShouldBeReturned(string rootTemplate, string inputFile, string expectedFile) diff --git a/src/Microsoft.Health.Fhir.Liquid.Converter.FunctionalTests/DiffHelper.cs b/src/Microsoft.Health.Fhir.Liquid.Converter.FunctionalTests/DiffHelper.cs new file mode 100644 index 00000000..9e3180d0 --- /dev/null +++ b/src/Microsoft.Health.Fhir.Liquid.Converter.FunctionalTests/DiffHelper.cs @@ -0,0 +1,63 @@ +using System.Linq; +using Newtonsoft.Json.Linq; + +namespace Microsoft.Health.Fhir.Liquid.Converter.FunctionalTests +{ + public static class DiffHelper + { + public static JObject FindDiff(this JToken Current, JToken Model) + { + var diff = new JObject(); + if (JToken.DeepEquals(Current, Model)) return diff; + + switch(Current.Type) + { + case JTokenType.Object: + { + var current = Current as JObject; + var model = Model as JObject; + var addedKeys = current.Properties().Select(c => c.Name).Except(model.Properties().Select(c => c.Name)); + var removedKeys = model.Properties().Select(c => c.Name).Except(current.Properties().Select(c => c.Name)); + var unchangedKeys = current.Properties().Where(c => JToken.DeepEquals(c.Value, Model[c.Name])).Select(c => c.Name); + foreach (var k in addedKeys) + { + diff[k] = new JObject + { + ["+"] = Current[k] + }; + } + foreach (var k in removedKeys) + { + diff[k] = new JObject + { + ["-"] = Model[k] + }; + } + var potentiallyModifiedKeys = current.Properties().Select(c => c.Name).Except(addedKeys).Except(unchangedKeys); + foreach (var k in potentiallyModifiedKeys) + { + var foundDiff = FindDiff(current[k], model[k]); + if(foundDiff.HasValues) diff[k] = foundDiff; + } + } + break; + case JTokenType.Array: + { + var current = Current as JArray; + var model = Model as JArray; + var plus = new JArray(current.Except(model, new JTokenEqualityComparer())); + var minus = new JArray(model.Except(current, new JTokenEqualityComparer())); + if (plus.HasValues) diff["+"] = plus; + if (minus.HasValues) diff["-"] = minus; + } + break; + default: + diff["+"] = Current; + diff["-"] = Model; + break; + } + + return diff; + } + } +} diff --git a/src/Microsoft.Health.Fhir.Liquid.Converter.FunctionalTests/TestData/Expected/eCR/EICR/eCR_full-expected.json b/src/Microsoft.Health.Fhir.Liquid.Converter.FunctionalTests/TestData/Expected/eCR/EICR/eCR_full-expected.json new file mode 100644 index 00000000..8905be9b --- /dev/null +++ b/src/Microsoft.Health.Fhir.Liquid.Converter.FunctionalTests/TestData/Expected/eCR/EICR/eCR_full-expected.json @@ -0,0 +1,6024 @@ +{ + "resourceType": "Bundle", + "type": "batch", + "entry": [ + { + "fullUrl": "urn:uuid:1.2.840.114350.1.13.297.3.7.8.688883.538441", + "resource": { + "resourceType": "Composition", + "id": "1.2.840.114350.1.13.297.3.7.8.688883.538441", + "meta": { + "profile": [ + "http://hl7.org/fhir/us/ecr/StructureDefinition/eicr-composition" + ] + }, + "identifier": [ + { + "use": "official", + "type": { + "coding": [ + { + "code": "55751-2", + "system": "http://loinc.org", + "display": "Initial Public Health Case Report" + } + ] + }, + "value": "7a89f990-3f70-11ed-9549-c301d81100b2", + "assigner": { + "display": "EPC" + } + } + ], + "extension": [ + { + "url": "http://hl7.org/fhir/StructureDefinition/composition-clinicaldocument-versionNumber", + "valueString": "15" + }, + { + "url": "https://www.hl7.org/implement/standards/product_brief.cfm?product_id=436", + "valueString": "2016-12-01" + } + ], + "status": "final", + "type": { + "coding": [ + { + "code": "55751-2", + "system": "http://loinc.org", + "display": "Initial Public Health Case Report" + } + ] + }, + "date": "2022-09-28T14:01:01-07:00", + "title": "Initial Public Health Case Report", + "confidentiality": "N", + "section": [ + { + "id": "59ecd3e2-c425-9925-b7ad-7440009463e5", + "title": "Miscellaneous Notes", + "text": { + "status": "generated", + "div": "Not on filedocumented in this encounter" + }, + "code": { + "coding": [ + { + "code": "10164-2", + "system": "http://loinc.org", + "display": "HISTORY OF PRESENT ILLNESS" + } + ] + }, + "mode": "snapshot" + }, + { + "id": "A84C7F7E-3F70-11ED-9549-C301D81100B2", + "title": "Immunizations", + "text": { + "status": "generated", + "div": "
NameAdministration DatesNext Due
DTAP-HIB-IPV (PENTACEL)04/16/2010
HEP A (ADULT) 2 DOSE11/11/2011
HEP B (PED,ADOLESCENT) 3 DOSE03/21/1974
MENINGOCOCCAL CONJUGATE,MENACTRA (PED/ADOL/ADULT)11/16/2020
TDAP, (ADOL/ADULT)11/10/2020
documented as of this encounter" + }, + "code": { + "coding": [ + { + "code": "11369-6", + "system": "http://loinc.org", + "display": "History of Immunization Narrative" + } + ] + }, + "mode": "snapshot" + }, + { + "id": "A853DBC0-3F70-11ED-9549-C301D81100B2", + "title": "Administered Medications", + "text": { + "status": "generated", + "div": "Not on filedocumented in this encounter" + }, + "code": { + "coding": [ + { + "code": "29549-3", + "system": "http://loinc.org", + "display": "MEDICATIONS ADMINISTERED" + } + ] + }, + "mode": "snapshot" + }, + { + "id": "2a6a9ce3-c605-ff37-1f76-86650fe02739", + "title": "Plan of Treatment", + "text": { + "status": "generated", + "div": "Not on filedocumented as of this encounter" + }, + "code": { + "coding": [ + { + "code": "18776-5", + "system": "http://loinc.org", + "display": "Plan of care note" + } + ] + }, + "mode": "snapshot", + "entry": [ + { + "reference": "CarePlan/42008b73-bc71-2c3e-1078-9799e5db7fe1" + } + ] + }, + { + "id": "A8648114-3F70-11ED-9549-C301D81100B2", + "title": "Problems", + "text": { + "status": "generated", + "div": "
Active ProblemsNoted Date
Bipolar I disorder11/19/20
Reactive depression11/19/20
Rheumatoid arthritis with negative rheumatoid factor11/16/20
Arthralgia of both ankles11/16/20
Anxiety11/10/20
Asthma11/10/20
Knee pain4/29/19
Sprain of calcaneofibular ligament of right ankle4/16/19
A note:Last Assessment & Plan: Formatting of this note might be different from the original.
This is my note about this problem.
documented as of this encounter (statuses as of 09/28/2022)" + }, + "code": { + "coding": [ + { + "code": "11450-4", + "system": "http://loinc.org", + "display": "Problem list - Reported" + } + ] + }, + "mode": "snapshot", + "entry": [ + { + "display": "Problem - Sprain of calcaneofibular ligament of right ankle", + "reference": "Condition/34728086-4b53-a5f0-8eaa-61f72b79a78c" + }, + { + "display": "Problem - Knee pain", + "reference": "Condition/b3f9a35e-828c-e0aa-f083-b95837e69a31" + }, + { + "display": "Problem - Anxiety", + "reference": "Condition/9e83e83e-8c39-c58f-d96c-72bb94b75531" + }, + { + "display": "Problem - Asthma", + "reference": "Condition/b8166f2c-ad38-da4b-aec4-974cc2c6664f" + }, + { + "display": "Problem - Rheumatoid arthritis with negative rheumatoid factor", + "reference": "Condition/5dad7636-f4ae-0823-a58d-3536ce82c42b" + }, + { + "display": "Problem - Arthralgia of both ankles", + "reference": "Condition/f5840e99-3485-96c0-ee31-139f1cdb7c36" + }, + { + "display": "Problem - Bipolar I disorder", + "reference": "Condition/650e3ee3-148d-3895-2406-7dc0da609ae0" + }, + { + "display": "Problem - Reactive depression", + "reference": "Condition/e6367140-81af-9ccf-c974-c2170bc95500" + } + ] + }, + { + "id": "bbec169d-3c40-32f9-03df-b5594fe80c34", + "title": "Reason for Visit", + "text": { + "status": "generated", + "div": "Not on file" + }, + "code": { + "coding": [ + { + "code": "29299-5", + "system": "http://loinc.org", + "display": "REASON FOR VISIT" + } + ] + }, + "mode": "snapshot", + "extension": [ + { + "url": "http://hl7.org/fhir/cda/ccda/StructureDefinition/2.16.840.1.113883.10.20.22.2.12", + "valueString": "Not on file" + } + ] + }, + { + "id": "A87B29AA-3F70-11ED-9549-C301D81100B2", + "title": "Results", + "text": { + "status": "generated", + "div": "Stool Pathogens, NAAT, 12 to 25 Targets (09/28/2022 1:51 PM PDT)
ComponentValueRef RangeTest MethodAnalysis TimePerformed AtPathologist Signature
Campylobacter, NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
Plesiomonas shigelloides, NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
Salmonella, NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
Vibrio, NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
Vibrio cholerae, NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
Yersinia enterocolitica, NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
E. Coli (EAEC), NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
E. Coli (EPEC), NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
E. Coli (ETEC), NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
Shiga-Like Toxin E. Coli (STEC), NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
Shigella/EIEC, NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
Cryptosporidium, NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
Cyclospora cayetanensis, NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
E. histolytica, NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
Giardia lamblia, NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
Adenovirus F 40/41, NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
Astrovirus, NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
Norovirus, NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
Rotavirus A, NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
Sapovirus, NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 1:59 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
StoolSTOOL SPECIMEN / Unknown09/28/2022 1:51 PM PDT09/28/2022 1:51 PM PDT
Authorizing ProviderResult Type
Ambhp1 Test MDMICROBIOLOGY - GENERAL ORDERABLES
Performing OrganizationAddressCity/State/ZIP CodePhone Number
PROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)501 S. Buena Vista StreetBurbank, CA 91505818-847-6000
(ABNORMAL) Stool Pathogens, NAAT, 12 to 25 Targets (09/28/2022 1:51 PM PDT)
ComponentValueRef RangeTest MethodAnalysis TimePerformed AtPathologist Signature
Campylobacter, NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
Plesiomonas shigelloides, NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
Salmonella, NAATDETECTED (AA)Not DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
Vibrio, NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
Vibrio cholerae, NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
Yersinia enterocolitica, NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
E. Coli O157, NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
E. Coli (EAEC), NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
E. Coli (EPEC), NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
E. Coli (ETEC), NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
Shiga-Like Toxin E. Coli (STEC), NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
Shigella/EIEC, NAATDETECTED (AA)Not DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
Cryptosporidium, NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
Cyclospora cayetanensis, NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
E. histolytica, NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
Giardia lamblia, NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
Adenovirus F 40/41, NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
Astrovirus, NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
Norovirus, NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
Rotavirus A, NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
Sapovirus, NAATNot DetectedNot DetectedLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
GI Pathogens PanelAcceptableLAB DEVICE: BIOFIRE® FILMARRAY® 2.0 SYSTEM09/28/2022 2:00 PM PDTPROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)
Specimen (Source)Anatomical Location / LateralityCollection Method / VolumeCollection TimeReceived Time
StoolSTOOL SPECIMEN / Unknown09/28/2022 1:51 PM PDT09/28/2022 1:51 PM PDT
Authorizing ProviderResult Type
Ambhp1 Test MDMICROBIOLOGY - GENERAL ORDERABLES
Performing OrganizationAddressCity/State/ZIP CodePhone Number
PROVIDENCE ST. JOSEPH MEDICAL CENTER LABORATORY (CLIA 05D0672675)501 S. Buena Vista StreetBurbank, CA 91505818-847-6000
documented in this encounter" + }, + "code": { + "coding": [ + { + "code": "30954-2", + "system": "http://loinc.org", + "display": "Relevant diagnostic tests/laboratory data Narrative" + } + ] + }, + "mode": "snapshot", + "entry": [ + { + "reference": "Observation/a00006e4-f2d8-0c10-b96b-6b56def874e1", + "display": "Campylobacter, NAAT" + }, + { + "reference": "Observation/386f91f9-9bb9-44f2-4e99-284e3d0051c8", + "display": "Plesiomonas shigelloides, NAAT" + }, + { + "reference": "Observation/db2ddcd3-de40-a980-701d-3295256719bb", + "display": "Salmonella, NAAT" + }, + { + "reference": "Observation/ef277bb4-7302-f66e-0585-a90c6fe7b63f", + "display": "Vibrio, NAAT" + }, + { + "reference": "Observation/28949844-281e-0581-70e8-38ecd287116b", + "display": "Vibrio cholerae, NAAT" + }, + { + "reference": "Observation/38af00cb-3319-514b-3a9c-b6f71d57a6a4", + "display": "Yersinia enterocolitica, NAAT" + }, + { + "reference": "Observation/9256f7d3-98ec-fce8-90d1-57aec284c887", + "display": "E. Coli O157, NAAT" + }, + { + "reference": "Observation/9f4402c6-0783-bc2d-926f-3c7b96146cfd", + "display": "E. Coli (EAEC), NAAT" + }, + { + "reference": "Observation/06e693a9-b5c4-51ac-8888-086131261c46", + "display": "E. Coli (EPEC), NAAT" + }, + { + "reference": "Observation/b33d223c-9947-0795-a25d-bc0510716509", + "display": "E. Coli (ETEC), NAAT" + }, + { + "reference": "Observation/7086a08a-8e86-6354-8c0c-88d42a1c5234", + "display": "Shiga-Like Toxin E. Coli (STEC), NAAT" + }, + { + "reference": "Observation/d41aae21-a91a-74d8-3423-260256bc48b5", + "display": "Shigella/EIEC, NAAT" + }, + { + "reference": "Observation/93caad24-d8f1-6b8d-82f7-7e757c5f145b", + "display": "Cryptosporidium, NAAT" + }, + { + "reference": "Observation/63537cc7-04fe-9788-5390-25547813e41d", + "display": "Cyclospora cayetanensis, NAAT" + }, + { + "reference": "Observation/23ce6d59-e5cb-a803-97d0-28e9c9ea9cf5", + "display": "E. histolytica, NAAT" + }, + { + "reference": "Observation/1bace839-10e5-14ad-eb5d-1017c1b563ed", + "display": "Giardia lamblia, NAAT" + }, + { + "reference": "Observation/0b6a2f7f-6ee8-c00d-8519-70ae47a94d01", + "display": "Adenovirus F 40/41, NAAT" + }, + { + "reference": "Observation/993fdfcb-0d15-1ce5-7652-d9cbccd77d7f", + "display": "Astrovirus, NAAT" + }, + { + "reference": "Observation/b8746e9c-ed12-1069-1168-095692b463fb", + "display": "Norovirus, NAAT" + }, + { + "reference": "Observation/a04992b6-9980-8866-55b9-1187c93c378c", + "display": "Rotavirus A, NAAT" + }, + { + "reference": "Observation/9b963591-7fdd-96a5-69ec-1d56d9dec3a3", + "display": "Sapovirus, NAAT" + }, + { + "reference": "Observation/3d694e5a-92cc-9af5-4365-cfede30abe3c", + "display": "Lab Interpretation" + }, + { + "reference": "Observation/57c969ce-4656-9526-8d27-e39eb8e33625", + "display": "Campylobacter, NAAT" + }, + { + "reference": "Observation/af92101a-6b5d-50b3-ebdb-45658ec25808", + "display": "Plesiomonas shigelloides, NAAT" + }, + { + "reference": "Observation/c0b99528-7b83-6cdb-b4af-4376e969e11d", + "display": "Salmonella, NAAT" + }, + { + "reference": "Observation/a13fc3f5-06ed-2105-98c7-e2e0094fa1f6", + "display": "Vibrio, NAAT" + }, + { + "reference": "Observation/f74c4591-b7a0-eceb-f8be-f1441c4bb5f1", + "display": "Vibrio cholerae, NAAT" + }, + { + "reference": "Observation/87f76719-5e72-e3cd-cf52-5fc8635eebbd", + "display": "Yersinia enterocolitica, NAAT" + }, + { + "reference": "Observation/84ba7cd9-c570-9a62-7b1f-d08b19af0973", + "display": "E. Coli (EAEC), NAAT" + }, + { + "reference": "Observation/ee4f7291-130b-ae27-8b59-60b93c8c6e1b", + "display": "E. Coli (EPEC), NAAT" + }, + { + "reference": "Observation/3351c512-bc9e-0bda-3b51-6c6f807b772d", + "display": "E. Coli (ETEC), NAAT" + }, + { + "reference": "Observation/4d20693f-fe7d-5c98-e585-a89ac8088a59", + "display": "Shiga-Like Toxin E. 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This is my note about this problem.
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9b76856614f253dbf9105c695306fbf1ea7dd03e Mon Sep 17 00:00:00 2001 From: Mary McGrath Date: Fri, 13 Dec 2024 10:06:21 -0500 Subject: [PATCH 7/8] fix: attribution --- .../DiffHelper.cs | 1 + 1 file changed, 1 insertion(+) diff --git a/src/Microsoft.Health.Fhir.Liquid.Converter.FunctionalTests/DiffHelper.cs b/src/Microsoft.Health.Fhir.Liquid.Converter.FunctionalTests/DiffHelper.cs index 9e3180d0..2c22e509 100644 --- a/src/Microsoft.Health.Fhir.Liquid.Converter.FunctionalTests/DiffHelper.cs +++ b/src/Microsoft.Health.Fhir.Liquid.Converter.FunctionalTests/DiffHelper.cs @@ -3,6 +3,7 @@ namespace Microsoft.Health.Fhir.Liquid.Converter.FunctionalTests { + // from https://stackoverflow.com/questions/24876082/find-and-return-json-differences-using-newtonsoft-in-c public static class DiffHelper { public static JObject FindDiff(this JToken Current, JToken Model) From 0cd1e3a84a6e738c0099ee2cd5d8b99ae7656cdc Mon Sep 17 00:00:00 2001 From: Mary McGrath Date: Fri, 13 Dec 2024 10:32:32 -0500 Subject: [PATCH 8/8] test: update snapshot with latest from main --- .../TestData/Expected/eCR/EICR/eCR_full-expected.json | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/src/Microsoft.Health.Fhir.Liquid.Converter.FunctionalTests/TestData/Expected/eCR/EICR/eCR_full-expected.json b/src/Microsoft.Health.Fhir.Liquid.Converter.FunctionalTests/TestData/Expected/eCR/EICR/eCR_full-expected.json index 8905be9b..82ea16cb 100644 --- a/src/Microsoft.Health.Fhir.Liquid.Converter.FunctionalTests/TestData/Expected/eCR/EICR/eCR_full-expected.json +++ b/src/Microsoft.Health.Fhir.Liquid.Converter.FunctionalTests/TestData/Expected/eCR/EICR/eCR_full-expected.json @@ -974,7 +974,10 @@ "city": "NEWPORT BEACH", "state": "CA", "country": "USA", - "postalCode": "92663" + "postalCode": "92663", + "period": { + "start": "2019-04-10" + } } ], "maritalStatus": {