Merge pull request #465 from samply/release-0.11.1

Release 0.11.1
samply · Aug 30, 2021 · 95c8130 · 95c8130
2 parents 4174606 + 2832fb7
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diff --git a/.github/scripts/evaluate-measure.sh b/.github/scripts/evaluate-measure.sh
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+#!/usr/bin/env bash
+
+# Usage: ./evaluate-measure.sh -f <query>.cql <expected-count>
+
+# Takes a CQL file, creates a Library resource from it, references that from a
+# Measure resource and calls $evaluate-measure on it.
+
+library() {
+cat <<END
+{
+  "resourceType": "Library",
+  "status": "active",
+  "type" : {
+    "coding" : [
+      {
+        "system": "http://terminology.hl7.org/CodeSystem/library-type",
+        "code" : "logic-library"
+      }
+    ]
+  },
+  "content": [
+    {
+      "contentType": "text/cql"
+    }
+  ]
+}
+END
+}
+
+measure() {
+cat <<END
+{
+  "resourceType": "Measure",
+  "status": "active",
+  "scoring": {
+    "coding": [
+      {
+        "system": "http://terminology.hl7.org/CodeSystem/measure-scoring",
+        "code": "cohort"
+      }
+    ]
+  },
+  "group": [
+    {
+      "population": [
+        {
+          "code": {
+            "coding": [
+              {
+                "system": "http://terminology.hl7.org/CodeSystem/measure-population",
+                "code": "initial-population"
+              }
+            ]
+          },
+          "criteria": {
+            "language": "text/cql",
+            "expression": "InInitialPopulation"
+          }
+        }
+      ]
+    }
+  ]
+}
+END
+}
+
+create-library() {
+  library | jq -cM ".url = \"urn:uuid:$1\" | .content[0].data = \"$2\""
+}
+
+create-measure() {
+  measure | jq -cM ".url = \"urn:uuid:$1\" | .library[0] = \"urn:uuid:$2\""
+}
+
+post() {
+  curl -sH "Content-Type: application/fhir+json" -d @- "http://localhost:8080/fhir/$1"
+}
+
+evaluate-measure() {
+  curl -s "http://localhost:8080/fhir/Measure/$1/\$evaluate-measure?periodStart=2000&periodEnd=2030"
+}
+
+FILE=$1
+EXPECTED_COUNT=$2
+
+DATA=$(base64 "$FILE" | tr -d '\n')
+LIBRARY_URI=$(uuidgen | tr '[:upper:]' '[:lower:]')
+MEASURE_URI=$(uuidgen | tr '[:upper:]' '[:lower:]')
+
+create-library "$LIBRARY_URI" "$DATA" | post "Library" > /dev/null
+
+MEASURE_ID=$(create-measure "$MEASURE_URI" "$LIBRARY_URI" | post "Measure" | jq -r .id)
+COUNT=$(evaluate-measure "$MEASURE_ID" | jq -r ".group[0].population[0].count")
+
+if [ "$COUNT" = "$EXPECTED_COUNT" ]; then
+  echo "Success: count ($COUNT) equals the expected count"
+else
+  echo "Fail: count ($LAB_COUNT) != $EXPECTED_COUNT"
+  exit 1
+fi
diff --git a/.github/test-data/0-hospitalInformation1625911868739.json.bz2 b/.github/test-data/0-hospitalInformation1625911868739.json.bz2
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diff --git a/.github/test-data/README.md b/.github/test-data/README.md
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+# FHIR Test Data
+
+Generates with Synthea v2.7.0 using openjdk 11.
+
+```sh
+java -jar synthea-with-dependencies.jar -p 100 --exporter.use_uuid_filenames=true
+```
+
+```text
+Scanned 66 modules and 67 submodules.
+Loading submodule modules/breast_cancer/tnm_diagnosis.json
+Loading submodule modules/allergies/allergy_incidence.json
+Loading submodule modules/covid19/nonsurvivor_lab_values.json
+Loading submodule modules/covid19/outcomes.json
+Loading submodule modules/covid19/survivor_lab_values.json
+Loading submodule modules/dermatitis/moderate_cd_obs.json
+Loading submodule modules/covid19/diagnose_blood_clot.json
+Loading submodule modules/dermatitis/severe_cd_obs.json
+Loading submodule modules/contraceptives/female_sterilization.json
+Loading submodule modules/allergies/outgrow_env_allergies.json
+Loading submodule modules/covid19/medications.json
+Loading submodule modules/encounter/vitals.json
+Loading submodule modules/heart/chf_meds.json
+Loading submodule modules/lung_cancer/lung_cancer_probabilities.json
+Loading submodule modules/contraceptives/patch_contraceptive.json
+Loading submodule modules/heart/chf_lvad.json
+Loading submodule modules/allergies/allergy_panel.json
+Loading submodule modules/covid19/supplies_hospitalization.json
+Loading submodule modules/breast_cancer/surgery_therapy_breast.json
+Loading submodule modules/allergies/severe_allergic_reaction.json
+Loading submodule modules/covid19/supplies_intubation.json
+Loading submodule modules/covid19/infection.json
+Loading submodule modules/dermatitis/early_severe_eczema_obs.json
+Loading submodule modules/total_joint_replacement/functional_status_assessments.json
+Loading submodule modules/weight_loss/mend_week.json
+Loading submodule modules/heart/chf_lab_work.json
+Loading submodule modules/contraceptives/ring_contraceptive.json
+Loading submodule modules/covid19/end_symptoms.json
+Loading submodule modules/covid19/diagnose_bacterial_infection.json
+Loading submodule modules/anemia/anemia_sub.json
+Loading submodule modules/heart/chf_transplant.json
+Loading submodule modules/medications/otc_pain_reliever.json
+Loading submodule modules/breast_cancer/hormone_diagnosis.json
+Loading submodule modules/covid19/supplies_icu.json
+Loading submodule modules/medications/strong_opioid_pain_reliever.json
+Loading submodule modules/medications/ear_infection_antibiotic.json
+Loading submodule modules/allergies/immunotherapy.json
+Loading submodule modules/dermatitis/mid_moderate_eczema_obs.json
+Loading submodule modules/contraceptives/clear_contraceptive.json
+Loading submodule modules/heart/chf_meds_hfmef.json
+Loading submodule modules/covid19/end_outcomes.json
+Loading submodule modules/heart/chf_nyha_panel.json
+Loading submodule modules/surgery/general_anesthesia.json
+Loading submodule modules/veterans/veteran_suicide_probabilities.json
+Loading submodule modules/contraceptives/oral_contraceptive.json
+Loading submodule modules/medications/moderate_opioid_pain_reliever.json
+Loading submodule modules/covid19/measurements_vitals.json
+Loading submodule modules/medications/otc_antihistamine.json
+Loading submodule modules/covid19/determine_risk.json
+Loading Lookup Table: covid-19-severity-outcomes.csv
+Loading Lookup Table: covid-19-survival-outcomes.csv
+Loading submodule modules/covid19/admission.json
+Loading submodule modules/covid19/measurements_frequent.json
+Loading submodule modules/dermatitis/mid_severe_eczema_obs.json
+Loading submodule modules/dermatitis/early_moderate_eczema_obs.json
+Loading submodule modules/covid19/symptoms.json
+Loading submodule modules/contraceptives/intrauterine_device.json
+Loading submodule modules/contraceptives/male_sterilization.json
+Loading submodule modules/heart/chf_meds_hfref_nyha3.json
+Loading submodule modules/contraceptives/implant_contraceptive.json
+Loading submodule modules/heart/chf_meds_hfref_nyha4.json
+Loading submodule modules/breast_cancer/hormonetherapy_breast.json
+Loading submodule modules/heart/chf_meds_hfref_nyha2.json
+Loading submodule modules/contraceptives/injectable_contraceptive.json
+Loading submodule modules/covid19/measurements_daily.json
+Loading submodule modules/covid19/treat_blood_clot.json
+Loading submodule modules/medications/hypertension_medication.json
+Loading submodule modules/allergies/outgrow_food_allergies.json
+Loading submodule modules/breast_cancer/chemotherapy_breast.json
+Loading module modules/opioid_addiction.json
+Loading module modules/cerebral_palsy.json
+Loading module modules/dialysis.json
+Loading module modules/allergic_rhinitis.json
+Loading module modules/pregnancy.json
+Loading module modules/atopy.json
+Loading module modules/self_harm.json
+Loading module modules/asthma.json
+Loading module modules/covid19.json
+Loading Lookup Table: covid19_prob.csv
+Loading module modules/ear_infections.json
+Loading module modules/sinusitis.json
+Loading module modules/dementia.json
+Loading module modules/veteran_hyperlipidemia.json
+Loading module modules/mTBI.json
+Loading module modules/veteran_prostate_cancer.json
+Loading module modules/anemia___unknown_etiology.json
+Loading module modules/urinary_tract_infections.json
+Loading module modules/hypothyroidism.json
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+Loading module modules/fibromyalgia.json
+Loading module modules/veteran_substance_abuse_treatment.json
+Loading module modules/veteran_lung_cancer.json
+Loading module modules/total_joint_replacement.json
+Loading module modules/prescribing_opioids_for_chronic_pain_and_treatment_of_oud.json
+Loading module modules/rheumatoid_arthritis.json
+Loading module modules/sore_throat.json
+Loading module modules/gallstones.json
+Loading module modules/bronchitis.json
+Loading module modules/spina_bifida.json
+Loading module modules/sexual_activity.json
+Loading module modules/homelessness.json
+Loading module modules/epilepsy.json
+Loading module modules/wellness_encounters.json
+Loading module modules/injuries.json
+Loading module modules/colorectal_cancer.json
+Loading module modules/med_rec.json
+Loading module modules/congestive_heart_failure.json
+Loading module modules/veteran_self_harm.json
+Loading module modules/veteran_mdd.json
+Loading module modules/lung_cancer.json
+Loading module modules/contraceptives.json
+Loading module modules/osteoporosis.json
+Loading module modules/breast_cancer.json
+Loading module modules/female_reproduction.json
+Loading module modules/veteran.json
+Loading module modules/gout.json
+Loading module modules/metabolic_syndrome_disease.json
+Loading module modules/sepsis.json
+Loading module modules/allergies.json
+Loading module modules/metabolic_syndrome_care.json
+Loading module modules/lupus.json
+Loading module modules/cystic_fibrosis.json
+Loading module modules/attention_deficit_disorder.json
+Loading module modules/dermatitis.json
+Loading module modules/food_allergies.json
+Loading module modules/mend_program.json
+Loading module modules/veteran_ptsd.json
+Loading module modules/veteran_substance_abuse_conditions.json
+Loading module modules/hypertension.json
+Running with options:
+Population: 100
+Seed: 1625911868501
+Provider Seed:1625911868501
+Reference Time: 1625911868501
+Location: Massachusetts
+Min Age: 0
+Max Age: 140
+1 -- Patricio639 Fonseca493 (3 y/o M) North Andover, Massachusetts 
+8 -- Foster87 Heidenreich818 (9 y/o M) Norwood, Massachusetts 
+6 -- Isela504 Rempel203 (19 y/o F) Boxborough, Massachusetts 
+2 -- Rosario163 Medhurst46 (24 y/o M) Boston, Massachusetts 
+3 -- Boyd728 Hackett68 (45 y/o M) Barnstable, Massachusetts 
+7 -- Zena758 Powlowski563 (49 y/o F) New Bedford, Massachusetts 
+4 -- Yang129 Rosenbaum794 (63 y/o F) Springfield, Massachusetts 
+5 -- Reena181 Reilly981 (60 y/o F) Acushnet, Massachusetts 
+12 -- Ernesto186 Villareal516 (18 y/o M) Swampscott, Massachusetts 
+11 -- Sudie246 Bechtelar572 (26 y/o F) Boston, Massachusetts 
+10 -- Keven605 Shanahan202 (49 y/o M) Chelsea, Massachusetts 
+13 -- Delicia67 Mueller846 (33 y/o F) Quincy, Massachusetts 
+9 -- Denisha680 Kassulke119 (53 y/o F) Barnstable, Massachusetts 
+14 -- Gabriel934 Granado100 (58 y/o M) Sandwich, Massachusetts DECEASED
+16 -- Pierre431 Nikolaus26 (66 y/o M) Worcester, Massachusetts 
+21 -- Berenice603 Marvin195 (9 y/o F) Foxborough, Massachusetts 
+18 -- Rafaela464 Zboncak558 (45 y/o F) Concord, Massachusetts 
+20 -- Ruben688 Medhurst46 (29 y/o M) East Sandwich, Massachusetts 
+22 -- Dusty207 Bernier607 (11 y/o M) Nantucket, Massachusetts 
+15 -- Roselia779 Thompson596 (91 y/o F) Easton, Massachusetts DECEASED
+25 -- Chere867 Daniel959 (4 y/o F) Hudson, Massachusetts 
+24 -- Brent147 Harris789 (10 y/o M) Dracut, Massachusetts 
+23 -- Raymundo71 Labadie908 (10 y/o M) Abington, Massachusetts 
+19 -- Rafael239 Franecki195 (57 y/o M) Weymouth, Massachusetts 
+17 -- Chi716 Cormier289 (91 y/o F) East Douglas, Massachusetts DECEASED
+14 -- Rodrigo242 Rodr?quez611 (54 y/o M) Sandwich, Massachusetts DECEASED
+29 -- Ned189 Mills423 (13 y/o M) Marlborough, Massachusetts 
+28 -- Trinidad33 Sauer652 (26 y/o M) Williamstown, Massachusetts 
+26 -- Mikel238 Baumbach677 (54 y/o M) Topsfield, Massachusetts 
+30 -- Mose244 Gislason620 (34 y/o M) Dracut, Massachusetts 
+27 -- Britteny287 Pagac496 (44 y/o F) Billerica, Massachusetts 
+32 -- Rudy520 Abshire638 (10 y/o M) Arlington, Massachusetts 
+17 -- Camila223 Ankunding277 (20 y/o F) East Douglas, Massachusetts DECEASED
+15 -- Nathalie366 Mitchell808 (85 y/o F) Easton, Massachusetts DECEASED
+31 -- Adriana394 Preciado125 (55 y/o F) Worcester, Massachusetts 
+33 -- Leila837 Smitham825 (48 y/o F) Springfield, Massachusetts 
+35 -- Taylor21 Stiedemann542 (35 y/o M) Brimfield, Massachusetts 
+38 -- Valerie954 Walker122 (5 y/o F) Peabody, Massachusetts 
+34 -- Rosario163 Fadel536 (60 y/o M) Shrewsbury, Massachusetts 
+36 -- Elsie248 Witting912 (16 y/o F) Adams, Massachusetts 
+37 -- Chang901 Stroman228 (18 y/o F) Everett, Massachusetts 
+41 -- Marco578 Yundt842 (16 y/o M) Walpole, Massachusetts 
+17 -- Janis361 Gutmann970 (81 y/o F) East Douglas, Massachusetts DECEASED
+43 -- Donnie175 Swaniawski813 (26 y/o F) Springfield, Massachusetts 
+40 -- Lane844 Rath779 (42 y/o M) Charlton, Massachusetts 
+39 -- Numbers230 Barton704 (52 y/o M) Taunton, Massachusetts 
+14 -- Armando772 Cort?s936 (60 y/o M) Sandwich, Massachusetts 
+42 -- Kassandra256 Wiegand701 (41 y/o F) Chelsea, Massachusetts 
+44 -- Lucas404 Le?n820 (52 y/o M) Medford, Massachusetts 
+49 -- Bok974 Rau926 (8 y/o F) Stoughton, Massachusetts 
+48 -- Vennie613 Bogan287 (15 y/o F) Norwood, Massachusetts 
+15 -- Charisse42 Parisian75 (102 y/o F) Easton, Massachusetts 
+47 -- Annabelle638 Spencer878 (64 y/o F) Marlborough, Massachusetts 
+17 -- Loida499 Rosenbaum794 (89 y/o F) East Douglas, Massachusetts DECEASED
+52 -- Zana914 Gusikowski974 (41 y/o F) Hampden, Massachusetts 
+46 -- Stacia109 Schowalter414 (68 y/o F) Auburn, Massachusetts 
+45 -- Christian753 Bruen238 (73 y/o F) Pocasset, Massachusetts 
+50 -- Quintin944 Willms744 (55 y/o M) Norwood, Massachusetts 
+54 -- Aida517 Wiza601 (4 y/o F) Taunton, Massachusetts 
+53 -- Sybil495 Braun514 (22 y/o F) Upton, Massachusetts 
+51 -- Kristie55 Treutel973 (69 y/o F) Worcester, Massachusetts DECEASED
+57 -- Glen190 Zemlak964 (13 y/o M) Lawrence, Massachusetts 
+55 -- Mindi87 Homenick806 (65 y/o F) Acton, Massachusetts 
+56 -- Jacinto644 Bauch723 (48 y/o M) Worcester, Massachusetts 
+59 -- Arielle168 Robel940 (22 y/o F) Harvard, Massachusetts 
+61 -- Alva958 Ryan260 (20 y/o M) Medford, Massachusetts 
+60 -- Mathew182 Kuphal363 (43 y/o M) Somerville, Massachusetts 
+58 -- August363 Wiza601 (52 y/o M) Methuen, Massachusetts 
+62 -- Mel236 Mayer370 (21 y/o M) Newton, Massachusetts 
+17 -- Ginny287 Streich926 (83 y/o F) East Douglas, Massachusetts DECEASED
+64 -- Dexter530 Shields502 (22 y/o M) Ludlow, Massachusetts DECEASED
+66 -- Zandra428 O'Hara248 (0 y/o F) Amherst, Massachusetts 
+63 -- Tyron580 Abbott774 (67 y/o M) Lexington, Massachusetts DECEASED
+68 -- Florine959 Wolf938 (10 y/o F) Hingham, Massachusetts 
+67 -- Gerry91 Powlowski563 (35 y/o M) Worcester, Massachusetts 
+64 -- Ollie731 Funk324 (53 y/o M) Ludlow, Massachusetts 
+65 -- Rose199 Wehner319 (81 y/o F) Greenfield, Massachusetts 
+17 -- Onita767 Conn188 (44 y/o F) East Douglas, Massachusetts DECEASED
+72 -- Kyle55 Hilll811 (23 y/o M) Somerville, Massachusetts DECEASED
+70 -- Delinda651 Casper496 (59 y/o F) Winchester, Massachusetts 
+69 -- Lavera253 Langworth352 (77 y/o F) Haverhill, Massachusetts 
+73 -- Ayesha583 Hauck852 (36 y/o F) Newton, Massachusetts 
+63 -- Quincy153 Kohler843 (73 y/o M) Lexington, Massachusetts DECEASED
+51 -- Louis204 Little434 (76 y/o F) Worcester, Massachusetts 
+71 -- Lurlene215 Torp761 (71 y/o F) Plymouth, Massachusetts 
+77 -- Soledad678 Guzm?n14 (5 y/o F) Winchendon, Massachusetts 
+75 -- Margarita164 Legros616 (32 y/o F) Boston, Massachusetts 
+76 -- Corey514 Balistreri607 (28 y/o M) Boston, Massachusetts 
+72 -- Robt687 Morissette863 (69 y/o M) Somerville, Massachusetts 
+74 -- Darrel772 Davis923 (59 y/o M) Grafton, Massachusetts 
+17 -- Luna60 Will178 (92 y/o F) East Douglas, Massachusetts 
+79 -- Mercy752 Ankunding277 (49 y/o F) Taunton, Massachusetts 
+84 -- Gary33 Boehm581 (3 y/o F) Boston, Massachusetts 
+80 -- Roscoe437 Windler79 (45 y/o M) Marlborough, Massachusetts 
+78 -- Dexter530 Price929 (73 y/o M) Waltham, Massachusetts DECEASED
+63 -- Eliseo499 Wyman904 (75 y/o M) Lexington, Massachusetts 
+85 -- Yuriko393 Jakubowski832 (10 y/o F) Lancaster, Massachusetts 
+82 -- Ka422 Ryan260 (56 y/o F) Plymouth, Massachusetts 
+83 -- Raymon366 Sauer652 (48 y/o M) Cambridge, Massachusetts 
+81 -- Karren465 Little434 (79 y/o F) Rehoboth, Massachusetts 
+86 -- Gwyneth692 Will178 (49 y/o F) Worcester, Massachusetts 
+88 -- Alphonso102 Collins926 (26 y/o M) Boston, Massachusetts 
+89 -- Neal874 Kovacek682 (36 y/o M) Worcester, Massachusetts 
+87 -- Kris249 Welch179 (58 y/o M) Plymouth, Massachusetts 
+90 -- Stevie682 Russel238 (52 y/o F) Framingham, Massachusetts 
+94 -- Maximo817 Bartell116 (30 y/o M) Milford, Massachusetts 
+95 -- Lupe126 Gulgowski816 (26 y/o M) Brockton, Massachusetts 
+92 -- Maricela194 Grant908 (61 y/o F) Boston, Massachusetts 
+91 -- Karren465 Stoltenberg489 (73 y/o F) Boston, Massachusetts 
+93 -- Elinor7 Wilderman619 (48 y/o F) Worcester, Massachusetts DECEASED
+78 -- Jayson808 Johnston597 (74 y/o M) Waltham, Massachusetts 
+97 -- Garfield38 Kessler503 (51 y/o M) Attleboro, Massachusetts DECEASED
+96 -- Sarina640 Kilback373 (39 y/o F) Fall River, Massachusetts 
+99 -- Tula326 Gulgowski816 (24 y/o F) Watertown, Massachusetts 
+98 -- Demarcus108 Rosenbaum794 (62 y/o M) Newton, Massachusetts DECEASED
+100 -- Joelle163 Feeney44 (46 y/o F) Rehoboth, Massachusetts DECEASED
+97 -- Carmine137 Harber290 (62 y/o M) Attleboro, Massachusetts 
+100 -- Loree183 Keebler762 (47 y/o F) Rehoboth, Massachusetts 
+98 -- Billy698 Homenick806 (78 y/o M) Newton, Massachusetts 
+93 -- Karine844 Blanda868 (58 y/o F) Worcester, Massachusetts 
+Records: total=120, alive=100, dead=20
+```
diff --git a/.github/test-data/a1935ff2-8d78-6259-e537-1036c451d997.json.bz2 b/.github/test-data/a1935ff2-8d78-6259-e537-1036c451d997.json.bz2
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