+
-
+
Python FHIR converter, fastish, most nuts and bolts included, ready for production
@@ -25,6 +25,10 @@
+
+
+ 
Generated Narrative with Details
id: example
identifier: 49476534
clinicalStatus: active
verificationStatus: confirmed
type: allergy
category: food
criticality: high
code: Cashew nuts (Details : {SNOMED CT code '227493005' = 'Cashew nuts', given as 'Cashew nuts'})
patient: Patient/example
onset: 01/01/2004
assertedDate: 09/10/2014 2:58:00 PM
recorder: Practitioner/example
asserter: Patient/example
lastOccurrence: 01/06/2012
note: The criticality is high becasue of the observed anaphylactic reaction when challenged with cashew extract.
reaction
substance: cashew nut allergenic extract Injectable Product (Details : {RxNorm code '1160593' = '1160593', given as 'cashew nut allergenic extract Injectable Product'})
manifestation: Anaphylactic reaction (Details : {SNOMED CT code '39579001' = 'Anaphylaxis', given as 'Anaphylactic reaction'})
description: Challenge Protocol. Severe reaction to subcutaneous cashew extract. Epinephrine administered
onset: 12/06/2012
severity: severe
exposureRoute: Subcutaneous route (Details : {SNOMED CT code '34206005' = 'Subcutaneous route', given as 'Subcutaneous route'})
reaction
manifestation: Urticaria (Details : {SNOMED CT code '64305001' = 'Urticaria', given as 'Urticaria'})
onset: 01/01/2004
severity: moderate
note: The patient reports that the onset of urticaria was within 15 minutes of eating cashews.
Generated Narrative with Details
id: f201
identifier: 12345
clinicalStatus: resolved
verificationStatus: confirmed
category: Problem (Details : {SNOMED CT code '55607006' = 'Problem', given as 'Problem'}; {http://hl7.org/fhir/condition-category code 'problem-list-item' = 'Problem List Item)
severity: Mild (Details : {SNOMED CT code '255604002' = 'Mild', given as 'Mild'})
code: Fever (Details : {SNOMED CT code '386661006' = 'Fever', given as 'Fever'})
bodySite: Entire body as a whole (Details : {SNOMED CT code '38266002' = 'Body as a whole', given as 'Entire body as a whole'})
subject: Roel
context: Encounter/f201
onset: 02/04/2013
abatement: around April 9, 2013
assertedDate: 04/04/2013
asserter: Practitioner/f201
| - | Code | Detail |
| * | degrees C (Details : {SNOMED CT code '258710007' = 'degrees C', given as 'degrees C'}) | Temperature |
Generated Narrative with Details
id: f202
identifier: Encounter_Roel_20130128 (TEMP)
status: finished
class: ambulatory (Details: http://hl7.org/fhir/v3/ActCode code AMB = 'ambulatory', stated as 'ambulatory')
type: Chemotherapy (Details : {SNOMED CT code '367336001' = 'Chemotherapy', given as 'Chemotherapy'})
priority: Urgent (Details : {SNOMED CT code '103391001' = 'Urgency', given as 'Urgent'})
subject: Roel
| - | Individual |
| * | Practitioner/f201 |
length: 56 minutes (Details: UCUM code min = 'min')
reason: The patient is treated for a tumor. (Details )
| - | Condition | Role | Rank |
| * | Complications from Roel's TPF chemotherapy on January 28th, 2013 | Admission diagnosis (Details : {http://hl7.org/fhir/diagnosis-role code 'AD' = 'Admission diagnosis', given as 'Admission diagnosis'}) | 1 |
serviceProvider: Organization/f201
Generated Narrative with Details
id: example
identifier: urn:oid:1.3.6.1.4.1.21367.2005.3.7.1234
status: completed
notGiven: false
vaccineCode: Fluvax (Influenza) (Details : {urn:oid:1.2.36.1.2001.1005.17 code 'FLUVAX' = 'Fluvax)
patient: Patient/example
encounter: Encounter/example
date: 10/01/2013
primarySource: true
location: Location/1
manufacturer: Organization/hl7
lotNumber: AAJN11K
expirationDate: 15/02/2015
site: left arm (Details : {http://hl7.org/fhir/v3/ActSite code 'LA' = 'left arm', given as 'left arm'})
route: Injection, intramuscular (Details : {http://hl7.org/fhir/v3/RouteOfAdministration code 'IM' = 'Injection, intramuscular', given as 'Injection, intramuscular'})
doseQuantity: 5 mg (Details: UCUM code mg = 'mg')
practitioner
role: Ordering Provider (Details : {http://hl7.org/fhir/v2/0443 code 'OP' = 'Ordering Provider)
actor: Practitioner/example
practitioner
role: Administering Provider (Details : {http://hl7.org/fhir/v2/0443 code 'AP' = 'Administering Provider)
actor: Practitioner/example
note: Notes on adminstration of vaccine
| - | Reason |
| * | Procedure to meet occupational requirement (Details : {SNOMED CT code '429060002' = 'Procedure to meet occupational requirement) |
| - | Date | Detail | Reported |
| * | 10/01/2013 | Observation/example | true |
| - | DoseSequence | Description | Authority | Series | SeriesDoses | TargetDisease | DoseStatus | DoseStatusReason |
| * | 1 | Vaccination Protocol Sequence 1 | Organization/hl7 | Vaccination Series 1 | 2 | Gestational rubella syndrome (Details : {SNOMED CT code '1857005' = 'Gestational rubella syndrome) | Counts (Details : {http://hl7.org/fhir/vaccination-protocol-dose-status code 'count' = 'Counts', given as 'Counts'}) | Cold chain break (Details : {http://hl7.org/fhir/vaccination-protocol-dose-status-reason code 'coldchbrk' = 'Cold chain break', given as 'Cold chain break'}) |
Generated Narrative with Details
id: med0303
contained:
code: Alemtuzumab 10mg/ml (Lemtrada) (Details : {RxNorm code '1594660' = '1594660', given as 'Alemtuzumab 10mg/ml (Lemtrada)'})
isBrand: true
manufacturer: id: org6; name: Genzyme
form: Injection solution (qualifier vallue) (Details : {SNOMED CT code '385219001' = 'Injection solution', given as 'Injection solution (qualifier vallue)'})
| - | Item[x] | Amount |
| * | Alemtuzamab (substance) (Details : {SNOMED CT code '129472003' = 'Alemtuzumab', given as 'Alemtuzamab (substance)'}) | 12 mg (Details: UCUM code mg = 'mg')/1.2 mL (Details: UCUM code mL = 'mL') |
package
container: Vial (Details : {SNOMED CT code '415818006' = 'Vial', given as 'Vial'})
Contents
- Item[x] Amount * Alemtuzumab 30mg/3mL infusion concentrate (product) (Details : {SNOMED CT code '408596005' = 'Alemtuzumab 30mg/3mL infusion concentrate', given as 'Alemtuzumab 30mg/3mL infusion concentrate (product)'}) 3 mL (Details: UCUM code mL = 'mL') Batches
- LotNumber ExpirationDate * 9494788 22/05/2017
Generated Narrative with Details
id: example-TPMT-haplotype-two
status: unknown
code: Haplotype Call (Details : {SNOMED CT code '363779003' = '363779003', given as 'Genotype determination'})
subject: E***********
issued: 03/04/2013 3:30:10 PM
value: *4 (Details : {http://pharmakb.org code 'PA166128353' = 'PA166128353', given as '*4'})
| - | Type | Target |
| * | derived-from | Sequence/example-TPMT-two |
Generated Narrative with Details
id: f003
active: true
type: Hospital Department (Details : {http://hl7.org/fhir/organization-type code 'dept' = 'Hospital Department', given as 'Hospital Department'})
name: Burgers UMC Ear,Nose,Throat unit
telecom: ph: 022-655 6780
address: West Wing, floor 5
partOf: Organization/f001
| - | Purpose | Name | Telecom | Address |
| * | Administrative (Details : {http://hl7.org/fhir/contactentity-type code 'ADMIN' = 'Administrative) | mr. F. de Hond | ph: 022-655 7654 | West Wing, floor 5 |
| Id | \n \nKenzi (Dog: Golden Retriever) | \n \n
| Owner | \n \nPeter Chalmers, 534 Erewhon, Pleasantville, Vic, 3999 | \n \n
| Contacts | \n \nWork: (03) 5555 6473 | \n \n
| Id | \n \nDog Tag: 1234123 (Maroondah City Council) | \n \n
| Name | \nPeter James Chalmers ("Jim") | \n
| Address | \n534 Erewhon, Pleasantville, Vic, 3999 | \n
| Contacts | \nHome: unknown. Work: (03) 5555 6473 | \n
| Id | \nMRN: 12345 (Acme Healthcare) | \n
5$RJ~*(4e_yI#U|1N;sTcR1b&~DTMSu>J;3pAGQj%DEWTU
z10~#{@1@>?Fb&D$h{)|$3PG>Iz=b&5;J9vz%2Cn<2TqbmL42E@h?BEU2Y|stxmR8T
zDRHyL)vOjb3=ew?{Pp){*OejzWE$z%ukxi8%I|E;Q}$kg`ec!gs+fEmHNAh84xX#P
zvOWu4jn;`wiL3xs15K&pCM~7i42UNQr5^f}hnu9}indCQV~$}j$MN`|6lvQjvaL<6
z74F1VF6R>$UbM$)$Nsu#k224rC{83AqrHK>x_Am+uT7cWu^8SZ48D;I Generated Narrative with Details id: example identifier: urn:oid:1.3.6.1.4.1.21367.2005.3.7.1234 status: completed notGiven: false vaccineCode: Fluvax (Influenza) (Details : {urn:oid:1.2.36.1.2001.1005.17 code 'FLUVAX' = 'Fluvax) patient: Patient/example encounter: Encounter/example date: 10/01/2013 primarySource: true location: Location/1 manufacturer: Organization/hl7 lotNumber: AAJN11K expirationDate: 15/02/2015 site: left arm (Details : {http://hl7.org/fhir/v3/ActSite code 'LA' = 'left arm', given as 'left arm'}) route: Injection, intramuscular (Details : {http://hl7.org/fhir/v3/RouteOfAdministration code 'IM' = 'Injection, intramuscular', given as 'Injection, intramuscular'}) doseQuantity: 5 mg (Details: UCUM code mg = 'mg') practitioner role: Ordering Provider (Details : {http://hl7.org/fhir/v2/0443 code 'OP' = 'Ordering Provider) actor: Practitioner/example practitioner role: Administering Provider (Details : {http://hl7.org/fhir/v2/0443 code 'AP' = 'Administering Provider) actor: Practitioner/example note: Notes on adminstration of vaccine"
+ },
+ "identifier": [
+ {
+ "system": "urn:ietf:rfc:3986",
+ "value": "urn:oid:1.3.6.1.4.1.21367.2005.3.7.1234"
+ }
+ ],
+ "status": "completed",
+ "notGiven": false,
+ "vaccineCode": {
+ "coding": [
+ {
+ "system": "urn:oid:1.2.36.1.2001.1005.17",
+ "code": "FLUVAX"
+ }
+ ],
+ "text": "Fluvax (Influenza)"
+ },
+ "patient": {
+ "reference": "Patient/example"
+ },
+ "encounter": {
+ "reference": "Encounter/example"
+ },
+ "date": "2017-01-01T00:00:00.000Z",
+ "primarySource": true,
+ "location": {
+ "reference": "Location/1"
+ },
+ "manufacturer": {
+ "reference": "Organization/hl7"
+ },
+ "lotNumber": "AAJN11K",
+ "expirationDate": "2015-02-15",
+ "site": {
+ "coding": [
+ {
+ "system": "http://hl7.org/fhir/v3/ActSite",
+ "code": "LA",
+ "display": "left arm"
+ }
+ ]
+ },
+ "route": {
+ "coding": [
+ {
+ "system": "http://hl7.org/fhir/v3/RouteOfAdministration",
+ "code": "IM",
+ "display": "Injection, intramuscular"
+ }
+ ]
+ },
+ "doseQuantity": {
+ "value": 5,
+ "system": "http://unitsofmeasure.org",
+ "code": "mg"
+ },
+ "practitioner": [
+ {
+ "role": {
+ "coding": [
+ {
+ "system": "http://hl7.org/fhir/v2/0443",
+ "code": "OP"
+ }
+ ]
+ },
+ "actor": {
+ "reference": "Practitioner/example"
+ }
+ },
+ {
+ "role": {
+ "coding": [
+ {
+ "system": "http://hl7.org/fhir/v2/0443",
+ "code": "AP"
+ }
+ ]
+ },
+ "actor": {
+ "reference": "Practitioner/example"
+ }
+ }
+ ],
+ "note": [
+ {
+ "text": "Notes on adminstration of vaccine"
+ }
+ ],
+ "explanation": {
+ "reason": [
+ {
+ "coding": [
+ {
+ "system": "http://snomed.info/sct",
+ "code": "429060002"
+ }
+ ]
+ }
+ ]
+ },
+ "reaction": [
+ {
+ "date": "2013-01-10",
+ "detail": {
+ "reference": "Observation/example"
+ },
+ "reported": true
+ }
+ ],
+ "vaccinationProtocol": [
+ {
+ "doseSequence": 1,
+ "description": "Vaccination Protocol Sequence 1",
+ "authority": {
+ "reference": "Organization/hl7"
+ },
+ "series": "Vaccination Series 1",
+ "seriesDoses": 2,
+ "targetDisease": [
+ {
+ "coding": [
+ {
+ "system": "http://snomed.info/sct",
+ "code": "1857005"
+ }
+ ]
+ }
+ ],
+ "doseStatus": {
+ "coding": [
+ {
+ "system": "http://hl7.org/fhir/vaccination-protocol-dose-status",
+ "code": "count",
+ "display": "Counts"
+ }
+ ]
+ },
+ "doseStatusReason": {
+ "coding": [
+ {
+ "system": "http://hl7.org/fhir/vaccination-protocol-dose-status-reason",
+ "code": "coldchbrk",
+ "display": "Cold chain break"
+ }
+ ]
+ }
+ }
+ ]
+}
\ No newline at end of file
diff --git a/tests/data/stu3/Person.json b/tests/data/stu3/Person.json
new file mode 100644
index 0000000..ccf6e1e
--- /dev/null
+++ b/tests/data/stu3/Person.json
@@ -0,0 +1,88 @@
+{
+ "resourceType": "Person",
+ "id": "example",
+ "text": {
+ "status": "generated",
+ "div": "Explanations
- Reason * Procedure to meet occupational requirement (Details : {SNOMED CT code '429060002' = 'Procedure to meet occupational requirement) Reactions
- Date Detail Reported * 10/01/2013 Observation/example true VaccinationProtocols
- DoseSequence Description Authority Series SeriesDoses TargetDisease DoseStatus DoseStatusReason * 1 Vaccination Protocol Sequence 1 Organization/hl7 Vaccination Series 1 2 Gestational rubella syndrome (Details : {SNOMED CT code '1857005' = 'Gestational rubella syndrome) Counts (Details : {http://hl7.org/fhir/vaccination-protocol-dose-status code 'count' = 'Counts', given as 'Counts'}) Cold chain break (Details : {http://hl7.org/fhir/vaccination-protocol-dose-status-reason code 'coldchbrk' = 'Cold chain break', given as 'Cold chain break'}) \n "
+ },
+ "identifier": [
+ {
+ "use": "usual",
+ "type": {
+ "coding": [
+ {
+ "system": "http://hl7.org/fhir/v2/0203",
+ "code": "MR"
+ }
+ ]
+ },
+ "system": "urn:oid:1.2.36.146.595.217.0.1",
+ "value": "12345",
+ "period": {
+ "start": "2001-05-06"
+ },
+ "assigner": {
+ "display": "Acme Healthcare"
+ }
+ }
+ ],
+ "name": [
+ {
+ "use": "official",
+ "family": "Chalmers",
+ "given": [
+ "Peter",
+ "James"
+ ]
+ },
+ {
+ "use": "usual",
+ "given": [
+ "Jim"
+ ]
+ }
+ ],
+ "telecom": [
+ {
+ "use": "home"
+ },
+ {
+ "system": "phone",
+ "value": "(03) 5555 6473",
+ "use": "work"
+ },
+ {
+ "system": "email",
+ "value": "Jim@example.org",
+ "use": "home"
+ }
+ ],
+ "gender": "male",
+ "birthDate": "1974-12-25",
+ "address": [
+ {
+ "use": "home",
+ "line": [
+ "534 Erewhon St"
+ ],
+ "city": "PleasantVille",
+ "state": "Vic",
+ "postalCode": "3999"
+ }
+ ],
+ "active": true,
+ "link": [
+ {
+ "target": {
+ "reference": "RelatedPerson/peter",
+ "display": "Peter Chalmers"
+ }
+ },
+ {
+ "target": {
+ "reference": "Patient/example",
+ "display": "Peter Chalmers"
+ }
+ }
+ ]
+}
\ No newline at end of file
diff --git a/tests/test_filters.py b/tests/test_filters.py
index 26d853a..070aee6 100644
--- a/tests/test_filters.py
+++ b/tests/test_filters.py
@@ -1,5 +1,5 @@
from base64 import b64decode
-from datetime import timezone
+from datetime import datetime, timezone
from unittest import TestCase
from zlib import decompress
@@ -25,15 +25,15 @@ class FilterTest:
def setup_template(self, **kwargs) -> None:
Environment.output_stream_limit = None
- env = Environment(strict_filters=True, **kwargs)
- register_filters(env, all_filters)
-
- self.template = self.template.strip()
+ env = Environment(**kwargs)
+ register_filters(env, all_filters, replace=True)
self.bound_template = env.from_string(self.template)
def test_unregistered(self) -> None:
with raises(NoSuchFilterFunc):
- Environment().from_string(self.template).render()
+ env = Environment()
+ env.filters.clear()
+ env.from_string(self.template).render()
class ToJsonStringTest(TestCase, FilterTest):
@@ -62,7 +62,7 @@ class ToArrayTest(TestCase, FilterTest):
template = """
{% assign keys = el.key | to_array -%}
{% for key in keys -%}{{key}},{% endfor -%}
- """
+ """.strip()
def setUp(self) -> None:
self.setup_template()
@@ -200,6 +200,236 @@ def test(self) -> None:
self.assertEqual(result, "2024-01-10T06:35:57.920Z")
+class DateTest(TestCase, FilterTest):
+ template = """{{ dt | date: format }}"""
+ iso_datetime_complete = "2014-10-09T11:58:10.001981+08:00"
+
+ def setUp(self) -> None:
+ self.setup_template()
+
+ def test_undefined(self) -> None:
+ result = self.bound_template.render()
+ self.assertEqual(result, "")
+
+ def test_format_undefined(self) -> None:
+ result = self.bound_template.render(dt=self.iso_datetime_complete)
+ self.assertEqual(result, self.iso_datetime_complete)
+
+ def test_format_empty_str(self) -> None:
+ result = self.bound_template.render(dt=self.iso_datetime_complete, format="")
+ self.assertEqual(result, self.iso_datetime_complete)
+
+ def test_format_not_str(self) -> None:
+ result = self.bound_template.render(dt=self.iso_datetime_complete, format=[])
+ self.assertEqual(result, self.iso_datetime_complete)
+
+ def test_liquid_date_str(self) -> None:
+ result = self.bound_template.render(dt="March 14, 2016", format="%b %d, %y")
+ self.assertEqual(result, "Mar 14, 16")
+
+ def test_liquid_date_datetime(self) -> None:
+ result = self.bound_template.render(
+ dt=datetime(2002, 1, 1, 11, 45, 13), format="%a, %b %d, %y"
+ )
+ self.assertEqual(result, "Tue, Jan 01, 02")
+
+ def test_liquid_date_now(self) -> None:
+ result = self.bound_template.render(dt="now", format="%Y")
+ self.assertEqual(result, datetime.now().strftime("%Y"))
+
+ def test_liquid_date_today(self) -> None:
+ result = self.bound_template.render(dt="today", format="%Y")
+ self.assertEqual(result, datetime.now().strftime("%Y"))
+
+ def test_liquid_date_unsupported_format(self) -> None:
+ result = self.bound_template.render(dt="today", format="YYYY")
+ self.assertEqual(result, "YYYY")
+
+ def test_unsupported_format(self) -> None:
+ result = self.bound_template.render(dt=self.iso_datetime_complete, format="ffff")
+ self.assertEqual(result, "ffff")
+
+ def test_year(self) -> None:
+ result = self.bound_template.render(dt=self.iso_datetime_complete, format="yyyy")
+ self.assertEqual(result, "2014")
+
+ def test_year_python(self) -> None:
+ result = self.bound_template.render(dt=self.iso_datetime_complete, format="%Y")
+ self.assertEqual(result, "2014")
+
+ def test_without_century(self) -> None:
+ result = self.bound_template.render(dt=self.iso_datetime_complete, format="%y")
+ self.assertEqual(result, "14")
+
+ def test_month(self) -> None:
+ result = self.bound_template.render(dt=self.iso_datetime_complete, format="MM")
+ self.assertEqual(result, "10")
+
+ def test_month_python(self) -> None:
+ result = self.bound_template.render(dt=self.iso_datetime_complete, format="%m")
+ self.assertEqual(result, "10")
+
+ def test_month_locale(self) -> None:
+ result = self.bound_template.render(dt=self.iso_datetime_complete, format="%b")
+ self.assertEqual(result, "Oct")
+
+ def test_month_locale_full(self) -> None:
+ result = self.bound_template.render(dt=self.iso_datetime_complete, format="%B")
+ self.assertEqual(result, "October")
+
+ def test_day(self) -> None:
+ result = self.bound_template.render(dt=self.iso_datetime_complete, format="dd")
+ self.assertEqual(result, "09")
+
+ def test_day_python(self) -> None:
+ result = self.bound_template.render(dt=self.iso_datetime_complete, format="%d")
+ self.assertEqual(result, "09")
+
+ def test_hour(self) -> None:
+ result = self.bound_template.render(dt=self.iso_datetime_complete, format="HH")
+ self.assertEqual(result, "11")
+
+ def test_hour_python(self) -> None:
+ result = self.bound_template.render(dt=self.iso_datetime_complete, format="%H")
+ self.assertEqual(result, "11")
+
+ def test_minute(self) -> None:
+ result = self.bound_template.render(dt=self.iso_datetime_complete, format="mm")
+ self.assertEqual(result, "58")
+
+ def test_minute_python(self) -> None:
+ result = self.bound_template.render(dt=self.iso_datetime_complete, format="%M")
+ self.assertEqual(result, "58")
+
+ def test_second(self) -> None:
+ result = self.bound_template.render(dt=self.iso_datetime_complete, format="ss")
+ self.assertEqual(result, "10")
+
+ def test_second_python(self) -> None:
+ result = self.bound_template.render(dt=self.iso_datetime_complete, format="%S")
+ self.assertEqual(result, "10")
+
+ def test_milli(self) -> None:
+ result = self.bound_template.render(dt=self.iso_datetime_complete, format="fff")
+ self.assertEqual(result, "001")
+
+ def test_micro(self) -> None:
+ result = self.bound_template.render(
+ dt=self.iso_datetime_complete, format="ffffff"
+ )
+ self.assertEqual(result, "001981")
+
+ def test_micro_python(self) -> None:
+ result = self.bound_template.render(dt=self.iso_datetime_complete, format="%f")
+ self.assertEqual(result, "001981")
+
+ def test_k_specifier_tz_undefined(self) -> None:
+ result = self.bound_template.render(dt="2014-10-09T11:58:10", format="%K")
+ self.assertEqual(result, "")
+
+ def test_k_specifier_tz_offset(self) -> None:
+ result = self.bound_template.render(dt=self.iso_datetime_complete, format="%K")
+ self.assertEqual(result, "+08:00")
+
+ def test_k_specifier_tz_offset_zero(self) -> None:
+ result = self.bound_template.render(dt="2014-10-09T11:58:10+00:00", format="%K")
+ self.assertEqual(result, "Z")
+
+ def test_k_specifier_tz_utc(self) -> None:
+ result = self.bound_template.render(dt="2014-10-09T11:58:10Z", format="%K")
+ self.assertEqual(result, "Z")
+
+ def test_tz_hour_min_offset(self) -> None:
+ result = self.bound_template.render(dt=self.iso_datetime_complete, format="zzz")
+ self.assertEqual(result, "+08:00")
+
+ def test_tz_hour_min_offset_python(self) -> None:
+ result = self.bound_template.render(dt=self.iso_datetime_complete, format="%z")
+ self.assertEqual(result, "+0800")
+
+ def test_tz_hour_offset(self) -> None:
+ result = self.bound_template.render(dt=self.iso_datetime_complete, format="zz")
+ self.assertEqual(result, "+08")
+
+ def test_year_month(self) -> None:
+ result = self.bound_template.render(
+ dt=self.iso_datetime_complete, format="yyyy-MM"
+ )
+ self.assertEqual(result, "2014-10")
+
+ def test_year_month_day(self) -> None:
+ result = self.bound_template.render(
+ dt=self.iso_datetime_complete, format="yyyy-MM-dd"
+ )
+ self.assertEqual(result, "2014-10-09")
+
+ def test_year_month_day_python(self) -> None:
+ result = self.bound_template.render(
+ dt=self.iso_datetime_complete, format="%Y-%m-%d"
+ )
+ self.assertEqual(result, "2014-10-09")
+
+ def test_year_month_day_hour(self) -> None:
+ result = self.bound_template.render(
+ dt=self.iso_datetime_complete, format="yyyy-MM-ddTHH"
+ )
+ self.assertEqual(result, "2014-10-09T11")
+
+ def test_year_month_day_hour_minute(self) -> None:
+ result = self.bound_template.render(
+ dt=self.iso_datetime_complete, format="yyyy-MM-ddTHH:mm"
+ )
+ self.assertEqual(result, "2014-10-09T11:58")
+
+ def test_year_month_day_hour_minute_second(self) -> None:
+ result = self.bound_template.render(
+ dt=self.iso_datetime_complete, format="yyyy-MM-ddTHH:mm:ss"
+ )
+ self.assertEqual(result, "2014-10-09T11:58:10")
+
+ def test_year_month_day_hour_minute_second_python(self) -> None:
+ result = self.bound_template.render(
+ dt=self.iso_datetime_complete, format="%Y-%m-%dT%H:%M:%S"
+ )
+ self.assertEqual(result, "2014-10-09T11:58:10")
+
+ def test_year_month_day_hour_minute_second_k_specifier(self) -> None:
+ result = self.bound_template.render(
+ dt=self.iso_datetime_complete, format="yyyy-MM-ddTHH:mm:ss%K"
+ )
+ self.assertEqual(result, "2014-10-09T11:58:10+08:00")
+
+ def test_year_month_day_hour_minute_second_milli(self) -> None:
+ result = self.bound_template.render(
+ dt=self.iso_datetime_complete, format="yyyy-MM-ddTHH:mm:ss.fff"
+ )
+ self.assertEqual(result, "2014-10-09T11:58:10.001")
+
+ def test_year_month_day_hour_minute_second_milli_k_specifier(self) -> None:
+ result = self.bound_template.render(
+ dt=self.iso_datetime_complete, format="yyyy-MM-ddTHH:mm:ss.fff%K"
+ )
+ self.assertEqual(result, "2014-10-09T11:58:10.001+08:00")
+
+ def test_year_month_day_hour_minute_second_milli_micro(self) -> None:
+ result = self.bound_template.render(
+ dt=self.iso_datetime_complete, format="yyyy-MM-ddTHH:mm:ss.ffffff"
+ )
+ self.assertEqual(result, "2014-10-09T11:58:10.001981")
+
+ def test_year_month_day_hour_minute_second_milli_micro_python(self) -> None:
+ result = self.bound_template.render(
+ dt=self.iso_datetime_complete, format="%Y-%m-%dT%H:%M:%S.%f"
+ )
+ self.assertEqual(result, "2014-10-09T11:58:10.001981")
+
+ def test_year_month_day_hour_minute_second_milli_micro_k_specifier(self) -> None:
+ result = self.bound_template.render(
+ dt=self.iso_datetime_complete, format="yyyy-MM-ddTHH:mm:ss.ffffff%K"
+ )
+ self.assertEqual(result, "2014-10-09T11:58:10.001981+08:00")
+
+
class NowTest(TestCase, FilterTest):
template = """{{ "" | now }}"""
@@ -472,7 +702,7 @@ def test_found_flatten_ids(self) -> None:
class BatchRenderTest(TestCase, FilterTest):
template = """{{ batch | batch_render: template, 'data' }}"""
- inner_template = """{{ data }},"""
+ inner_template = """{{ data }}"""
def setUp(self) -> None:
self.setup_template(loader=DictLoader({"__template__": self.inner_template}))
@@ -495,6 +725,18 @@ def test_batch(self) -> None:
)
self.assertEqual(result, "one,two,three,")
+ def test_batch_with_trailing_comma(self) -> None:
+ result = self.bound_template.render(
+ batch=["one,", "two,", "three,"], template="__template__"
+ )
+ self.assertEqual(result, "one,two,three,")
+
+ def test_batch_with_trailing_comma_blank_space_line_endings(self) -> None:
+ result = self.bound_template.render(
+ batch=["one, \n", "two, \n\n", "three, \n\n\n"], template="__template__"
+ )
+ self.assertEqual(result, "one, \ntwo, \n\nthree, \n\n\n")
+
def test_template_not_found(self) -> None:
with raises(TemplateNotFound):
self.bound_template.render(batch=["one"], template="undefined")
diff --git a/tests/test_renderers.py b/tests/test_renderers.py
index dd35016..5e7e38e 100644
--- a/tests/test_renderers.py
+++ b/tests/test_renderers.py
@@ -1,19 +1,23 @@
from collections.abc import Mapping
from io import StringIO
from json import loads
+from pathlib import Path
from unittest import TestCase
-from liquid import FileExtensionLoader
+from liquid import Environment, FileExtensionLoader
from liquid.utils import LRUCache
from pyexpat import ExpatError
+from pyjson5 import Json5EOF
from pytest import raises
from fhir_converter.loaders import TemplateSystemLoader
from fhir_converter.renderers import (
CcdaRenderer,
RenderingError,
+ Stu3FhirRenderer,
ccda_default_loader,
get_environment,
+ stu3_default_loader,
)
@@ -64,7 +68,107 @@ def test_additional_loaders(self) -> None:
self.assertEqual([loader, ccda_default_loader], env.loader.loaders) # type: ignore
+class Stu3FhirRendererTest(TestCase):
+ stu3_file = Path("tests/data/stu3/Immunization.json")
+
+ def validate_str(self, fhir_str: str) -> None:
+ self.validate(loads(fhir_str))
+
+ def validate(self, fhir: Mapping) -> None:
+ self.assertEqual(fhir["resourceType"], "Immunization")
+ self.assertEqual(fhir["status"], "completed")
+ self.assertNotIn("notGiven", fhir)
+ # TODO validation!
+
+ def test_render_fhir_string_json_error(self) -> None:
+ with raises(RenderingError, match="Failed to render FHIR") as exc_info:
+ Stu3FhirRenderer().render_fhir_string("Immunization", "")
+ self.assertIsInstance(exc_info.value.__cause__, Json5EOF)
+
+ def test_render_fhir_string_text(self) -> None:
+ self.validate_str(
+ Stu3FhirRenderer().render_fhir_string(
+ "Immunization", self.stu3_file.read_text()
+ )
+ )
+
+ def test_render_fhir_string_bytes(self) -> None:
+ self.validate_str(
+ Stu3FhirRenderer().render_fhir_string(
+ "Immunization", self.stu3_file.read_bytes()
+ )
+ )
+
+ def test_render_fhir_string_text_io(self) -> None:
+ with self.stu3_file.open() as fhir_in:
+ self.validate_str(
+ Stu3FhirRenderer().render_fhir_string("Immunization", fhir_in)
+ )
+
+ def test_render_fhir_string_binary_io(self) -> None:
+ with self.stu3_file.open("rb") as fhir_in:
+ self.validate_str(
+ Stu3FhirRenderer().render_fhir_string("Immunization", fhir_in)
+ )
+
+ def test_render_to_fhir_json_error(self) -> None:
+ with raises(RenderingError, match="Failed to render FHIR") as exc_info:
+ Stu3FhirRenderer().render_to_fhir("Immunization", "")
+ self.assertIsInstance(exc_info.value.__cause__, Json5EOF)
+
+ def test_render_to_fhir_text(self) -> None:
+ self.validate(
+ Stu3FhirRenderer().render_to_fhir("Immunization", self.stu3_file.read_text())
+ )
+
+ def test_render_to_fhir_bytes(self) -> None:
+ self.validate(
+ Stu3FhirRenderer().render_to_fhir("Immunization", self.stu3_file.read_bytes())
+ )
+
+ def test_render_to_fhir_text_io(self) -> None:
+ with self.stu3_file.open() as fhir_in:
+ self.validate(Stu3FhirRenderer().render_to_fhir("Immunization", fhir_in))
+
+ def test_render_to_fhir_binary_io(self) -> None:
+ with self.stu3_file.open("rb") as fhir_in:
+ self.validate(Stu3FhirRenderer().render_to_fhir("Immunization", fhir_in))
+
+ def test_render_fhir_serialize_error(self) -> None:
+ buffer = StringIO()
+ buffer.close()
+
+ with raises(RenderingError, match="Failed to serialize FHIR") as exc_info:
+ with self.stu3_file.open() as fhir_in:
+ Stu3FhirRenderer().render_fhir("Immunization", fhir_in, buffer)
+ self.assertIsInstance(exc_info.value.__cause__, ValueError)
+ self.assertEqual(str(exc_info.value.__cause__), "I/O operation on closed file")
+
+ def test_render_fhir_text(self) -> None:
+ buffer = StringIO()
+ Stu3FhirRenderer().render_fhir("Immunization", self.stu3_file.read_text(), buffer)
+ self.validate_str(buffer.getvalue())
+
+ def test_render_fhir_bytes(self) -> None:
+ buffer = StringIO()
+ Stu3FhirRenderer().render_fhir(
+ "Immunization", self.stu3_file.read_bytes(), buffer
+ )
+ self.validate_str(buffer.getvalue())
+
+ def test_render_env_provided(self) -> None:
+ renderer = Stu3FhirRenderer(
+ Environment(loader=TemplateSystemLoader(loaders=[stu3_default_loader]))
+ )
+ self.validate(renderer.render_to_fhir("Immunization", self.stu3_file.read_text()))
+
+
class CcdaRendererTest(TestCase):
+ ccda_file = Path("tests/data/ccda/CCD.ccda")
+
+ def validate_str(self, fhir_str: str) -> None:
+ self.validate(loads(fhir_str))
+
def validate(self, fhir: Mapping) -> None:
self.assertEqual(fhir["resourceType"], "Bundle")
self.assertEqual(fhir["type"], "batch")
@@ -76,17 +180,23 @@ def test_render_fhir_string_xml_error(self) -> None:
CcdaRenderer().render_fhir_string("CCD", "")
self.assertIsInstance(exc_info.value.__cause__, ExpatError)
- def test_render_fhir_string_text_str(self) -> None:
- with open("tests/data/ccda/CCD.ccda") as xml_in:
- self.validate(loads(CcdaRenderer().render_fhir_string("CCD", xml_in.read())))
-
def test_render_fhir_string_text(self) -> None:
- with open("tests/data/ccda/CCD.ccda") as xml_in:
- self.validate(loads(CcdaRenderer().render_fhir_string("CCD", xml_in)))
+ self.validate_str(
+ CcdaRenderer().render_fhir_string("CCD", self.ccda_file.read_text())
+ )
+
+ def test_render_fhir_string_bytes(self) -> None:
+ self.validate_str(
+ CcdaRenderer().render_fhir_string("CCD", self.ccda_file.read_bytes())
+ )
+
+ def test_render_fhir_string_text_io(self) -> None:
+ with self.ccda_file.open() as xml_in:
+ self.validate_str(CcdaRenderer().render_fhir_string("CCD", xml_in))
- def test_render_fhir_string_binary(self) -> None:
- with open("tests/data/ccda/CCD.ccda", "rb") as xml_in:
- self.validate(loads(CcdaRenderer().render_fhir_string("CCD", xml_in)))
+ def test_render_fhir_string_binary_io(self) -> None:
+ with self.ccda_file.open("rb") as xml_in:
+ self.validate_str(CcdaRenderer().render_fhir_string("CCD", xml_in))
def test_render_to_fhir_xml_error(self) -> None:
with raises(RenderingError, match="Failed to render FHIR") as exc_info:
@@ -96,16 +206,18 @@ def test_render_to_fhir_xml_error(self) -> None:
str(exc_info.value.__cause__), "no element found: line 1, column 0"
)
- def test_render_to_fhir_text_str(self) -> None:
- with open("tests/data/ccda/CCD.ccda") as xml_in:
- self.validate(CcdaRenderer().render_to_fhir("CCD", xml_in.read()))
-
def test_render_to_fhir_text(self) -> None:
- with open("tests/data/ccda/CCD.ccda") as xml_in:
+ self.validate(CcdaRenderer().render_to_fhir("CCD", self.ccda_file.read_text()))
+
+ def test_render_to_fhir_bytes(self) -> None:
+ self.validate(CcdaRenderer().render_to_fhir("CCD", self.ccda_file.read_bytes()))
+
+ def test_render_to_fhir_text_io(self) -> None:
+ with self.ccda_file.open() as xml_in:
self.validate(CcdaRenderer().render_to_fhir("CCD", xml_in))
- def test_render_to_fhir_binary(self) -> None:
- with open("tests/data/ccda/CCD.ccda", "rb") as xml_in:
+ def test_render_to_fhir_binary_io(self) -> None:
+ with self.ccda_file.open("rb") as xml_in:
self.validate(CcdaRenderer().render_to_fhir("CCD", xml_in))
def test_render_fhir_serialize_error(self) -> None:
@@ -113,7 +225,23 @@ def test_render_fhir_serialize_error(self) -> None:
buffer.close()
with raises(RenderingError, match="Failed to serialize FHIR") as exc_info:
- with open("tests/data/ccda/CCD.ccda") as xml_in:
+ with self.ccda_file.open() as xml_in:
CcdaRenderer().render_fhir("CCD", xml_in, buffer)
self.assertIsInstance(exc_info.value.__cause__, ValueError)
self.assertEqual(str(exc_info.value.__cause__), "I/O operation on closed file")
+
+ def test_render_fhir_text(self) -> None:
+ buffer = StringIO()
+ CcdaRenderer().render_fhir("CCD", self.ccda_file.read_text(), buffer)
+ self.validate_str(buffer.getvalue())
+
+ def test_render_fhir_bytes(self) -> None:
+ buffer = StringIO()
+ CcdaRenderer().render_fhir("CCD", self.ccda_file.read_bytes(), buffer)
+ self.validate_str(buffer.getvalue())
+
+ def test_render_env_provided(self) -> None:
+ renderer = CcdaRenderer(
+ Environment(loader=TemplateSystemLoader(loaders=[ccda_default_loader]))
+ )
+ self.validate(renderer.render_to_fhir("CCD", self.ccda_file.read_text()))
diff --git a/tests/test_tags.py b/tests/test_tags.py
index c706938..8ab817c 100644
--- a/tests/test_tags.py
+++ b/tests/test_tags.py
@@ -1,12 +1,162 @@
+from typing import Optional
from unittest import TestCase
from liquid import BoundTemplate, DictLoader, Environment
from liquid.ast import ChildNode
from liquid.exceptions import LiquidSyntaxError, TemplateNotFound
from liquid.expression import Identifier, IdentifierPathElement, StringLiteral
+from liquid.loaders import BaseLoader
+from pyjson5 import Json5Exception
from pytest import raises
-from fhir_converter.tags import EvaluateNode, all_tags, register_tags
+from fhir_converter.tags import EvaluateNode, MergeDiffNode, all_tags, register_tags
+
+
+def get_template(
+ source: str,
+ register: bool = True,
+ loader: Optional[BaseLoader] = None,
+) -> BoundTemplate:
+ env = Environment(loader=loader)
+ if register:
+ register_tags(env, all_tags)
+ return env.from_string(source)
+
+
+class MergeDiffTest(TestCase):
+ missing_endmerge = "{% mergeDiff var -%}"
+ missing_identifier = "{% mergeDiff -%}{% endmergeDiff -%}"
+ block = "{% mergeDiff var -%}{{block}}{% endmergeDiff -%}"
+
+ def test_unregistered(self) -> None:
+ with raises(LiquidSyntaxError, match="unexpected tag 'mergeDiff'"):
+ get_template(source=self.block, register=False).render()
+
+ def test_missing_endmerge(self) -> None:
+ with raises(LiquidSyntaxError, match="expected tag with value 'endmergeDiff'"):
+ get_template(source=self.missing_endmerge).render()
+
+ def test_missing_identifier(self) -> None:
+ with raises(LiquidSyntaxError, match="expected 'expression', found 'tag'"):
+ get_template(source=self.missing_identifier).render()
+
+ def test_invalid(self) -> None:
+ with raises(Json5Exception):
+ template = get_template(source=self.block)
+ template.render(var={"test": "ok"}, block="{test:ok}")
+
+ def test_empty(self) -> None:
+ template = get_template(source=self.block)
+ self.assertEqual(template.render(var={"test": "ok"}, block=""), '{"test":"ok"}')
+
+ def test_space(self) -> None:
+ template = get_template(source=self.block)
+ self.assertEqual(template.render(var={"test": "ok"}, block=" "), '{"test":"ok"}')
+
+ def test_empty_quote(self) -> None:
+ template = get_template(source=self.block)
+ self.assertEqual(template.render(var={"test": "ok"}, block='""'), '{"test":"ok"}')
+
+ def test_str(self) -> None:
+ template = get_template(source=self.block)
+ self.assertEqual(
+ template.render(var={"test": "ok"}, block='"failed"'),
+ '{"test":"ok"}',
+ )
+
+ def test_variable_undefined(self) -> None:
+ template = get_template(source=self.block)
+ self.assertEqual(template.render(block={"test": "ok"}), "{}")
+
+ def test_variable_str(self) -> None:
+ template = get_template(source=self.block)
+ self.assertEqual(template.render(var="ok", block={"test": "ok"}), '"ok"')
+
+ def test_add(self) -> None:
+ template = get_template(source=self.block)
+ self.assertEqual(len(template.tree.statements), 1)
+
+ node = template.tree.statements[0]
+ self.assertIsInstance(node, MergeDiffNode)
+
+ self.assertEqual(
+ repr(node),
+ "MergeDiff(tok=Token(linenum=1, type='tag', value='mergeDiff') identifier=var)",
+ )
+ self.assertEqual(str(node), "mergeDiff var { `block` }")
+ self.assertTrue(len(node.children()) > 0)
+ self.assertEqual(template.render(var={}, block={"test": "add"}), '{"test":"add"}')
+
+ def test_update(self) -> None:
+ template = get_template(source=self.block)
+ self.assertEqual(
+ template.render(var={"test": "ok"}, block={"test": "update"}),
+ '{"test":"update"}',
+ )
+
+ def test_remove(self) -> None:
+ template = get_template(source=self.block)
+ self.assertEqual(
+ template.render(var={"test": "ok"}, block={"test": ""}), '{"test":""}'
+ )
+
+ def test_empty_dict(self) -> None:
+ template = get_template(source=self.block)
+ self.assertEqual(template.render(var={"test": "ok"}, block={}), '{"test":"ok"}')
+
+ def test_empty_dicts(self) -> None:
+ template = get_template(source=self.block)
+ self.assertEqual(template.render(var={}, block={}), "{}")
+
+ def test_choice_update(self) -> None:
+ template = get_template(source=self.block)
+ self.assertEqual(
+ template.render(var={"test_first": "ok"}, block={"test[x]": "update"}),
+ '{"test_first":"update"}',
+ )
+
+ def test_choice_update_first(self) -> None:
+ template = get_template(source=self.block)
+ self.assertEqual(
+ template.render(
+ var={"test_first": "ok", "test_second": "failed"},
+ block={"test[x]": "update"},
+ ),
+ '{"test_first":"update","test_second":"failed"}',
+ )
+
+ def test_choice_remove(self) -> None:
+ template = get_template(source=self.block)
+ self.assertEqual(
+ template.render(var={"test_first": "ok"}, block={"test[x]": ""}),
+ '{"test_first":""}',
+ )
+
+ def test_choice_remove_first(self) -> None:
+ template = get_template(source=self.block)
+ self.assertEqual(
+ template.render(
+ var={"test_first": "ok", "test_second": "failed"}, block={"test[x]": ""}
+ ),
+ '{"test_first":"","test_second":"failed"}',
+ )
+
+ def test_choice_remove_multiple(self) -> None:
+ template = get_template(source=self.block)
+ self.assertEqual(
+ template.render(
+ var={"test_first": "ok", "test_second": "failed"},
+ block={"test_f[x]": "", "test_s[x]": ""},
+ ),
+ '{"test_first":"","test_second":""}',
+ )
+
+ def test_choice_ignore(self) -> None:
+ template = get_template(source=self.block)
+ self.assertEqual(
+ template.render(var={"other": "unknown"}, block={"test[x]": "ok"}),
+ '{"other":"unknown"}',
+ )
class EvaluateTest(TestCase):
@@ -25,30 +175,24 @@ class EvaluateTest(TestCase):
}
)
- def get_template(self, source: str, register: bool = True) -> BoundTemplate:
- env = Environment(loader=self.loader)
- if register:
- register_tags(env, all_tags)
- return env.from_string(source)
-
def test_unregistered(self) -> None:
with raises(LiquidSyntaxError):
- self.get_template(source=self.no_arg, register=False).render()
+ get_template(source=self.no_arg, register=False).render()
def test_template_not_found(self) -> None:
with raises(TemplateNotFound):
- self.get_template(source=self.not_found).render()
+ get_template(source=self.not_found).render()
def test_missing_keyword(self) -> None:
with raises(LiquidSyntaxError):
- self.get_template(source=self.missing_keyword).render()
+ get_template(source=self.missing_keyword).render()
def test_missing_comma(self) -> None:
with raises(LiquidSyntaxError):
- self.get_template(source=self.missing_comma).render(val1="test", val2="ok")
+ get_template(source=self.missing_comma).render(val1="test", val2="ok")
def test_no_arg(self) -> None:
- template = self.get_template(source=self.no_arg)
+ template = get_template(source=self.no_arg, loader=self.loader)
self.assertEqual(len(template.tree.statements), 2)
node = template.tree.statements[0]
@@ -75,7 +219,7 @@ def test_no_arg(self) -> None:
self.assertEqual(template.render(), "ok")
def test_single_arg(self) -> None:
- template = self.get_template(source=self.single_arg)
+ template = get_template(source=self.single_arg, loader=self.loader)
self.assertEqual(len(template.tree.statements), 2)
node = template.tree.statements[0]
@@ -102,7 +246,7 @@ def test_single_arg(self) -> None:
self.assertEqual(template.render(val="test"), "test")
def test_multiple_args(self) -> None:
- template = self.get_template(source=self.multi_arg)
+ template = get_template(source=self.multi_arg, loader=self.loader)
self.assertEqual(len(template.tree.statements), 2)
node = template.tree.statements[0]
diff --git a/tests/test_utils.py b/tests/test_utils.py
index f97545a..250cff4 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -1,7 +1,10 @@
+from io import BytesIO, StringIO
from pathlib import Path
+from typing import Mapping
from unittest import TestCase
from unittest.mock import patch
+from liquid import Undefined
from pyexpat import ExpatError
from pyjson5 import Json5EOF
from pytest import raises
@@ -11,59 +14,63 @@
blank_str_to_empty,
del_empty_dirs_quietly,
del_path_quietly,
- is_none_or_empty,
+ is_undefined_none_or_blank,
join_subpath,
merge_dict,
mkdir,
parse_json,
parse_xml,
+ tail,
to_list_or_empty,
walk_path,
)
-class IsNoneOrEmptyTest(TestCase):
+class IsUndefinedNoneOrBlankTest(TestCase):
+ def test_undefined(self) -> None:
+ self.assertTrue(is_undefined_none_or_blank(Undefined("")))
+
def test_none(self) -> None:
- self.assertTrue(is_none_or_empty(None))
+ self.assertTrue(is_undefined_none_or_blank(None))
def test_false(self) -> None:
- self.assertFalse(is_none_or_empty(False))
+ self.assertFalse(is_undefined_none_or_blank(False))
def test_true(self) -> None:
- self.assertFalse(is_none_or_empty(True))
+ self.assertFalse(is_undefined_none_or_blank(True))
def test_zero(self) -> None:
- self.assertFalse(is_none_or_empty(0))
+ self.assertFalse(is_undefined_none_or_blank(0))
def test_one(self) -> None:
- self.assertFalse(is_none_or_empty(1))
+ self.assertFalse(is_undefined_none_or_blank(1))
def test_str_empty(self) -> None:
- self.assertTrue(is_none_or_empty(""))
+ self.assertTrue(is_undefined_none_or_blank(""))
def test_str_blank(self) -> None:
- self.assertTrue(is_none_or_empty(" "))
+ self.assertTrue(is_undefined_none_or_blank(" "))
def test_str(self) -> None:
- self.assertFalse(is_none_or_empty("test"))
+ self.assertFalse(is_undefined_none_or_blank("test"))
def test_list_empty(self) -> None:
- self.assertTrue(is_none_or_empty([]))
+ self.assertTrue(is_undefined_none_or_blank([]))
def test_list(self) -> None:
- self.assertFalse(is_none_or_empty(["test"]))
+ self.assertFalse(is_undefined_none_or_blank(["test"]))
def test_tuple_empty(self) -> None:
- self.assertTrue(is_none_or_empty(()))
+ self.assertTrue(is_undefined_none_or_blank(()))
def test_tuple(self) -> None:
- self.assertFalse(is_none_or_empty(("test", "ok")))
+ self.assertFalse(is_undefined_none_or_blank(("test", "ok")))
def test_dict_empty(self) -> None:
- self.assertTrue(is_none_or_empty({}))
+ self.assertTrue(is_undefined_none_or_blank({}))
def test_dict(self) -> None:
- self.assertFalse(is_none_or_empty({"test": "ok"}))
+ self.assertFalse(is_undefined_none_or_blank({"test": "ok"}))
class ToListOrEmptyTest(TestCase):
@@ -187,6 +194,12 @@ def test_ignore_empty_list(self) -> None:
class ParseJsonTest(TestCase):
+ stu3_file = Path("tests/data/stu3/Person.json")
+
+ def validate_fhir(self, fhir: Mapping) -> None:
+ self.assertIn("gender", fhir)
+ self.assertEqual("male", fhir["gender"])
+
def test_empty(self) -> None:
with raises(Json5EOF):
parse_json("")
@@ -256,41 +269,74 @@ def test_dict_ignore_lead_trail_spaces(self) -> None:
parse_json(' {"name": [{"family": "Relative","given": ["Ralph"]}]} '),
)
+ def test_include_empty_fields(self) -> None:
+ self.assertEqual(
+ {"name": [{"family": "", "given": [""]}]},
+ parse_json(
+ '{"name": [{"family": "","given": [""]}]}', ignore_empty_fields=False
+ ),
+ )
+
+ def test_text(self) -> None:
+ self.validate_fhir(parse_json(self.stu3_file.read_text()))
+
+ def test_bytes(self) -> None:
+ self.validate_fhir(parse_json(self.stu3_file.read_bytes()))
+
+ def test_text_io(self) -> None:
+ with self.stu3_file.open() as stu3_in:
+ self.validate_fhir(parse_json(stu3_in))
+
+ def test_binary_io(self) -> None:
+ with self.stu3_file.open("rb") as stu3_in:
+ self.validate_fhir(parse_json(stu3_in))
+
class ParseXmlTest(TestCase):
- def test_empty_str(self) -> None:
+ ccda_file = Path("tests/data/ccda/CCD.ccda")
+ empty_file = Path("tests/data/bad_data/empty.ccda")
+
+ def validate_ccda(self, xml: Mapping) -> None:
+ self.assertIn("ClinicalDocument", xml)
+ self.assertIsNotNone(
+ get_ccda_section(xml, search_template_ids="2.16.840.1.113883.10.20.22.2.6.1")
+ )
+
+ def test_empty_text(self) -> None:
with raises(ExpatError):
parse_xml("")
- def test_blank_str(self) -> None:
+ def test_blank_text(self) -> None:
with raises(ExpatError):
parse_xml(" ")
- def test_empty_file(self) -> None:
+ def test_empty_bytes(self) -> None:
+ with raises(ExpatError):
+ parse_xml(bytes())
+
+ def test_empty_text_io(self) -> None:
with raises(ExpatError):
- with Path("tests/data/bad_data/empty.ccda").open() as xml_in:
+ with self.empty_file.open() as xml_in:
parse_xml(xml_in)
- def test_empty_file_binary(self) -> None:
+ def test_empty_binary_io(self) -> None:
with raises(ExpatError):
- with Path("tests/data/bad_data/empty.ccda").open("rb") as xml_in:
+ with self.empty_file.open("rb") as xml_in:
parse_xml(xml_in)
- def test_file(self) -> None:
- with Path("tests/data/ccda/CCD.ccda").open() as xml_in:
- xml = parse_xml(xml_in)
- self.assertIn("ClinicalDocument", xml)
- self.assertIsNotNone(
- get_ccda_section(xml, search_template_ids="2.16.840.1.113883.10.20.22.2.6.1")
- )
+ def test_text(self) -> None:
+ self.validate_ccda(parse_xml(self.ccda_file.read_text()))
- def test_file_binary(self) -> None:
- with Path("tests/data/ccda/CCD.ccda").open("rb") as xml_in:
- xml = parse_xml(xml_in)
- self.assertIn("ClinicalDocument", xml)
- self.assertIsNotNone(
- get_ccda_section(xml, search_template_ids="2.16.840.1.113883.10.20.22.2.6.1")
- )
+ def test_bytes(self) -> None:
+ self.validate_ccda(parse_xml(self.ccda_file.read_bytes()))
+
+ def test_text_io(self) -> None:
+ with self.ccda_file.open() as xml_in:
+ self.validate_ccda(parse_xml(xml_in))
+
+ def test_binary_io(self) -> None:
+ with self.ccda_file.open("rb") as xml_in:
+ self.validate_ccda(parse_xml(xml_in))
class JoinSubpathTest(TestCase):
@@ -483,3 +529,43 @@ def test_walk_path(self) -> None:
with raises(StopIteration):
next(walk)
+
+
+class TailTest(TestCase):
+ def test_empty_text(self) -> None:
+ buffer = StringIO()
+ self.assertEqual("", tail(buffer))
+
+ def test_empty_bytes(self) -> None:
+ buffer = BytesIO()
+ self.assertEqual("", tail(buffer))
+
+ def test_read_all_text(self) -> None:
+ buffer = StringIO()
+ buffer.write("This is a test.")
+ self.assertEqual("This is a test.", tail(buffer))
+
+ def test_read_last_n_text(self) -> None:
+ buffer = StringIO()
+ buffer.write("This is a test.")
+ self.assertEqual("st.", tail(buffer, last_n=3))
+
+ def test_read_last_n_is_negative(self) -> None:
+ buffer = StringIO()
+ buffer.write("This is a test.")
+ self.assertEqual("", tail(buffer, last_n=-3))
+
+ def test_read_last_n_is_zero(self) -> None:
+ buffer = StringIO()
+ buffer.write("This is a test.")
+ self.assertEqual("", tail(buffer, last_n=0))
+
+ def test_read_all_bytes(self) -> None:
+ buffer = BytesIO()
+ buffer.write(b"This is a test.")
+ self.assertEqual("This is a test.", tail(buffer))
+
+ def test_read_last_n_bytes(self) -> None:
+ buffer = BytesIO()
+ buffer.write(b"This is a test.")
+ self.assertEqual("st.", tail(buffer, last_n=3))
\n \n
\n \n \n Name \n Peter James Chalmers ("Jim") \n \n \n Address \n 534 Erewhon, Pleasantville, Vic, 3999 \n \n \n Contacts \n Home: unknown. Work: (03) 5555 6473 \n \n \n \n Id \n MRN: 12345 (Acme Healthcare) \n