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Merge pull request #97 from mednax-it/nonprod
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PDIP-116,117,118,119 SMILECDR-894,898,897,916
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@amakineni
amakineni authored May 24, 2024
2 parents 586fc96 + fe60384 commit 0079c7a
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Showing 17 changed files with 92 additions and 26 deletions.
27 changes: 18 additions & 9 deletions hl7v2_default.json
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Original file line number Diff line number Diff line change
Expand Up @@ -67,6 +67,7 @@
{"name": "LAN","min": 0, "max": -1},
{"name": "ZPD","min": 0, "max": -1},
{"name": "PD1","min": 0, "max": -1},
{"name": "ARV","min": 0, "max": -1},
{"name": "ZOE","min": 0, "max": -1},
{"name": "NTE","min": 0, "max": -1},
{"name": "ZPI","min": 0, "max": -1},
Expand Down Expand Up @@ -99,6 +100,7 @@
{"name": "ZOE","min": 0, "max": -1},
{"name": "PV2","min": 0, "max": -1},
{"name": "PD1","min": 0, "max": -1},
{"name": "NK1","min": 0, "max": -1},
{"name": "ZPV","min": 0, "max": -1},
{"name": "ZVI","min": 0, "max": -1},
{"name": "ZIF","min": 0, "max": -1},
Expand All @@ -111,6 +113,7 @@
{"name": "allergy", "type":"segment_group","min": 0, "max": -1,
"child_segments": [
{"name": "AL1","min": 0,"max": -1},
{"name": "DG1","min": 0, "max": -1},
{"name": "ZAL","min": 0,"max": -1},
{"name": "NTE","min": 0, "max": -1}
]
Expand Down Expand Up @@ -223,6 +226,7 @@
},
{"name": "DG1","min": 0, "max": -1},
{"name": "AL1","min": 0, "max": -1},
{"name": "DG1","min": 0, "max": -1},
{"name": "PR1","min": 0, "max": -1},
{"name": "ACC","min": 0, "max": -1},
{"name": "UB1","min": 0, "max": -1},
Expand All @@ -234,16 +238,20 @@
{"name": "ZIN","min": 0, "max": -1},
{"name": "ZIM","min": 0, "max": -1},
{"name": "ZCN","min": 0, "max": -1},
{"name": "ZCS","min": 0, "max": -1},
{"name": "ZM1","min": 0, "max": -1},
{"name": "ZPV","min": 0, "max": -1},
{"name": "ZEX","min": 0, "max": -1},
{"name": "ZRE","min": 0, "max": -1},
{"name": "ZAC","min": 0, "max": -1},
{"name": "ZQA","min": 0, "max": -1},
{"name": "ZCS","min": 0, "max": -1},
{"name": "ZSU","min": 0, "max": -1},
{"name": "ZMP","min": 0, "max": -1},
{"name": "ZEM","min": 0, "max": -1},
{"name": "ZAD","min": 0, "max": -1},
{"name": "ZNM","min": 0, "max": -1},
{"name": "ZVQ","min": 0, "max": -1},
{"name": "ZMS","min": 0, "max": -1},
{"name": "ZMD","min": 0, "max": -1},
{"name": "ZET","min": 0, "max": -1},
{"name": "ZCQ","min": 0, "max": -1},
Expand Down Expand Up @@ -846,14 +854,15 @@
"relatedperson_guarantor_resource": {
"object": {
"fullUrl": {
"custom_func":{
"name": "concat",
"args": [
{"const": "urn:uuid:61ebe121-aa05-0001-000"},
{"xpath": "GT1/set_id"},
{"const": "-983a382abcd7"}
]
}
"custom_func":{
"name": "javascript",
"args": [
{"const": "prefix + index.toString() + suffix"},
{"const": "prefix"}, {"const": "urn:uuid:61ebe121-aa05-0001-000"},
{"const": "index"}, {"xpath": "GT1/set_id", "template": "transform_guarantor_set_id"},
{"const": "suffix"}, {"const": "-983a382abcd7"}
]
}
},
"resource": {
"object": {
Expand Down
27 changes: 18 additions & 9 deletions hl7v2_default_test.json
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Original file line number Diff line number Diff line change
Expand Up @@ -67,6 +67,7 @@
{"name": "LAN","min": 0, "max": -1},
{"name": "ZPD","min": 0, "max": -1},
{"name": "PD1","min": 0, "max": -1},
{"name": "ARV","min": 0, "max": -1},
{"name": "ZOE","min": 0, "max": -1},
{"name": "NTE","min": 0, "max": -1},
{"name": "ZPI","min": 0, "max": -1},
Expand Down Expand Up @@ -99,6 +100,7 @@
{"name": "ZOE","min": 0, "max": -1},
{"name": "PV2","min": 0, "max": -1},
{"name": "PD1","min": 0, "max": -1},
{"name": "NK1","min": 0, "max": -1},
{"name": "ZPV","min": 0, "max": -1},
{"name": "ZVI","min": 0, "max": -1},
{"name": "ZIF","min": 0, "max": -1},
Expand All @@ -111,6 +113,7 @@
{"name": "allergy", "type":"segment_group","min": 0, "max": -1,
"child_segments": [
{"name": "AL1","min": 0,"max": -1},
{"name": "DG1","min": 0, "max": -1},
{"name": "ZAL","min": 0,"max": -1},
{"name": "NTE","min": 0, "max": -1}
]
Expand Down Expand Up @@ -223,6 +226,7 @@
},
{"name": "DG1","min": 0, "max": -1},
{"name": "AL1","min": 0, "max": -1},
{"name": "DG1","min": 0, "max": -1},
{"name": "PR1","min": 0, "max": -1},
{"name": "ACC","min": 0, "max": -1},
{"name": "UB1","min": 0, "max": -1},
Expand All @@ -234,16 +238,20 @@
{"name": "ZIN","min": 0, "max": -1},
{"name": "ZIM","min": 0, "max": -1},
{"name": "ZCN","min": 0, "max": -1},
{"name": "ZCS","min": 0, "max": -1},
{"name": "ZM1","min": 0, "max": -1},
{"name": "ZPV","min": 0, "max": -1},
{"name": "ZEX","min": 0, "max": -1},
{"name": "ZRE","min": 0, "max": -1},
{"name": "ZAC","min": 0, "max": -1},
{"name": "ZQA","min": 0, "max": -1},
{"name": "ZCS","min": 0, "max": -1},
{"name": "ZSU","min": 0, "max": -1},
{"name": "ZMP","min": 0, "max": -1},
{"name": "ZEM","min": 0, "max": -1},
{"name": "ZAD","min": 0, "max": -1},
{"name": "ZNM","min": 0, "max": -1},
{"name": "ZVQ","min": 0, "max": -1},
{"name": "ZMS","min": 0, "max": -1},
{"name": "ZMD","min": 0, "max": -1},
{"name": "ZET","min": 0, "max": -1},
{"name": "ZCQ","min": 0, "max": -1},
Expand Down Expand Up @@ -846,14 +854,15 @@
"relatedperson_guarantor_resource": {
"object": {
"fullUrl": {
"custom_func":{
"name": "concat",
"args": [
{"const": "urn:uuid:61ebe121-aa05-0001-000"},
{"xpath": "GT1/set_id"},
{"const": "-983a382abcd7"}
]
}
"custom_func":{
"name": "javascript",
"args": [
{"const": "prefix + index.toString() + suffix"},
{"const": "prefix"}, {"const": "urn:uuid:61ebe121-aa05-0001-000"},
{"const": "index"}, {"xpath": "GT1/set_id", "template": "transform_guarantor_set_id"},
{"const": "suffix"}, {"const": "-983a382abcd7"}
]
}
},
"resource": {
"object": {
Expand Down
6 changes: 2 additions & 4 deletions src/omniparser_schemas/parser/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,10 +11,10 @@ def validate_ETL_parser(resource, file):
# The universal parser need to have carriage return
hl7content = hl7content.replace('\\r', '\r')

# call universal utl parser
# call universal etl parser
fhir_bundle_from_hl7 = fetch_parsed_text(hl7content)
# Remove first and last character of fhir bundle

# Remove first and last character of fhir bundle
fhir_bundle = fhir_bundle_from_hl7[1:-1]

json_data = json.loads(fhir_bundle)
Expand All @@ -26,5 +26,3 @@ def validate_ETL_parser(resource, file):

with open(PATH + "/regression_" + str(resource) + "_" + str(file) + ".json", "w") as f:
json.dump(json_data, f)


2 changes: 1 addition & 1 deletion src/omniparser_schemas/parser/universal_etl_parser.py
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Expand Up @@ -23,7 +23,7 @@ def fetch_parsed_text(text_to_parse):

if http_response.status_code != HTTPStatus.OK:
error_message = http_response.status_code
print(error_message)
print("Error code:",error_message, http_response.text)
exit(1)

return http_response.text
3 changes: 3 additions & 0 deletions tests/regression/main.py
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Expand Up @@ -22,6 +22,7 @@
from tests.regression.claim_1_resource import claim_1_test
from tests.regression.claim_2_resource import claim_2_test
from tests.regression.claim_3_resource import claim_3_test
from tests.regression.missing_segment import missing_segment_test


def run_tests():
Expand Down Expand Up @@ -72,6 +73,8 @@ def run_tests():
relatedperson_insurance_3_test(RESOURCE_NAME[7], "3", IDENTIFIER_URL, IDENTIFIER_ID[4])
relatedperson_insurance_3_test(RESOURCE_NAME[7], "4", IDENTIFIER_URL, IDENTIFIER_ID[4])

missing_segment_test()

def cli(args=None):
"""Process command line arguments."""
if not args:
Expand Down
39 changes: 39 additions & 0 deletions tests/regression/missing_segment.py
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@@ -0,0 +1,39 @@
import os
import importlib
import json
from omniparser_schemas.parser.universal_etl_parser import fetch_parsed_text



def missing_segment_test():

# Get the segments to be tested
segments = "MissingSegments"

missing_segment_test_data_dir = f"tests/regression/regression_test_data/{segments}"

filenames = os.listdir(missing_segment_test_data_dir)

for filename in filenames:
with importlib.resources.path("tests.regression.regression_test_data." + str(segments), str(filename)) as f:
hl7content = f.read_text()

# The universal parser need to have carriage return
hl7content = hl7content.replace('\\r', '\r')

# call universal etl parser
fhir_bundle_from_hl7=fetch_parsed_text(hl7content)
fhir_bundle = fhir_bundle_from_hl7[1:-1]

json_data = json.loads(fhir_bundle)

OUTPUT_ROOT_PATH = "tests/regression/regression_output/"
PATH = OUTPUT_ROOT_PATH + str(segments)
if not os.path.exists(PATH):
os.makedirs(PATH)

with open(PATH + "/regression_" + str(segments) + "_" + str(filename) + ".json", "w") as f:
json.dump(json_data, f)


print("FHIR bundle with missing segments tests were successful")
2 changes: 1 addition & 1 deletion tests/regression/practitioner_attending_resource.py
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Expand Up @@ -67,4 +67,4 @@ def practitioner_attending_test(resource_name, testfile, identifier_url, identif
assert not attphys[0]["resource"]["name"][0]["given"][0] == PRACTITIONER_FAMILY_NAME, "negative test case failed"


print("FHIR bundle attending practitioner resource tests were successful")
print("FHIR bundle attending practitioner resource tests were successful")
2 changes: 1 addition & 1 deletion tests/regression/practitioner_referring_resource.py
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Expand Up @@ -67,4 +67,4 @@ def practitioner_referring_test(resource_name, testfile, identifier_url, identif
assert not refphys[1]["resource"]["name"][0]["given"][0] == PRACTITIONER_FAMILY_NAME, "negative test case failed"


print("FHIR bundle referring practitioner resource tests were successful")
print("FHIR bundle referring practitioner resource tests were successful")
1 change: 1 addition & 0 deletions tests/regression/regression_test_data/MissingSegments/AL1DG1.txt
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@@ -0,0 +1 @@
MSH|^~\\&|MS4_NY|BAOM|PDX|437|20230907070903||ADT^A08|00000000300746007|P|2.3\rEVN|A08|20230907070902|||TUSER1\rPID|1|H1234^^^MS4^PN|MR4567^^^MS4^MR^437||WICK^JOHN||19960513|Male||2106-3|123 MAIN ST^^ANYTOWN^NY^11210^USA^^NYC|NYC|(555)888-1234||en|Single|OTH|31184017||||U|NY|||USA\rZPD||||ACTIVATED|||Y|20240507||||||||||N\rZTP|Health Maintenance Reminders^Health Maintenance Reminders|MYCH^Y\rZTP|Bulk Communication^Bulk Communication|MYCH^Y~Mail^Y\rZTP|Communication Management^Communication Management|MYCH^Y\rZTP|New Estimate^New Estimate|Email^Y~Push^Y~Text^Y\rPD1||||128303^BAUER^JANE^A|||N|||||N\rPV1||E||1|||116596^KAPUR^SIMRAN^S^^^MD|128303^BAUER^JANE^A||EER||||1||||E|00031184017437|2115|||||||||||||||||||BAOM|||||202309070619\rDG1|0001|I10||POV CP DIFF BREATHING||A|||||||||0\rOBX|0001|NM|PRICSN|1|735464236||||||M|||||||||||||||||||||\rOBX|0002|NM|HT^HEIGHT||51.5|cm||||||||20230745145100||||||||||||||||||\rOBX|0003|NM|WT^WEIGHT||2.872|kg||||||||20230752000000||||||||||||||||||\rOBX|0004|TX|ContactType^CONTACT TYPE|1|3|||||||||20240508||||||||||||||||||\rGT1|0001|00H1234^^^MS4^PN|WICK^JOHN||123 MAIN ST^^ANYTOWN^NY^11210^USA^^NYC|(555)888-1234||19960513|M||A|||||DISABLED||||2|||||||||0000000002|S||||||||Y|||YYY||||||||||||||C\rIN1|0001|INS123456|2115|MERCY CARE RBHA|PO BOX 64835^^PHOENIX^NY^85082||(866)796-5598||||||||MCD|WICK^JOHN|A|19960513|123 MAIN ST^^ANYTOWN^NY^11210^USA|||1|||||N|||||||||INS123456||||||3|M||N||||00H1234\rIN1|0002|INS222456|0094|PENDING MEDICAID IHMS|^^^^ |||999999|PENDING||||||COM|WICK^JOHN|A|19960513|123 MAIN ST^^ANYTOWN^NY^11210^USA|||2|||||N|||||||||INS222456||||||3|M||N||||00H1234\rAL1|1|SYSTEMIC|^NO KNOWN ALLERGIES^\rDG1|1||^Newborn|Newborn||^W\rUB1||||||||||||||||23^20230907\rZAC|EXPLOSIVE EXPLODED IN PT FACE\rZQA|1|589723|^589724~^589725~^589726~^589727~^589728~^589729~^589730~^589731~^589732~^589733~^589734~^589735~^589736~^589737~^589738~^589739~^589740~^589741~^589742~^589743~^589744~^589745~^589746~^589747~^589748~^589749~^589750~^589751~^589752~^589753~^589754~^589755~^589756~^589757~^589758~^589759~^589760~^589761~^589762\rZCS||^^^^||||00005\rZSU|A44\r
1 change: 1 addition & 0 deletions tests/regression/regression_test_data/MissingSegments/ARV.txt
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@@ -0,0 +1 @@
MSH|^~\\&|MS4_NY|BAOM|PDX|437|20230907070903||ADT^A08|00000000300746007|P|2.3\rEVN|A08|20230907070902|||TUSER1\rPID|1|H1234^^^MS4^PN|MR4567^^^MS4^MR^437||WICK^JOHN||19960513|Male||2106-3|123 MAIN ST^^ANYTOWN^NY^11210^USA^^NYC|NYC|(555)888-1234||en|Single|OTH|31184017||||U|NY|||USA\rZPD||||ACTIVATED|||Y|20240507||||||||||N\rZTP|Health Maintenance Reminders^Health Maintenance Reminders|MYCH^Y\rZTP|Bulk Communication^Bulk Communication|MYCH^Y~Mail^Y\rZTP|Communication Management^Communication Management|MYCH^Y\rZTP|New Estimate^New Estimate|Email^Y~Push^Y~Text^Y\rPD1||||128303^BAUER^JANE^A|||N|||||N\rARV|1|S|CELEBCONFIDENTIAL||Patient is a widely known celebrity. Restrict communication of parties involved.\rPV1||E||1|||116596^KAPUR^SIMRAN^S^^^MD|128303^BAUER^JANE^A||EER||||1||||E|00031184017437|2115|||||||||||||||||||BAOM|||||202309070619\rDG1|0001|I10||POV CP DIFF BREATHING||A|||||||||0\rOBX|0001|NM|PRICSN|1|735464236||||||M|||||||||||||||||||||\rOBX|0002|NM|HT^HEIGHT||51.5|cm||||||||20230745145100||||||||||||||||||\rOBX|0003|NM|WT^WEIGHT||2.872|kg||||||||20230752000000||||||||||||||||||\rOBX|0004|TX|ContactType^CONTACT TYPE|1|3|||||||||20240508||||||||||||||||||\rGT1|0001|00H1234^^^MS4^PN|WICK^JOHN||123 MAIN ST^^ANYTOWN^NY^11210^USA^^NYC|(555)888-1234||19960513|M||A|||||DISABLED||||2|||||||||0000000002|S||||||||Y|||YYY||||||||||||||C\rIN1|0001|INS123456|2115|MERCY CARE RBHA|PO BOX 64835^^PHOENIX^NY^85082||(866)796-5598||||||||MCD|WICK^JOHN|A|19960513|123 MAIN ST^^ANYTOWN^NY^11210^USA|||1|||||N|||||||||INS123456||||||3|M||N||||00H1234\rIN1|0002|INS222456|0094|PENDING MEDICAID IHMS|^^^^ |||999999|PENDING||||||COM|WICK^JOHN|A|19960513|123 MAIN ST^^ANYTOWN^NY^11210^USA|||2|||||N|||||||||INS222456||||||3|M||N||||00H1234\rAL1|1|SYSTEMIC|^NO KNOWN ALLERGIES^\rDG1|1||^Newborn|Newborn||^W\rUB1||||||||||||||||23^20230907\rZAC|EXPLOSIVE EXPLODED IN PT FACE\rZQA|1|589723|^589724~^589725~^589726~^589727~^589728~^589729~^589730~^589731~^589732~^589733~^589734~^589735~^589736~^589737~^589738~^589739~^589740~^589741~^589742~^589743~^589744~^589745~^589746~^589747~^589748~^589749~^589750~^589751~^589752~^589753~^589754~^589755~^589756~^589757~^589758~^589759~^589760~^589761~^589762\rZCS||^^^^||||00005\rZSU|A44\r
1 change: 1 addition & 0 deletions tests/regression/regression_test_data/MissingSegments/NK1.txt
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@@ -0,0 +1 @@
MSH|^~\\&|MS4_NY|BAOM|PDX|437|20230907070903||ADT^A08|00000000300746007|P|2.3\rEVN|A08|20230907070902|||TUSER1\rPID|1|H1234^^^MS4^PN|MR4567^^^MS4^MR^437||WICK^JOHN||19960513|Male||2106-3|123 MAIN ST^^ANYTOWN^NY^11210^USA^^NYC|NYC|(555)888-1234||en|Single|OTH|31184017||||U|NY|||USA\rZPD||||ACTIVATED|||Y|20240507||||||||||N\rZTP|Health Maintenance Reminders^Health Maintenance Reminders|MYCH^Y\rZTP|Bulk Communication^Bulk Communication|MYCH^Y~Mail^Y\rZTP|Communication Management^Communication Management|MYCH^Y\rZTP|New Estimate^New Estimate|Email^Y~Push^Y~Text^Y\rPD1||||128303^BAUER^JANE^A|||N|||||N\rNK1|1|ARES^ARES^^|F|MANOVER STREET^BLOCK 23 2077^NEW YORK^NY^10001^US|(555)111-2222^^PH^^^555^1112222||Emergency Contact 1\rNK1|2|ARES^ARES^^|F|MANOVER STREET^BLOCK 23 2077^NEW YORK^NY^10001^US|(555)111-2222^^PH^^^555^1112222||Partner\rPV1||E||1|||116596^KAPUR^SIMRAN^S^^^MD|128303^BAUER^JANE^A||EER||||1||||E|00031184017437|2115|||||||||||||||||||BAOM|||||202309070619\rDG1|0001|I10||POV CP DIFF BREATHING||A|||||||||0\rOBX|0001|NM|PRICSN|1|735464236||||||M|||||||||||||||||||||\rOBX|0002|NM|HT^HEIGHT||51.5|cm||||||||20230745145100||||||||||||||||||\rOBX|0003|NM|WT^WEIGHT||2.872|kg||||||||20230752000000||||||||||||||||||\rOBX|0004|TX|ContactType^CONTACT TYPE|1|3|||||||||20240508||||||||||||||||||\rGT1|0001|00H1234^^^MS4^PN|WICK^JOHN||123 MAIN ST^^ANYTOWN^NY^11210^USA^^NYC|(555)888-1234||19960513|M||A|||||DISABLED||||2|||||||||0000000002|S||||||||Y|||YYY||||||||||||||C\rIN1|0001|INS123456|2115|MERCY CARE RBHA|PO BOX 64835^^PHOENIX^NY^85082||(866)796-5598||||||||MCD|WICK^JOHN|A|19960513|123 MAIN ST^^ANYTOWN^NY^11210^USA|||1|||||N|||||||||INS123456||||||3|M||N||||00H1234\rIN1|0002|INS222456|0094|PENDING MEDICAID IHMS|^^^^ |||999999|PENDING||||||COM|WICK^JOHN|A|19960513|123 MAIN ST^^ANYTOWN^NY^11210^USA|||2|||||N|||||||||INS222456||||||3|M||N||||00H1234\rAL1|1|SYSTEMIC|^NO KNOWN ALLERGIES^\rDG1|1||^Newborn|Newborn||^W\rUB1||||||||||||||||23^20230907\rZAC|EXPLOSIVE EXPLODED IN PT FACE\rZQA|1|589723|^589724~^589725~^589726~^589727~^589728~^589729~^589730~^589731~^589732~^589733~^589734~^589735~^589736~^589737~^589738~^589739~^589740~^589741~^589742~^589743~^589744~^589745~^589746~^589747~^589748~^589749~^589750~^589751~^589752~^589753~^589754~^589755~^589756~^589757~^589758~^589759~^589760~^589761~^589762\rZCS||^^^^||||00005\rZSU|A44\r
1 change: 1 addition & 0 deletions tests/regression/regression_test_data/MissingSegments/ZAC.txt
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